@text "PROTEIN TOURIST #4: A SURVEY OF PROTEINS IN THE 'SMALL IRREGULAR' CATEGORY OF TERTIARY STRUCTURE" J.S. Richardson Contents of file PROTOUR4.KIN: Small SS-rich, C-centered overhand structures: Kin.1 - Cellobiohydrolase C-terminal domain: overhand topology and C-C beta hairpin Kin.2 - Potato carboxypeptidase inhibitor: very small SS-rich Kin.3 - Scorpion neurotoxin Kin.4 - Closeup of glycine roles, in scorpion toxin Small SS-rich, N-centered overhands and others: Kin.5 - Ovomucoid serine protease inhibitor: N-centered topology Kin.6 - Wheat germ agglutinin domain Kin.7 - Hirudin: up&down topology, with 3-SS core Small metal-rich structures: Kin.8 - Rubredoxin: one non-heme Fe Kin.9 - Ferredoxin (P. aer.): two Fe4S4 clusters Kin.10- Cytochrome C3: 4 hemes Kin.11- Metallothionein domain 2: 4 Cd sites in 31 residues Small proteins with neither disulfides nor metals: Kin.12- Immunoglobulin-binding domain of Strep. protein G (Procedural notes: With a text file this long, you may want to print out the first few pages of this *.kin file and refer to that rather than switching windows. Stereo is helpful; it is turned on in the "Other" pulldown menu. Either use a stereo viewer, or just relax your eyes, look "through" the screen toward infinity, let the two images drift together, and once they merge then focus on the merged image to see in 3-D. Note that alternative views are accessed on the "Graphics" pulldown menu.) In describing the overall, tertiary-structure, folding patterns of globular proteins, the three most obvious categories everyone agrees upon are the all-alpha, the antiparallel beta, and the parallel alpha/beta. (ProTour1.kin surveyed the doubly-wound alpha/beta proteins, or nucleotide-binding domains, which are the most common type of alpha/beta structure.) Beyond those three categories there are a good many examples that are somewhat harder to describe, classify, and assign clear dividing lines between groups; some of these proteins have been described as "alpha + beta" and some as "small irregular" (e.g., Levitt and Chothia 1976; Richardson, 1981; 1989). This Protein Tourist surveys the small irregular structures, within which there are several important subgroups: the small disulfide-rich proteins, the small metal-rich proteins, and a few cases of small proteins with neither. The number of known structures in this class is growing rapidly, because they are ideal subjects for structure solution by NMR methods as well as by xray crystallography. SMALL IRREGULAR, SS-RICH First we will survey a fairly complete sample of the small SS-rich structures: 12 unrelated proteins (or domains) of 35 to 70 residues, with 10% or more Cys. Shorter sequences seldom have high Cys content, and usually act more like peptides than proteins (having only one or two pieces of secondary structure, no interior, and often multiple conformations or needing to assemble as a multimer to form structure). Longer sequences almost never have disulfides as a major structural component (exception: phospholipase A2, with 7 SS in 123 residues) and have much more regular and dominant secondary structure; they are usuually most usefully considered as belonging to one of the other categories of structure, but the dividing line is sometimes arbitrary. These 12 SS-rich proteins are tabulated below, with descriptive statistics: number of amino acids, number and order of disulfides, number of helices, number and topology of beta strands, and presence of Cys on a characteristic type of beta hairpin. Note: SS order is abbreviated by writing out the SS connectivity in order of first-Cys (e.g., a-b, c-e, d-f) and then just listing the second letters (e.g., bef). These structures are all quite different in overall arrangement (except for a resemblance between EBX and WGA; see Drenth et al., 1980) and they each have a distinct order of SS connectivity except for BDS and OVO (which, however, use those SS in entirely different ways). We will find, however, that certain substructures appear with great consistency. Sample of small SS-rich proteins: #aa #SS order helix beta topol. hairpin hpin Cys name CBH 36 2 cd - 3 C-cntr. yes 2 opp. cellobiohydrolase PCI 39 3 def 1 3 C-cntr. yes 2 opp. potato CPA inhib. BDS 43 3 edf - 3 C-cntr. yes 2 opp., 1 anemone anti-viral SN3 65 4 hefg 1 3,2+ C-cntr. yes 2 opp., 1 scorpion toxin WGA 41 4 defh 1 3,2 N-cntr. yes 2 opp., 1 wh. germ agglutinin CRN 46 3 fed 2 3 N-cntr. ( ) 2 opp., 1 crambin OVO 56 3 edf 1 3+ N-cntr. yes 1 ovomucoid inhibitor PTI 58 3 fde 2 3 N-cntr. yes 1 panc. trypsin inhib. EBX 62 4 edfh - 3,2 N-cntr. yes 2 opp. erabutoxin HIR (49) 3 bef - 3 up&down yes 2 opp. hirudin EGF 39 3 cdf - 2 just hp yes 2 opp., 1 epid. growth factor INS 21,30 3 dfe 3 2+ (2 chain) - - insulin Kinemage 1 shows the C-terminal domain of cellobiohydrolase (file 1CBH), a small SS-rich structure, with mainchain and H-bonds for the secondary structure regions and Calpha backbone for the loops, plus disulfides. This domain has 36 residues, 2 SS bonds, and 3 beta strands, and it shows in a simple form most features that are common to many of the small disulfide-rich proteins. The cysteine content is greater than 10%, and the beta sheet, although important, is of modest size and quite irregular; it has a total of 12 Hbonds and 3 beta bulges. (A beta bulge is a place where an extra residue is squeezed in on one side of a pair of beta strands; it can usually be seen by a bifurcated Hbond or by the bulged shape of the backbone. The most obvious one here is at Leu 28.) Click repeatedly on the "animate grp" button to see a buildup of the 'C-centered overhand' topology of the beta strand connections. 'C-centered' means that the C-terminal strand is the central one of the three, and 'overhand' refers to the crossover connection between the two outer beta strands (refer to ProTour1.kin for an explanation of righthanded crossover connections). Almost all of the small disulfide-rich proteins can be described as either C-centered or N-centered overhands (9 out of these12). Simple up&down, 3-strand beta sheets are common as parts of larger proteins but are very rare in the small disulfide-rich structures (only hirudin, here). Also, neither lefthanded crossover connections nor mixed beta sheets (partly parallel and partly antiparallel) occur. The overhands are about equally distributed between N-centered and C-centered, and we will look at several of each. Most of the SS-rich proteins (8 out of 12) contain a pair of disulfides that come from positions opposite each other on adjacent beta strands, near the middle of the most H-bonded (or the only) beta hairpin in the structure. Turn on the "C-C hairpin" button to highlight in red and gold this beta hairpin in the CBH structure, with its two adjacent disulfides. (For those interested in the structural details, these disulfide pairs are on the "wide Hbond" side of the beta hairpin, and they have consistent conformations and sequence-connectivity orders.) Kinemage 2 shows potato carboxypeptidase inhibitor (PCI; from file 4CPA), which is also a C-centered overhand with a C-C hairpin, but in a rather different overall arrangement. Click on residues in the beta strands to confirm that the C-terminal strand is in the middle. Turn on the "C-C hairpin" button to see that feature highlighted in red and gold. The central core of PCI is small and the two chain termini are quite long. The C-terminus is the site of inhibition and, in the complex with carboxypeptidase, Gly 39 as shown has been cleaved (the complex can be seen in file Phillips.kin, PS 1_4). There are 39 residues, 3 SS bonds, 3 extremely short beta strands, and just over a turn of 3/10 helix (in the crossover connection). Two of the disulfides join the outer beta strands into a ring, and the third disulfide passes through the ring to firmly tether the C-terminal tail (seen best in View2). Kinemage 3 shows scorpion neurotoxin variant 3 (file 1SN3), a slightly larger protein with a C-centered overhand and a C-C hairpin. It has 65 residues, 4 disulfides, 3 major beta strands (in greentint), and an alpha helix (pinktint). The overall shape of the structure can be compared to a left hand, with the loop excursions at the right being the wrist, and the green beta-strand 'fingers' curling around the pink helix 'thumb'. Again, confirm the strand order as C-centered and use the "C-C hairpin" button to find the two adjacent disulfides on the major beta hairpin (best in View2). The scorpion toxin has both long chain termini and a complex crossover connection, including a three other regions that make two antiparallel-beta Hbonds (indicated by the '+' in the table above). The major hairpin makes seven H-bonds and the first strand makes four, with 2 bulges. The alpha helix illustrates another feature found in 3 of these SS-rich structures: a pair of disulfides separated by one turn (either 3 or 4 residues) along the helix. Cysteines on adjacent beta strands or on adjacent turns of helix cannot form a disulfide with each other unless the secondary-structure is very severely distorted; therefore both of these arrangements are probably a way of avoiding unwanted SS pairings, as well as rigidifying the structure. Seven of the proteins have Cys separated by only 1 or 2 in sequence, which are also virtually impossible to pair. The small SS-rich proteins have nearly 10 times the usual Cys content, but have significantly lower percentages of all the large hydrophobics: Val, Ile, Leu, Met, and Phe. The disulfides are hydrophobic as well as strong crosslinks, and they substitute for a normal hydrophobic core in stabilizing these structures. SS-rich proteins are also very low in Ala, especially those with no helix. They have a higher than average content of Tyr, Pro, Asn, and especially Gly. Kinemage 4 shows a part of the scorpion toxin structure that includes examples of several roles played by the glycines (labelled in cyan). The two major functions are: 1) providing room, either for an SS (Gly 36 and Gly 39 here) or for an aromatic (Gly 3 and Trp 47), and 2) adopting an unusual conformation that allows a loop to accomodate the additional constraints imposed by the disulfide connectivity (Gly 50, which has phi = +75). The cluster of 4 aromatics shown here is on the outside of the protein, which is not unusual in these SS-rich structures and helps explain why Tyr is favored for having a hydrophobic portion with a polar OH at the end. Kinemage 5 shows the serine protease inhibitor from silver pheasant ovomucoid (file 2OVO) as an example of a small SS-rich protein with an N-centered overhand topology. Click on the "animate grp" button to see a progressive buildup of the N-centered overhand. Like SN3, OVO has a well-formed alpha-helix as an important part of the structure, with two Cys a turn apart. In this case those two disulfides provide support for the binding loop (across the top in View1), which is held out in the extended but not H-bonded conformation that lets it fit well in the active site of a serine protease. Choose View2 for a closeup of the beta sheet. The major hairpin in OVO (residues 20-33) has only one disulfide, which goes to the C-terminus of the chain. Pancreatic trypsin inhibitor (see file Hurle.kin, PS 1_1) is also an N-centered overhand with only one SS (30-51) on its major hairpin, but it has a helix on each chain terminus instead of one on the crossover. Kinemage 6 shows the first domain of wheat germ agglutinin (file 3WGA), one of four similar domains making up the subunit. It is an irregular N-centered overhand, with a few other beta, helical, and turn Hbonds in the loops. The overall effect is rather like a loose stack of three rope coils, knit together by 4 disulfides. The snake neurotoxins (such as 3EBX) have a similar arrangement, but with much more prominent beta strands and the final SS loop flipped over. Choose View2 and turn on the "C-C hairpin" button, to see the major hairpin in WGA, with its two adjacent disulfides. Kinemage 7 shows hirudin (file 5HIR), an inhibitor of thrombin, which has 3 disulfides and a small beta sheet with simple up-and-down topology. Only the first 49 residues are shown here; residues 50-65 are disordered in solution but bind across the surface of thrombin (see file Karshikv.kin, PS 1_6); the N-terminus occupies the thrombin active site. The connection between beta strands 1 and 2 in hirudin is long and convoluted, but strands 2 and 3 form a hairpin with the now-familiar pair of adjacent disulfides (turn on "C-C hairpin" and choose View2). In hirudin the core of the structure consists mainly of the 3 SS bridges, which pack against each other, as seen in View3. Turn on the "core sc" button to see the 5 other sidechains on the inside, which are a Leu, the hydrophobic portion of a Gln, and 3 Asn's. For the small SS-rich proteins in general, the commonest sidechains to pack against the SS bridges are the other disulfides, aromatic rings, Gly, Asn, and occasionally the hydrophobes one might expect. Of the 12 SS-rich examples, only crambin and insulin are organized more around helices than beta sheets. In crambin the two helices are part of an enlarged hairpin connection, and the two adjacent hairpin Cys are past the end of the beta-sheet Hbonds and manage to pair with one another. Insulin folds as a longer single chain which is then cleaved into the two pieces we see in the mature protein subunit. SMALL IRREGULAR, METAL-RICH Kinemage 8 shows rubredoxin (file 5RXN), which has 54 residues, 4 Cys that bind a non-heme Fe, and some irregular beta sheet. The overall organization can be described either as a highly irregular beta barrel with only partial H-bonding, or as a 3-stranded beta sheet with complex loops and an N-centered overhand topology. View1 has the "barrel" vertical, while View2 looks down on the sheet. View3 is a closeup of the Fe-binding region, with the Cys in yellow and the bonds to the Fe in red. The Cys ligands are in pairs on two loops that are related by a quite good local two-fold axis; each loop has the sequence Cys-x-x-Cys-Gly, with a +phi angle for the Gly. Turn off the Calphas and turn on the mainchain, to see the loop conformations in more detail. Probably the smallest of the metal-rich domains are the Zinc fingers, two types of which are shown on file Summers.kin, PS 1_5. They are only 20-25 residues long, bind a Zn with His and Cys ligands, and interact with DNA. Kinemage 9 shows ferredoxin (from Peptococcus aerogenes; file 1FDX), a redox protein of 54 residues with two Fe4S4 clusters each bound by four Cys. The overall structure looks like a 4-stranded beta sheet with two righthanded crossover connections, but the helices in the connections are short and irregular, and there are no H-bonds between the central two beta strands. However, there is an elegant twofold symmetry to the metal binding (View1 looks down the 2-fold axis), with 3 ligands of each cluster contributed from one half of the protein and one ligand from the other half. This symmetry applies to the entire structure, except for the presence or absence of chain termini. Each cluster is a distorted cube, with the Cys bonded to the Fe atoms, which in turn are bonded to the inorganic S atoms at the pointed corners further from the cluster center (click on an atom to identify it). Kinemage 10 shows Cytochrome C3 (file 2CDV), which manages to bind four heme groups (shades of pink) with only 107 residues. Each heme has covalent links to two Cys and has two His as Fe ligands; turn on the "sidechain" button to see the ligands. One His ligand comes from the chain on one side of the heme, and the other His and the two Cys come from a 5- to 7-residue stretch of chain on the other side of the heme. The alternation of ligands to the various hemes along the sequence is reminiscent of the arrangement in ferredoxin, but cytochrome C3 is more complex and much less regular. Turn off hemes and sidechains to get a clearer idea of the polypeptide conformation; it is a series of loops and irregular short helices, and of course is not very compact without the hemes. In front in View2 is an unusual "interrupted helix"; there is a loop excursion between residues 70 and 78, but there are helical H-bonds between the two pieces. Kinemage 11 shows the second domain of metallothionein (human; file 1MHU), which represents the ultimate in both metal binding and in irregularity: this domain binds 4 metals (Cd here) with 11 Cys in 31 residues, with no secondary structure except a few H-bonded turns. Each metal has 4 Cys ligands (shown in yellow, with seagreen bonds to the green Cd atom markers), but many of them are shared, making a large Cd-S cluster. Domain 1 binds 3 Cd with 9 Cys in 30 residues. Among the small irregular proteins, the metal-rich group is much more heterogeneous than the SS-rich group in overall structure, in local structure, and in amino acid composition. Their main unifying characteristic is that their interactions with metals or metal-containing prosthetic groups are a dominant factor in their structure and stability, while secondary structure is relatively less regular and less important than for most proteins. OTHER VERY SMALL PROTEINS For comparison purposes, it is important to determine the nature of other very small proteins that do not have either disulfides or bound metals. In the size range between about 30 and 80 residues such proteins are not at all common but they do occur. One interesting case is that of eglin and chymotrypsin inhibitor II (file 2CI2), which are quite similar to the ovomucoid inhibitors such as 2OVO but have no disulfides. Eglin is shown on file Hyberts.kin, PS 1_6. They are somewhat longer than the ovomucoids (70 and 83 residues, versus 56) and have four well-formed beta strands with the crossover and tails differently arranged, but the resemblance is very clear. ROP protein (58 residues) and cro repressor (66 residues) both function as dimers and have well-formed secondary structure. The C-terminal fragment of ribosomal protein L7/L12 (file 1 CTF) is 68 residues long, with three beta strands 5 to 7 residues long and three regular alpha-helices of 12 to 16 residues each. Kinemage 12 shows one of the shortest plausible examples of a "bare" small protein: the immunoglobulin-binding domain from Streptococcal protein G (file 2GB1), which is known to be very stable in isolation. GB1 is 56 residues long, with one regular 17-residue alpha helix, four beta strands with 5 to 9 H-bonds per pair, and almost no loops. The topology is unusual, with the helix in the crossover between the two outer strands, and with the N-terminal and C-terminal strands parallel to each other and both buried on the inside of the sheet. There are 16 charged sidechains on the outside and a large hydrophobic core between the helix and the sheet, with 6 aromatics and 5 or 6 large aliphatics (choose View3 and turn on the "core sc"). Although GB1 is certainly a small, stable, disulfide-less structure, it also very definitely is not "irregular". Coordinates from Brookhaven Data Bank files: 1CBH, 4CPA, 1SN3, 2OVO, 3WGA, 5HIR, 5RXN, 1FDX, 2CDV, 1MHU, 2GB1. References: M. Levitt and C. Chothia (1976) Nature 261: 552 - structural patterns in globular proteins J.S. Richardson (1981) Adv. Prot. Chem. 34: 169 - protein anatomy and taxonomy: includes classification, details of SS conformations J.S. Richardson and D.C. Richardson (1989) chap. 1 in "Prediction of Protein Structure and Principles of Protein Conformation", ed. G. Fasman, Plenum Press - survey of protein structure, including classification system P.J. Kraulis, G.M. Clore, M. Nilges, T.A. Jones, G. Pettersson, J. Knowles, and A.M. Gronenborn (1989) Biochemistry 28: 7241 - structure of cellobiohydrolase C-terminal domain, by NMR and simulated annealing (file 1CBH) D.C. Rees and W.N. Lipscomb (1982) J. Mol. Biol. 160: 475 - crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 A resolution (4CPA) R.J. Almassy, J.C. Fontecilla-Camps, F.L. Suddath, and C.E. Bugg (1983) J. Mol. Biol. 170: 387 - crystal structure of variant-3 scorpion neurotoxin at 1.8 A resolution (1SN3) W. Bode, O. Epp, R. Huber, M. Laskowski Jr., and W. Ardelt (1985) Eur. J. Biochem. 147: 387 - crystal structure of 3rd domain of silver pheasant ovomucoid at 1.5 A resolution (2OVO) C.S. Wright (1987) J. Mol. Biol. 194: 501 - crystal structure of wheat germ agglutinin isolectin 2 at 1.8 A resolution J. Drenth, B.W. Low, J.S. Richardson, and C.S. Wright (1980) J. Biol. Chem. 255: 2652 - resemblance between erabutoxin and wheat germ agglutinin P.J.M. Folkers, G.M. Clore, P.C. Driscoll, J. Dodt, S. Koehler, and A.M. Gronenborn (1989) Biochemistry 28: 2601 - NMR structure of recombinant hirudin (5HIR) K.D. Watenpaugh, L.C. Sieker, and L.H. Jensen (1980) J. Mol. Biol. 138: 615 - crystal structure of rubredoxin at 1.2 A resolution (5RXN) E.T. Adman, L.C. Sieker, and L.H. Jensen (1976) J. Biol. Chem. 251: 3801 - crystal structure of Peptococcus aerogenes ferredoxin at 2 A resolution (1FDX) Y. Higuchi, M. Kusunoki, Y. Matsuura, N. Yasuoka, M. Kakudo (1984) J. Mol. Biol. 172: 109 - crystal structure of cytochrome C3 at 2 A resolution (2CDV) B.A. Messerle, A. Schaeffer, M. Vasak, J.H.R. Kaegi, and K. Wuthrich (1990) J. Mol. Biol. 214: 765 - NMR structure of human Cd7 metallothionein (files 1MHU) A.M. Gronenborn, D.R. Filpula, N.Z. Essig, A. Achari, M. Whitlow, P.T. Wingfield, and G.M. Clore (1991) Science 253: 657 - NMR structure of immunoglobulin-binding domain from Strep. protein G (2GB1) @kinemage 1 @caption Cellobiohydrolase C-terminal domain: mainchain and H-bonds for secondary structure (beta in greentint), Calphas for loops (white), and disulfides (yellow). Click repeatedly on "animate grp" to see the C-centered overhand topology, and turn on "C-C hairpin" to highlight the commonly-found pattern of two disulfides adjacent on the strands of the best-formed beta hairpin. @onewidth @matrix .211902 .969618 -.122224 -.954094 .232335 .189012 .211666 .076561 .974339 @2matrix .250941 .960263 .12216 -.741955 .271856 -.612860 -.621717 .063155 .780692 @3matrix -.304393 .952508 .008549 .939193 .30161 -.164158 -.15894 -.041938 -.986398 @group {cellobiohydr} @subgroup {beta sheet} @vectorlist {main ch} color=greentint {ca his 4}P -7.043 -2.057 -4.68 {c his 4}-5.769 -1.898 -5.543 {o his 4}-5.738 -1.081 -6.439 {c his 4}P -5.769 -1.898 -5.543 {n tyr 5}-4.744 -2.66 -5.234 {ca tyr 5}-3.449 -2.54 -5.998 {c tyr 5}-2.85 -1.148 -5.783 {o tyr 5}-2.047 -0.687 -6.571 {c tyr 5}P -2.85 -1.148 -5.783 {n gly 6}-3.254 -0.51 -4.715 {ca gly 6}-2.731 0.849 -4.429 {c gly 6}-1.523 0.799 -3.479 {o gly 6}-1.384 -0.115 -2.691 {c gly 6}P -1.523 0.799 -3.479 {n gln 7}-0.678 1.791 -3.581 {ca gln 7}0.525 1.834 -2.699 {c gln 7}0.17 2.372 -1.317 {o gln 7}-0.144 3.537 -1.178 {c gln 7}P 0.17 2.372 -1.317 {n cys 8}0.227 1.527 -0.317 {ca cys 8}-0.078 2. 1.034 {c cys 8}1.206 2.306 1.787 {o cys 8}1.199 3.074 2.728 {c cys 8}P 1.206 2.306 1.787 {n gly 9}2.293 1.7 1.367 {ca gly 9}3.569 1.962 2.086 {c gly 9}4.788 1.847 1.168 {o gly 9}4.668 1.865 -0.041 {c gly 9}P 4.788 1.847 1.168 {n gly 10}5.94 1.732 1.78 {ca gly 10}7.192 1.63 0.995 {ca thr 23}P -8.149 -5.132 1.033 {c thr 23}-7.273 -4.891 2.258 {o thr 23}-7.736 -4.45 3.291 {c thr 23}P -7.273 -4.891 2.258 {n thr 24}-6.022 -5.185 2.1 {ca thr 24}-5.062 -5.001 3.219 {c thr 24}-3.723 -4.551 2.664 {o thr 24}-3.473 -4.686 1.491 {c thr 24}P -3.723 -4.551 2.664 {n cys 25}-2.881 -4.041 3.512 {ca cys 25}-1.558 -3.578 3.01 {c cys 25}-0.553 -4.726 3.017 {o cys 25}-0.441 -5.452 3.985 {c cys 25}P -0.553 -4.726 3.017 {n gln 26}0.159 -4.858 1.928 {ca gln 26}1.165 -5.949 1.824 {c gln 26}2.5 -5.393 1.341 {o gln 26}2.615 -4.914 0.23 {c 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gln 34}0.871 -2.75 -2.412 {c gln 34}-0.315 -3.206 -1.544 {o gln 34}-0.145 -3.918 -0.577 {c gln 34}P -0.315 -3.206 -1.544 {n cys 35}-1.504 -2.778 -1.93 {ca cys 35}-2.732 -3.167 -1.157 {c cys 35}-3.49 -4.278 -1.882 {o cys 35}-4.037 -4.048 -2.937 {c cys 35}P -3.49 -4.278 -1.882 {n leu 36}-3.544 -5.447 -1.282 {ca leu 36}-4.253 -6.59 -1.946 {c leu 36}-5.201 -7.283 -0.965 {o leu 36}-5.29 -6.789 0.139 {c leu 36}P -5.201 -7.283 -0.965 {oxt leu 36}-5.777 -8.275 -1.38 @vectorlist {Hbonds} color=sea <1.90>{tyr 5 hn} P U -4.86 -3.31 -4.48 {cys 35 o} U -4.28 -3.83 -3.4 <1.98>{cys 8 hn} P U 0.48 0.57 -0.49 {ser 33 o} U 1.51 -0.27 -0.86 <2.37>{gly 9 hn} P U 2.23 1.08 0.58 {ser 33 o} U 2.04 -0.12 -0.54 <1.71>{thr 24 hn} P U -5.74 -5.53 1.21 {leu 36 o} U -5.42 -6.41 0.46 <1.79>{gln 26 hn} P U 0. -4.21 1.18 {gln 34 o} U -0.1 -4.01 -0.05 <1.95>{leu 28 hn} P U 5.49 -4.02 -0.44 {tyr 32 o} U 6.17 -2.95 -0.96 <1.91>{asn 29 hn} P U 7.79 -3.82 -1.56 {tyr 32 o} U 6.86 -2.89 -1.29 <2.03>{tyr 32 hn} P U 8.63 -0.98 -0.91 {asn 29 o} U 9.02 -2.14 -0.18 <2.25>{ser 33 hn} P U 4.68 0.03 -1.34 {gly 9 o} U 4.67 1.31 -0.43 <2.26>{gln 34 hn} P U 2.74 -3.59 -1.6 {gln 26 o} U 2.65 -4.52 -0.32 <2.09>{cys 35 hn} P U -1.55 -2.2 -2.74 {gly 6 o} U -1.43 -0.74 -2.71 <2.10>{leu 36 hn} P U -3.1 -5.54 -0.39 {thr 24 o} U -3.36 -4.94 0.93 @subgroup {loops} @vectorlist {Calpha} color= white {ca thr 1}P -7.649 5.995 1.626 {ca gln 2}-6.044 3.797 -1.009 {ca ser 3}-7.603 1.553 -3.65 {ca his 4}-7.043 -2.057 -4.68 {ca gly 10}P 7.192 1.63 0.995 {ca ile 11}10.162 3.959 1.531 {ca gly 12}9.851 7.221 -0.37 {ca tyr 13}6.067 6.978 0.042 {ca ser 14}4.425 9.987 1.72 {ca gly 15}0.761 9.01 1.333 {ca pro 16}-1.915 7.368 3.484 {ca thr 17}-1.445 3.706 4.325 {ca val 18}-5.069 2.651 4.805 {ca cys 19}-6.176 0.279 2.041 {ca ala 20}-9.755 0.451 0.784 {ca ser 21}-12.21 -1.867 2.562 {ca gly 22}-11.908 -5.53 1.594 {ca thr 23}-8.149 -5.132 1.033 {ca pro 30}P 11.684 -2.059 1.12 {ca tyr 31}10.548 0.563 -1.398 @vectorlist off {Hbonds} color=brown <1.93>{gln 2 hn} P U -6.77 3.76 1.05 {val 18 o} U -6.3 3.17 2.18 <2.22>{gly 6 hn} P U -3.91 -0.96 -4.11 {ser 3 o} U -5.23 -0.29 -3.64 <2.08>{tyr 13 hn} P U 7.93 6. 0.68 {gly 10 o} U 7.63 4.61 0.94 <2.25>{thr 23 hn} P U -9.93 -3.99 1.63 {ala 20 o} U -9.74 -2.43 1.67 <1.85>{tyr 31 hn} P U 10.27 -1.54 -0.88 {asn 29 o} U 9.51 -2.31 -0.17 @subgroup dominant {SS} @vectorlist {SS} color= yellow {ca cys 8}P -0.078 2. 1.034 {cb cys 8}-0.814 0.913 1.778 {sg cys 8}-0.36 -0.803 1.441 {sg cys 25}0.327 -1.466 3.226 {cb cys 25}-1.042 -2.447 3.889 {ca cys 25}-1.558 -3.578 3.01 {ca cys 19}P -6.176 0.279 2.041 {cb cys 19}-5.712 -1.145 1.901 {sg cys 19}-3.929 -1.46 1.927 {sg cys 35}-3.259 -0.698 0.179 {cb cys 35}-3.66 -1.956 -1.047 {ca cys 35}-2.732 -3.167 -1.157 @group {0} dominant animate @vectorlist {dummy} @group {1} dominant animate @vectorlist {4-10} color=sky {ca his 4}P -7.043 -2.057 -4.68 {c his 4}-5.769 -1.898 -5.543 {n tyr 5}-4.744 -2.66 -5.234 {ca tyr 5}-3.449 -2.54 -5.998 {c tyr 5}-2.85 -1.148 -5.783 {n gly 6}-3.254 -0.51 -4.715 {ca gly 6}-2.731 0.849 -4.429 {c gly 6}-1.523 0.799 -3.479 {n gln 7}-0.678 1.791 -3.581 {ca gln 7}0.525 1.834 -2.699 {c gln 7}0.17 2.372 -1.317 {n cys 8}0.227 1.527 -0.317 {ca cys 8}-0.078 2. 1.034 {c cys 8}1.206 2.306 1.787 {n gly 9}2.293 1.7 1.367 {ca gly 9}3.569 1.962 2.086 {c gly 9}4.788 1.847 1.168 {n gly 10}5.94 1.732 1.78 {ca gly 10}7.192 1.63 0.995 @group {2} dominant animate @vectorlist {2a} instance={4-10} @vectorlist {10-23} color=purple {ca gly 10}P 7.192 1.63 0.995 {ca ile 11}10.162 3.959 1.531 {ca gly 12}9.851 7.221 -0.37 {ca tyr 13}6.067 6.978 0.042 {ca ser 14}4.425 9.987 1.72 {ca gly 15}0.761 9.01 1.333 {ca pro 16}-1.915 7.368 3.484 {ca thr 17}-1.445 3.706 4.325 {ca val 18}-5.069 2.651 4.805 {ca cys 19}-6.176 0.279 2.041 {ca ala 20}-9.755 0.451 0.784 {ca ser 21}-12.21 -1.867 2.562 {ca gly 22}-11.908 -5.53 1.594 {ca thr 23}-8.149 -5.132 1.033 @group {3} dominant animate @vectorlist {3a} instance={4-10} @vectorlist {3b} instance={10-23} @vectorlist {23-30} color=magenta {ca thr 23}P -8.149 -5.132 1.033 {c thr 23}-7.273 -4.891 2.258 {n thr 24}-6.022 -5.185 2.1 {ca thr 24}-5.062 -5.001 3.219 {c thr 24}-3.723 -4.551 2.664 {n cys 25}-2.881 -4.041 3.512 {ca cys 25}-1.558 -3.578 3.01 {c cys 25}-0.553 -4.726 3.017 {n gln 26}0.159 -4.858 1.928 {ca gln 26}1.165 -5.949 1.824 {c gln 26}2.5 -5.393 1.341 {n val 27}3.482 -5.462 2.193 {ca val 27}4.816 -4.942 1.807 {c val 27}5.343 -5.711 0.607 {n leu 28}5.636 -5.007 -0.454 {ca leu 28}6.174 -5.713 -1.632 {c leu 28}7.698 -5.804 -1.427 {n asn 29}8.331 -4.642 -1.395 {ca asn 29}9.816 -4.586 -1.117 {c asn 29}10.093 -3.381 -0.187 {n pro 30}11.35 -3.192 0.239 {ca pro 30}11.684 -2.059 1.12 @group {4} dominant animate @vectorlist {4a} instance={4-10} @vectorlist {4b} instance={10-23} @vectorlist {4c} instance={23-30} @vectorlist {30-36} color=hotpink {ca pro 30}P 11.684 -2.059 1.12 {ca tyr 31}10.548 0.563 -1.398 {c tyr 31}9.158 0.575 -2.029 {n tyr 32}8.328 -0.344 -1.616 {ca tyr 32}6.972 -0.406 -2.212 {c tyr 32}6.076 -1.374 -1.452 {n ser 33}4.899 -0.922 -1.116 {ca ser 33}3.938 -1.816 -0.427 {c ser 33}2.591 -1.687 -1.082 {n gln 34}2.168 -2.767 -1.668 {ca gln 34}0.871 -2.75 -2.412 {c gln 34}-0.315 -3.206 -1.544 {n cys 35}-1.504 -2.778 -1.93 {ca cys 35}-2.732 -3.167 -1.157 {c cys 35}-3.49 -4.278 -1.882 {n leu 36}-3.544 -5.447 -1.282 {ca leu 36}-4.253 -6.59 -1.946 {c leu 36}-5.201 -7.283 -0.965 @group dominant off {C-C hairpin} @vectorlist {2SS} instance={SS} color=gold @vectorlist {mc1 HP} instance={23-30} color=red @vectorlist {mc2 HP} instance={30-36} color=red @vectorlist {HP Hb} color=gold <1.71>{thr 24 hn} P U -5.74 -5.53 1.21 {leu 36 o} U -5.42 -6.41 0.46 <1.79>{gln 26 hn} P U 0. -4.21 1.18 {gln 34 o} U -0.1 -4.01 -0.05 <1.95>{leu 28 hn} P U 5.49 -4.02 -0.44 {tyr 32 o} U 6.17 -2.95 -0.96 <1.91>{asn 29 hn} P U 7.79 -3.82 -1.56 {tyr 32 o} U 6.86 -2.89 -1.29 <2.03>{tyr 32 hn} P U 8.63 -0.98 -0.91 {asn 29 o} U 9.02 -2.14 -0.18 <2.26>{gln 34 hn} P U 2.74 -3.59 -1.6 {gln 26 o} U 2.65 -4.52 -0.32 <2.10>{leu 36 hn} P U -3.1 -5.54 -0.39 {thr 24 o} U -3.36 -4.94 0.93 @kinemage 2 @caption Potato carboxypeptidase inhibitor, with disulfides in yellow and inhibitor site in skyblue. Mainchain atoms and H-bonds are included for secondary structure; the 3-10 helix is pink and the beta sheet seagreen. @onewidth @center -20.7 -7.9 10. @zoom .7 @matrix .508631 -.739576 .440818 .826065 .563523 -.007701 -.242716 .368061 .897563 @2zoom 1.05 @2zslab 140 @2matrix -.511517 -.826085 .236504 .012596 .268 .963337 -.85918 .495742 -.126681 @group {PCI} @subgroup {3-10 helix} @vectorlist {main ch} color=pinktint {ca thr 14}P -23.412 -11.218 18.288 {c thr 14}-22.169 -11.038 17.373 {o thr 14}-22.258 -10.963 16.112 {c thr 14}P -22.169 -11.038 17.373 {n his 15}-20.98 -11.098 17.892 {ca his 15}-19.767 -11.018 16.972 {c his 15}-19.5 -12.386 16.327 {o his 15}-18.613 -12.811 15.476 {c his 15}P -19.5 -12.386 16.327 {n asp 16}-20.293 -13.268 16.936 {ca asp 16}-20.271 -14.73 16.847 {c asp 16}-21.061 -15.133 15.633 {o asp 16}-20.594 -16.006 14.9 {c asp 16}P -21.061 -15.133 15.633 {n asp 17}-22.113 -14.383 15.348 {ca asp 17}-22.97 -14.61 14.205 {c asp 17}-22.323 -14.149 12.925 {o asp 17}-22.955 -14.186 11.865 {c asp 17}P -22.323 -14.149 12.925 {n cys 18}-21.038 -13.831 13.011 {ca cys 18}-20.14 -13.403 11.934 @vectorlist {hlx Hb} color=pink <2.66>{asp 17 hn} P U -22.33 -13.62 15.95 {thr 14 o} U -22.28 -11.76 16.06 <2.77>{cys 18 hn} P U -20.64 -13.89 13.93 {his 15 o} U -19.22 -13.14 15.01 @subgroup {beta sheet} @vectorlist {strand 1} color=greentint {ca cys 8}P -18.994 -8.773 5.437 {c cys 8}-20.433 -8.446 5.096 {o cys 8}-20.753 -9.096 4.082 {c cys 8}P -20.433 -8.446 5.096 {n asn 9}-21.146 -7.57 5.723 {ca asn 9}-22.499 -7.22 5.301 {c asn 9}-23.481 -8.345 5.575 {o asn 9}-24.653 -8.212 5.22 {c asn 9}P -23.481 -8.345 5.575 {n lys 10}-23.09 -9.338 6.316 {ca lys 10}-24.021 -10.404 6.769 {c lys 10}-24.749 -9.88 7.984 {o lys 10}-24.124 -9.257 8.865 {c lys 10}P -24.749 -9.88 7.984 {n pro 11}-26.037 -10.135 8.12 {ca pro 11}-26.849 -9.783 9.298 @vectorlist {hairpin} color=greentint {ca gln 25}P -15.649 -9.853 12.195 {c gln 25}-16.168 -9.168 13.445 {o gln 25}-16.356 -9.774 14.544 {c gln 25}P -16.168 -9.168 13.445 {n ala 26}-16.628 -7.93 13.339 {ca ala 26}-17.281 -7.193 14.41 {c ala 26}-18.764 -7.038 14.032 {o ala 26}-18.962 -6.583 12.902 {c ala 26}P -18.764 -7.038 14.032 {n cys 27}-19.605 -7.183 15.017 {ca cys 27}-21.026 -6.779 14.769 {c cys 27}-21.084 -5.253 15.054 {o cys 27}-20.556 -4.873 16.081 {c cys 27}P -21.084 -5.253 15.054 {n trp 28}-21.827 -4.604 14.177 {ca trp 28}-22.008 -3.147 14.359 {c trp 28}-23.383 -2.989 14.956 {o trp 28}-24.149 -3.552 14.188 {c trp 28}P -23.383 -2.989 14.956 {n asn 29}-23.595 -2.535 16.144 {ca asn 29}-24.828 -2.463 16.88 {ca arg 32}P -26.529 -5.074 12.677 {c arg 32}-26.121 -5.992 11.506 {o arg 32}-26.918 -6.861 11.113 {c arg 32}P -26.121 -5.992 11.506 {n thr 33}-24.908 -5.807 11.038 {ca thr 33}-24.221 -6.283 9.876 {c thr 33}-22.781 -6.631 10.169 {o thr 33}-22.127 -5.614 10.625 {c thr 33}P -22.781 -6.631 10.169 {n cys 34}-22.134 -7.748 9.942 {ca cys 34}-20.66 -7.893 9.983 {c cys 34}-19.893 -6.859 9.135 {o cys 34}-20.239 -6.56 7.994 {c cys 34}P -19.893 -6.859 9.135 {n gly 35}-18.978 -6.174 9.761 {ca gly 35}-18.121 -5.122 9.273 {c gly 35}-16.85 -5.473 10.072 {o gly 35}-17.022 -6.404 10.898 {c gly 35}P -16.85 -5.473 10.072 {n pro 36}-15.774 -4.8 9.741 {ca pro 36}-14.481 -5.009 10.378 @vectorlist {beta Hb} color=sea <1.66>{asn 9 hn} P U -20.73 -7.13 6.52 {cys 34 o} U -20.39 -6.73 7.55 <1.81>{cys 34 hn} P U -22.7 -8.54 9.73 {lys 10 o} U -23.7 -9.04 9.12 <1.96>{ala 26 hn} P U -16.52 -7.47 12.46 {gly 35 o} U -16.87 -6.72 11.37 <2.84>{trp 28 hn} P U -22.25 -5.1 13.42 {thr 33 o} U -22.16 -5.46 11.46 <3.07>{thr 33 hn} P U -24.34 -5.21 11.61 {trp 28 o} U -24.21 -4.05 13.41 <2.19>{gly 35 hn} P U -18.86 -6.42 10.72 {ala 26 o} U -18.93 -6.53 12.25 @subgroup {loops} @vectorlist {Calphas} color=white {glx 2}P -13.386 -16.604 -2.426 {his 3}-12.977 -12.861 -3.454 {ala 4}-12.434 -11.231 -0.009 {asp 5}-14.967 -11.385 2.743 {pro 6}-18.06 -13.355 2.128 {ile 7}-19.249 -12.559 5.712 {cys 8}-18.994 -8.773 5.437 {pro 11}P -26.849 -9.783 9.298 {cys 12}-25.321 -10.1 12.72 {lys 13}-26.564 -10.035 16.367 {thr 14}-23.412 -11.218 18.288 {cys 18}P -20.14 -13.403 11.934 {ser 19}-18.67 -16.941 11.062 {gly 20}-15.109 -15.751 10.125 {ala 21}-14.266 -13.32 7.542 {trp 22}-10.618 -12.468 8.207 {phe 23}-12.109 -8.98 7.477 {cys 24}-15.628 -8.292 8.727 {gln 25}-15.649 -9.853 12.195 {asn 29}P -24.828 -2.463 16.88 {ser 30}-26.255 0.165 14.648 {ala 31}-26.407 -1.554 11.183 {arg 32}-26.529 -5.074 12.677 {pro 36}P -14.481 -5.009 10.378 {tyr 37}-13.229 -3.379 13.624 {val 38}-12.622 0.372 12.941 @vectorlist off {turn Hb} color=brown <2.26>{cys 8 hn} P U -18.08 -10.54 4.7 {asp 5 o} U -17.53 -10.68 3.22 <2.13>{lys 10 hn} P U -22.12 -9.35 6.57 {ile 7 o} U -21. -10.33 6.63 <2.15>{cys 12 hn} P U -26.21 -8.88 11.3 {arg 32 o} U -26.7 -7.47 11.17 <2.97>{lys 13 hn} P U -25.06 -10.78 15.13 {thr 14 o} U -23.1 -10.91 15.82 <1.11>{phe 23 hn} P U -12.54 -11.03 7.05 {ala 21 o} U -12.53 -11.76 6.77 <2.14>{ser 30 hn} P U -25.23 -1.75 14.58 {trp 28 o} U -24.47 -3.01 14.31 <2.61>{ala 31 hn} P U -26.01 -1.98 13.25 {trp 28 o} U -24.71 -3.08 13.91 @subgroup dominant {SS} @vectorlist {SSa} color=yellow {cys 8}P -18.994 -8.773 5.437 {cb cys 8}-18.069 -8.012 4.468 {sg cys 8}-16.346 -7.999 5.058 {sg cys 24}-16.513 -6.758 6.575 {cb cys 24}-16.809 -8.035 7.811 {cys 24}-15.628 -8.292 8.727 @vectorlist {SS} color=yellow {cys 12}P -25.321 -10.1 12.72 {cb cys 12}-24.148 -9.061 12.675 {sg cys 12}-23.368 -8.99 14.286 {sg cys 27}-23.838 -7.194 14.887 {cb cys 27}-22.118 -7.371 15.633 {cys 27}-21.026 -6.779 14.769 {cys 18}P -20.14 -13.403 11.934 {cb cys 18}-19.341 -12.105 12.232 {sg cys 18}-20.358 -10.549 12.153 {sg cys 34}-21.277 -10.483 10.392 {cb cys 34}-20.267 -9.273 9.485 {cys 34}-20.66 -7.893 9.983 @subgroup {inhib site} @vectorlist {Gly 39} color=sky {n gly 39} P -11.303 0.403 17.922 {n gly 39} -11.303 0.403 17.922 {ca gly 39} -12.735 0.68 17.882 {c gly 39} -13.053 2.177 18.164 {o gly 39} -13.624 2.944 17.307 {c gly 39} P -13.053 2.177 18.164 {oxt gly 39} -13.281 2.474 19.404 @group dominant off {C-C hairpin} @vectorlist {2SS} instance={SS} color=gold @vectorlist {mc HP} instance={hairpin} color=red @vectorlist {HP end} color=red {asn 29}P -24.828 -2.463 16.88 {ser 30}-26.255 0.165 14.648 {ala 31}-26.407 -1.554 11.183 {arg 32}-26.529 -5.074 12.677 @vectorlist {HP Hb} color=gold <1.96>{ala 26 hn} P U -16.52 -7.47 12.46 {gly 35 o} U -16.87 -6.72 11.37 <2.84>{trp 28 hn} P U -22.25 -5.1 13.42 {thr 33 o} U -22.16 -5.46 11.46 <3.07>{thr 33 hn} P U -24.34 -5.21 11.61 {trp 28 o} U -24.21 -4.05 13.41 <2.19>{gly 35 hn} P U -18.86 -6.42 10.72 {ala 26 o} U -18.93 -6.53 12.25 @kinemage 3 @caption Scorpion neurotoxin 3: mainchain for secondary structures (beta seagreen, helix pink), Calphas on loops (white), plus Hbonds and disulfides (yellow). @onewidth @zoom .85 @matrix .510442 .855111 -.09074 -.253783 .250626 .934227 .82161 -.453841 .344942 @2matrix .539156 -.73883 -.404277 -.836217 -.412474 -.361394 .100256 .532912 -.84021 @group {SN3} @subgroup {helix} @vectorlist {main ch} color=pinktint {ca asn 22}P 10.56 28.236 19.013 {c asn 22}11.011 29.597 18.855 {o asn 22}12.179 29.86 18.592 {c asn 22}P 11.011 29.597 18.855 {n glu 23}10.103 30.461 18.691 {ca glu 23}10.487 31.701 18.273 {c glu 23}11.265 32.54 19.287 {o glu 23}12.049 33.429 18.849 {c glu 23}P 11.265 32.54 19.287 {n gly 24}11.224 32.273 20.585 {ca gly 24}12.07 33.02 21.525 {c gly 24}13.538 32.59 21.379 {o gly 24}14.467 33.429 21.424 {c gly 24}P 13.538 32.59 21.379 {n cys 25}13.772 31.333 21.133 {ca cys 25}15.142 30.928 20.927 {c cys 25}15.676 31.417 19.611 {o cys 25}16.885 31.73 19.473 {c cys 25}P 15.676 31.417 19.611 {n asp 26}14.856 31.404 18.589 {ca asp 26}15.297 31.918 17.302 {c asp 26}15.645 33.392 17.373 {o asp 26}16.688 33.772 16.901 {c asp 26}P 15.645 33.392 17.373 {n thr 27}14.887 34.197 18.118 {ca thr 27}15.178 35.592 18.203 {c thr 27}16.511 35.842 18.81 {o thr 27}17.17 36.79 18.592 {c thr 27}P 16.511 35.842 18.81 {n glu 28}16.698 35.179 19.826 {ca glu 28}17.866 35.35 20.608 {c glu 28}19.106 34.861 19.834 {o glu 28}20.139 35.517 19.792 {c glu 28}P 19.106 34.861 19.834 {n cys 29}19.018 33.763 19.16 {ca cys 29}20.211 33.237 18.46 {c cys 29}20.548 34.202 17.285 {o cys 29}21.726 34.427 17.04 {c cys 29}P 20.548 34.202 17.285 {n lys 30}19.583 34.774 16.611 {ca lys 30}19.822 35.634 15.476 {c lys 30}20.258 37.061 15.823 {o lys 30}20.813 37.767 14.925 {c lys 30}P 20.258 37.061 15.823 {n ala 31}20.04 37.504 17.042 {ca ala 31}20.372 38.853 17.37 @vectorlist {Hb} color=pink <2.12>{asp 26 hn} P U 13.93 31.04 18.7 {asn 22 o} U 12.7 30.21 18.63 <2.11>{thr 27 hn} P U 14.1 33.84 18.63 {glu 23 o} U 12.67 33.55 18.78 <2.31>{glu 28 hn} P U 15.99 34.52 20.07 {gly 24 o} U 14.92 33.76 21.02 <2.03>{cys 29 hn} P U 18.13 33.3 19.13 {cys 25 o} U 17.26 32.2 19.37 <2.12>{lys 30 hn} P U 18.64 34.6 16.9 {asp 26 o} U 17.27 34.02 16.9 <2.62>{ala 31 hn} P U 19.65 36.9 17.74 {thr 27 o} U 17.91 36.82 18.34 <2.53>{ala 31 hn} P U 19.65 36.9 17.74 {glu 28 o} U 19.99 35.93 19.18 @subgroup {beta sheet} @vectorlist {strand 1} color=greentint {n lys 1}P 29.816 27.747 14.107 {ca lys 1}29.634 26.971 15.354 {c lys 1}28.13 26.632 15.479 {o lys 1}27.336 27.559 15.312 {c lys 1}P 28.13 26.632 15.479 {n glu 2}27.834 25.543 16.221 {ca glu 2}26.542 25.359 16.873 {c glu 2}26.703 25.05 18.358 {o glu 2}27.72 24.503 18.798 {c glu 2}P 26.703 25.05 18.358 {n gly 3}25.67 25.309 19.12 {ca gly 3}25.644 24.866 20.484 {c gly 3}24.492 25.526 21.243 {o gly 3}23.88 26.461 20.738 {c gly 3}P 24.492 25.526 21.243 {n tyr 4}24.456 25.321 22.55 {ca tyr 4}23.574 26.09 23.414 {c tyr 4}24.093 27.442 23.631 {o tyr 4}25.229 27.605 24.097 {c tyr 4}P 24.093 27.442 23.631 {n leu 5}23.2 28.398 23.643 {ca leu 5}23.563 29.722 24.035 @vectorlist {hairpin} color=greentint {ca gly 36}P 23.797 32.962 14.626 {c gly 36}22.816 33.079 13.522 {o gly 36}22.297 34.16 13.209 {c gly 36}P 22.816 33.079 13.522 {n ser 37}22.567 31.96 12.87 {ca ser 37}21.68 31.893 11.665 {c ser 37}20.227 31.521 12.074 {o ser 37}19.262 32.131 11.583 {c ser 37}P 20.227 31.521 12.074 {n tyr 38}20.04 30.448 12.825 {ca tyr 38}18.706 29.897 13.164 {c tyr 38}18.795 29.3 14.55 {o tyr 38}19.723 28.582 14.781 {c tyr 38}P 18.795 29.3 14.55 {n gly 39}17.85 29.517 15.431 {ca gly 39}17.861 28.791 16.704 {c gly 39}16.548 28.048 16.949 {o gly 39}15.515 28.436 16.399 {c gly 39}P 16.548 28.048 16.949 {n tyr 40}16.543 27.133 17.898 {ca tyr 40}15.333 26.428 18.324 {c tyr 40}15.536 25.872 19.719 {o tyr 40}16.594 26.044 20.32 {c tyr 40}P 15.536 25.872 19.719 {n cys 41}14.498 25.204 20.244 {ca cys 41}14.55 24.699 21.573 {c cys 41}14.783 23.175 21.599 {o cys 41}14.078 22.428 20.941 {c cys 41}P 14.783 23.175 21.599 {n tyr 42}15.894 22.754 22.177 {ca tyr 42}16.288 21.355 22.161 {c tyr 42}16.683 20.888 23.597 {o tyr 42}17.409 21.581 24.314 {c tyr 42}P 16.683 20.888 23.597 {n ala 43}15.956 19.936 24.052 {ca ala 43}16.076 19.564 25.396 {ca phe 44}P 14.581 22.583 27.146 {c phe 44}15.603 23.706 27.281 {o phe 44}15.52 24.491 28.207 {c phe 44}P 15.603 23.706 27.281 {n ala 45}16.444 23.914 26.265 {ca ala 45}17.305 25.012 26.24 {c ala 45}17.513 25.48 24.823 {o ala 45}17.373 24.67 23.894 {c ala 45}P 17.513 25.48 24.823 {n cys 46}17.866 26.72 24.611 {ca cys 46}17.959 27.217 23.202 {c cys 46}19.272 26.783 22.595 {o cys 46}20.315 27.208 23.072 {c cys 46}P 19.272 26.783 22.595 {n trp 47}19.158 26.261 21.396 {ca trp 47}20.294 25.793 20.611 {c trp 47}20.346 26.653 19.363 {o trp 47}19.277 27.125 18.914 {c trp 47}P 20.346 26.653 19.363 {n cys 48}21.55 27.096 18.985 {ca cys 48}21.69 28.114 17.923 {c cys 48}22.691 27.534 16.887 {o cys 48}23.719 26.916 17.299 {c cys 48}P 22.691 27.534 16.887 {n glu 49}22.37 27.618 15.6 {ca glu 49}23.231 27.146 14.536 {c glu 49}23.89 28.327 13.793 {o glu 49}23.345 29.425 13.83 {c glu 49}P 23.89 28.327 13.793 {n gly 50}25.11 28.156 13.251 {ca gly 50}25.753 29.25 12.526 {c gly 50}26.308 30.352 13.381 {o gly 50}26.422 31.5 12.932 {c gly 50}P 26.308 30.352 13.381 {n leu 51}26.687 30.056 14.595 {ca leu 51}27.362 31.104 15.374 @vectorlist {Hb} color=sea <2.16>{gly 3 hn} P U 24.9 25.82 18.75 {cys 48 o} U 24.07 26.59 17.73 <2.20>{leu 5 hn} P U 22.26 28.2 23.38 {cys 46 o} U 20.9 27.51 23.16 <1.84>{ser 37 hn} P U 23.01 31.13 13.22 {glu 49 o} U 23.24 29.94 13.65 <2.63>{tyr 38 hn} P U 20.86 30. 13.18 {glu 49 o} U 22.6 29.6 13.63 <1.96>{tyr 40 hn} P U 17.41 26.92 18.34 {trp 47 o} U 18.72 27.06 18.74 <1.98>{tyr 42 hn} P U 16.48 23.42 22.64 {ala 45 o} U 17.1 24.3 23.52 <2.27>{ala 45 hn} P U 16.49 23.29 25.49 {tyr 42 o} U 17.13 22.09 24.67 <1.79>{trp 47 hn} P U 18.24 26.19 21.01 {tyr 40 o} U 17.09 26.09 20.53 <1.94>{glu 49 hn} P U 21.49 28.03 15.35 {tyr 38 o} U 20.25 28.42 14.95 <2.02>{cys 48 hn} P U 22.36 26.73 19.43 {gly 3 o} U 23.43 26.54 20.35 <1.82>{leu 51 hn} P U 26.51 29.14 14.96 {lys 1 o} U 27.09 28.03 15.21 @subgroup {loops} @vectorlist {Calpha} color= white {ca leu 5}P 23.563 29.722 24.035 {ca val 6}24.886 30.832 27.488 {ca lys 7}24.217 33.863 29.506 {ca lys 8}27.263 35.909 30.356 {ca ser 9}25.888 37.07 33.619 {ca asp 10}25.265 33.788 35.234 {ca gly 11}26.806 31.116 32.964 {ca cys 12}23.579 29.313 32.577 {ca lys 13}21.581 28.16 29.404 {ca tyr 14}18.571 30.039 28.126 {ca gly 15}15.775 27.78 29.136 {ca cys 16}12.692 27.213 26.886 {ca leu 17}9.465 25.15 27.171 {ca lys 18}8.344 24.353 23.612 {ca leu 19}10.58 21.885 22.017 {ca gly 20}11.395 22.328 18.451 {ca glu 21}10.487 25.468 16.509 {ca asn 22}10.56 28.236 19.013 {ca ala 31}P 20.372 38.853 17.37 {ca lys 32}23.657 40.239 16.043 {ca asn 33}25.016 40.23 19.354 {ca gln 34}25.006 36.348 19.354 {ca gly 35}25.369 36.31 15.512 {ca gly 36}23.797 32.962 14.626 {ca ala 43}P 16.076 19.564 25.396 {ca phe 44}14.581 22.583 27.146 {ca leu 51}P 27.362 31.104 15.374 {ca pro 52}30.75 32.69 14.88 {ca glu 53}33.552 31.087 16.698 {ca ser 54}33.853 34.106 18.917 {ca thr 55}30.418 33.584 20.444 {ca pro 56}30.47 31.709 23.73 {ca thr 57}28.394 28.553 24.035 {ca tyr 58}27.522 26.432 27.154 {ca pro 59}29.458 25.906 29.311 {ca leu 60}31.077 29.375 29.723 {ca pro 61}34.559 28.803 31.307 {ca asn 62}34.299 32.022 33.278 {ca lys 63}31.357 31.095 35.482 {ca ser 64}29.489 27.793 36.021 {ca cys 65}25.737 27.856 36.12 @vectorlist off {other Hb} color=brown <1.78>{lys 7 hn} P U 23.97 31.81 29.7 {cys 12 o} U 23.39 30.8 30.14 <1.94>{gly 11 hn} P U 26.07 33.08 32.86 {lys 7 o} U 26.05 33.37 31.53 <2.09>{cys 16 hn} P U 14.26 26.15 27.97 {phe 44 o} U 15.14 24.99 28.14 <1.84>{gly 20 hn} P U 12.34 22.23 20.39 {cys 41 o} U 13.56 22.37 20.78 <2.03>{cys 41 hn} P U 13.66 25.05 19.72 {gly 20 o} U 12.56 24.75 18.87 <2.08>{cys 46 hn} P U 18.06 27.3 25.4 {tyr 14 o} U 17.62 27.96 26.62 <1.98>{tyr 58 hn} P U 26.72 27.17 25.32 {tyr 4 o} U 25.68 27.48 24.46 <2.01>{gly 35 hn} P U 23.92 36.77 17.03 {ala 31 o} U 23.04 37.77 17.48 <2.08>{gly 36 hn} P U 23.56 34.47 16.07 {cys 29 o} U 22.28 34.44 16.75 <2.07>{thr 55 hn} P U 31.49 33.23 18.53 {pro 52 o} U 31.12 32.25 17.52 <2.55>{lys 63 hn} P U 32.08 30.68 33.5 {leu 60 o} U 31.99 29.31 32.35 @subgroup dominant {SS} @vectorlist {SS} color= yellow {ca cys 16}P 12.692 27.213 26.886 {cb cys 16}13.185 27.271 25.427 {sg cys 16}14.285 25.889 24.93 {sg cys 41}13.128 24.528 23.973 {cb cys 41}13.211 24.996 22.189 {ca cys 41}14.55 24.699 21.573 {ca cys 25}P 15.142 30.928 20.927 {cb cys 25}15.261 29.413 20.896 {sg cys 25}15.001 28.519 22.471 {sg cys 46}16.299 29.396 23.702 {cb cys 46}17.928 28.72 23.242 {ca cys 46}17.959 27.217 23.202 @vectorlist {SSb} color= yellow {ca cys 29}P 20.211 33.237 18.46 {cb cys 29}19.744 31.926 17.889 {sg cys 29}20.756 31.12 16.563 {sg cys 48}22.489 30.741 17.553 {cb cys 48}22.188 29.359 18.635 {ca cys 48}21.69 28.114 17.923 {ca cys 12}P 23.579 29.313 32.577 {cb cys 12}22.38 29.613 33.467 {sg cys 12}22.738 29.359 35.225 {sg cys 65}23.107 27.43 35.324 {cb cys 65}24.886 27.242 35.005 {ca cys 65}25.737 27.856 36.12 @group dominant off {C-C hairpin} @vectorlist {2SS} instance={SS} color=gold @vectorlist {mc HP} instance={hairpin} color=red @vectorlist {HP end} color=red {ca ala 43}P 16.076 19.564 25.396 {ca phe 44}14.581 22.583 27.146 @vectorlist {HP Hb} color=gold <1.84>{ser 37 hn} P U 23.01 31.13 13.22 {glu 49 o} U 23.24 29.94 13.65 <2.63>{tyr 38 hn} P U 20.86 30. 13.18 {glu 49 o} U 22.6 29.6 13.63 <1.96>{tyr 40 hn} P U 17.41 26.92 18.34 {trp 47 o} U 18.72 27.06 18.74 <1.98>{tyr 42 hn} P U 16.48 23.42 22.64 {ala 45 o} U 17.1 24.3 23.52 <2.27>{ala 45 hn} P U 16.49 23.29 25.49 {tyr 42 o} U 17.13 22.09 24.67 <1.79>{trp 47 hn} P U 18.24 26.19 21.01 {tyr 40 o} U 17.09 26.09 20.53 <1.94>{glu 49 hn} P U 21.49 28.03 15.35 {tyr 38 o} U 20.25 28.42 14.95 @kinemage 4 @caption Scorpion neurotoxin 3: closeup showing interactions of Gly (cyan), aromatics (seagreen), and disulfides (yellow) around the beta sheet. @onewidth @zoom 1.4 @center 21. 27. 19.3 @matrix -.79318 .570729 .212444 .028159 .382847 -.923382 -.608335 -.726427 -.319737 @group {SN3} @subgroup {mainchain} @vectorlist {Calpha} color= white {ca lys 1}P 29.634 26.971 15.354 {ca glu 2}26.542 25.359 16.873 {ca gly 3}25.644 24.866 20.484 {ca tyr 4}23.574 26.09 23.414 {ca leu 5}23.563 29.722 24.035 {ca val 6}24.886 30.832 27.488 {ca lys 7}24.217 33.863 29.506 {ca lys 8}27.263 35.909 30.356 {ca ser 9}25.888 37.07 33.619 {ca asp 10}25.265 33.788 35.234 {ca gly 11}26.806 31.116 32.964 {ca cys 12}23.579 29.313 32.577 {ca lys 13}21.581 28.16 29.404 {ca tyr 14}18.571 30.039 28.126 {ca gly 15}15.775 27.78 29.136 {ca cys 16}12.692 27.213 26.886 {ca leu 17}9.465 25.15 27.171 {ca lys 18}8.344 24.353 23.612 {ca leu 19}10.58 21.885 22.017 {ca gly 20}11.395 22.328 18.451 {ca glu 21}10.487 25.468 16.509 {ca asn 22}10.56 28.236 19.013 {ca glu 23}10.487 31.701 18.273 {ca gly 24}12.07 33.02 21.525 {ca cys 25}15.142 30.928 20.927 {ca asp 26}15.297 31.918 17.302 {ca thr 27}15.178 35.592 18.203 {ca glu 28}17.866 35.35 20.608 {ca cys 29}20.211 33.237 18.46 {ca lys 30}19.822 35.634 15.476 {ca ala 31}20.372 38.853 17.37 {ca lys 32}23.657 40.239 16.043 {ca asn 33}25.016 40.23 19.354 {ca gln 34}25.006 36.348 19.354 {ca gly 35}25.369 36.31 15.512 {ca gly 36}23.797 32.962 14.626 {ca ser 37}21.68 31.893 11.665 {ca tyr 38}18.706 29.897 13.164 {ca gly 39}17.861 28.791 16.704 {ca tyr 40}15.333 26.428 18.324 {ca cys 41}14.55 24.699 21.573 {ca tyr 42}16.288 21.355 22.161 {ca ala 43}16.076 19.564 25.396 {ca phe 44}14.581 22.583 27.146 {ca ala 45}17.305 25.012 26.24 {ca cys 46}17.959 27.217 23.202 {ca trp 47}20.294 25.793 20.611 {ca cys 48}21.69 28.114 17.923 {ca glu 49}23.231 27.146 14.536 {ca gly 50}25.753 29.25 12.526 {ca leu 51}27.362 31.104 15.374 {ca pro 52}30.75 32.69 14.88 {ca glu 53}33.552 31.087 16.698 {ca ser 54}33.853 34.106 18.917 {ca thr 55}30.418 33.584 20.444 {ca pro 56}30.47 31.709 23.73 {ca thr 57}28.394 28.553 24.035 {ca tyr 58}27.522 26.432 27.154 {ca pro 59}29.458 25.906 29.311 {ca leu 60}31.077 29.375 29.723 {ca pro 61}34.559 28.803 31.307 {ca asn 62}34.299 32.022 33.278 {ca lys 63}31.357 31.095 35.482 {ca ser 64}29.489 27.793 36.021 {ca cys 65}25.737 27.856 36.12 @vectorlist off {beta Hb} color=brown <2.16>{gly 3 hn} P U 24.9 25.82 18.75 {cys 48 o} U 24.07 26.59 17.73 <2.20>{leu 5 hn} P U 22.26 28.2 23.38 {cys 46 o} U 20.9 27.51 23.16 <2.08>{gly 36 hn} P U 23.56 34.47 16.07 {cys 29 o} U 22.28 34.44 16.75 <1.84>{ser 37 hn} P U 23.01 31.13 13.22 {glu 49 o} U 23.24 29.94 13.65 <2.63>{tyr 38 hn} P U 20.86 30. 13.18 {glu 49 o} U 22.6 29.6 13.63 <1.96>{tyr 40 hn} P U 17.41 26.92 18.34 {trp 47 o} U 18.72 27.06 18.74 <1.98>{tyr 42 hn} P U 16.48 23.42 22.64 {ala 45 o} U 17.1 24.3 23.52 <2.27>{ala 45 hn} P U 16.49 23.29 25.49 {tyr 42 o} U 17.13 22.09 24.67 <1.79>{trp 47 hn} P U 18.24 26.19 21.01 {tyr 40 o} U 17.09 26.09 20.53 <2.02>{cys 48 hn} P U 22.36 26.73 19.43 {gly 3 o} U 23.43 26.54 20.35 <1.94>{glu 49 hn} P U 21.49 28.03 15.35 {tyr 38 o} U 20.25 28.42 14.95 <1.82>{leu 51 hn} P U 26.51 29.14 14.96 {lys 1 o} U 27.09 28.03 15.21 <1.98>{tyr 58 hn} P U 26.72 27.17 25.32 {tyr 4 o} U 25.68 27.48 24.46 @subgroup {sidechain} @vectorlist {SS} color= yellow {ca cys 16}P 12.692 27.213 26.886 {cb cys 16}13.185 27.271 25.427 {sg cys 16}14.285 25.889 24.93 {sg cys 41}13.128 24.528 23.973 {cb cys 41}13.211 24.996 22.189 {ca cys 41}14.55 24.699 21.573 {ca cys 25}P 15.142 30.928 20.927 {cb cys 25}15.261 29.413 20.896 {sg cys 25}15.001 28.519 22.471 {sg cys 46}16.299 29.396 23.702 {cb cys 46}17.928 28.72 23.242 {ca cys 46}17.959 27.217 23.202 {ca cys 29}P 20.211 33.237 18.46 {cb cys 29}19.744 31.926 17.889 {sg cys 29}20.756 31.12 16.563 {sg cys 48}22.489 30.741 17.553 {cb cys 48}22.188 29.359 18.635 {ca cys 48}21.69 28.114 17.923 @labellist {Gly} color=cyan {Gly} 25.644 24.866 20.484 <3>{Gly} 23.797 32.962 14.626 <36>{Gly} 17.861 28.791 16.704 <39>{Gly} 25.753 29.25 12.526 <50>@vectorlist {arom} color=sea {ca tyr 4}P 23.574 26.09 23.414 {cb tyr 4}23.423 25.334 24.727 {cg tyr 4}22.733 24.015 24.571 {cd1 tyr 4}21.368 23.973 24.252 {ce1 tyr 4}20.709 22.737 24.086 {cz tyr 4}21.431 21.576 24.255 {oh tyr 4}20.829 20.428 24.176 {cg tyr 4}P 22.733 24.015 24.571 {cd2 tyr 4}23.434 22.833 24.684 {ce2 tyr 4}22.764 21.61 24.535 {cz tyr 4}21.431 21.576 24.255 {ca tyr 40}P 15.333 26.428 18.324 {cb tyr 40}15.048 25.28 17.316 {cg tyr 40}16.205 24.474 16.817 {cd1 tyr 40}16.973 24.958 15.831 {ce1 tyr 40}18.032 24.207 15.397 {cz tyr 40}18.286 22.971 15.944 {oh tyr 40}19.288 22.265 15.462 {cg tyr 40}P 16.205 24.474 16.817 {cd2 tyr 40}16.465 23.196 17.381 {ce2 tyr 40}17.513 22.449 16.938 {cz tyr 40}18.286 22.971 15.944 {ca tyr 42}P 16.288 21.355 22.161 {cb tyr 42}17.497 21.176 21.243 {cg tyr 42}17.617 19.752 20.845 {cd1 tyr 42}18.369 18.904 21.63 {ce1 tyr 42}18.462 17.552 21.305 {cz tyr 42}17.783 17.051 20.204 {oh tyr 42}17.84 15.731 19.925 {cg tyr 42}P 17.617 19.752 20.845 {cd2 tyr 42}16.963 19.284 19.727 {ce2 tyr 42}17.046 17.932 19.394 {cz tyr 42}17.783 17.051 20.204 {ca trp 47}P 20.294 25.793 20.611 {cb trp 47}20.035 24.307 20.204 {cg trp 47}21.073 23.664 19.27 {cd1 trp 47}21.114 23.722 17.929 {ne1 trp 47}22.282 22.983 17.457 {ce2 trp 47}22.909 22.47 18.533 {cz2 trp 47}24.072 21.739 18.541 {ch2 trp 47}24.513 21.372 19.843 {cg trp 47}P 21.073 23.664 19.27 {cd2 trp 47}22.214 22.866 19.702 {ce2 trp 47}22.909 22.47 18.533 {cd2 trp 47}P 22.214 22.866 19.702 {ce3 trp 47}22.66 22.474 20.949 {cz3 trp 47}23.854 21.723 20.983 {ch2 trp 47}24.513 21.372 19.843 @vectorlist {hphobic} color=orange {ca leu 5}P 23.563 29.722 24.035 {cb leu 5}22.468 30.69 23.612 {cg leu 5}22.204 30.891 22.115 {cd1 leu 5}21.124 31.926 21.977 {cg leu 5}P 22.204 30.891 22.115 {cd2 leu 5}23.382 31.534 21.503 {ca ala 45}P 17.305 25.012 26.24 {cb ala 45}18.67 24.641 26.799 {ca leu 51}P 27.362 31.104 15.374 {cb leu 51}27.439 30.682 16.814 {cg leu 51}26.173 30.59 17.593 {cd1 leu 51}26.485 29.947 18.937 {cg leu 51}P 26.173 30.59 17.593 {cd2 leu 51}25.597 31.964 17.864 @kinemage 5 @caption Ovomucoid inhibitor: mainchain for secondary structures (helix pink, beta greentint), Calphas for loops, Hbonds, and disulfides (yellow). View2 is a closeup of the beta sheet; the animation builds up the N-centered overhand topology. @onewidth @zoom .75 @matrix .446555 -.889375 -.09798 -.894755 -.443665 -.05075 .001666 .110331 -.993893 @center 3.4 .3 11.8 @2zoom 1.1 @2center 9.9 2.6 13.4 @2zslab 170 @2matrix .166314 -.546492 .820784 .864052 .481845 .145739 -.475135 .684961 .552336 @3matrix -.493961 -.104801 -.863145 -.64936 .704629 .286061 .578217 .701794 -.416112 @group {ovomuc inh} @subgroup {beta sheet} @vectorlist {main ch} color=greentint {ca tyr 20}10.947 -5.489 4.06 {c tyr 20}11.37 -4.061 3.847 {o tyr 20}12.286 -3.784 3.021 {c tyr 20}P 11.37 -4.061 3.847 {n arg 21}10.479 -3.198 4.244 {ca arg 21}10.561 -1.759 4.048 {c arg 21}10.324 -1.02 5.359 {o arg 21}9.214 -0.437 5.503 {c arg 21}P 10.324 -1.02 5.359 {n pro 22}11.254 -1.114 6.32 {ca pro 22}10.998 -0.893 7.77 {c pro 22}10.624 0.504 8.231 {o pro 22}11.048 1.546 7.666 {c pro 22}P 10.624 0.504 8.231 {n leu 23}9.815 0.538 9.269 {ca leu 23}9.251 1.77 9.857 {c leu 23}9.399 1.638 11.357 {o leu 23}9.093 0.554 11.918 {c leu 23}P 9.399 1.638 11.357 {n cys 24}9.807 2.679 11.992 {ca cys 24}9.944 2.59 13.445 {c cys 24}8.753 3.279 14.147 {o cys 24}8.567 4.522 14.031 {c cys 24}P 8.753 3.279 14.147 {n gly 25}8.008 2.482 14.931 {ca gly 25}6.874 3.021 15.698 {c gly 25}7.28 3.81 16.928 {o gly 25}8.359 3.527 17.52 {c gly 25}P 7.28 3.81 16.928 {n ser 26}6.357 4.63 17.413 {ca ser 26}6.539 5.313 18.695 {c ser 26}6.586 4.372 19.887 {o ser 26}7.014 4.76 20.998 {c ser 26}P 6.586 4.372 19.887 {n asp 27}6.24 3.149 19.665 {ca asp 27}6.31 2.142 20.698 {c asp 27}7.67 1.42 20.727 {o asp 27}7.799 0.411 21.471 {c asp 27}P 7.67 1.42 20.727 {n asn 28}8.594 1.918 19.856 {ca asn 28}10.016 1.413 19.777 {c asn 28}10.06 -0.016 19.226 {o asn 28}11.036 -0.76 19.469 {c asn 28}P 10.06 -0.016 19.226 {n lys 29}9.084 -0.33 18.357 {ca lys 29}9.086 -1.483 17.486 {c lys 29}9.399 -1.125 16.039 {o lys 29}8.799 -0.195 15.451 {c lys 29}P 9.399 -1.125 16.039 {n thr 30}10.18 -1.97 15.418 {ca thr 30}10.333 -1.897 13.996 {c thr 30}9.227 -2.75 13.337 {o thr 30}9.296 -4.003 13.379 {c thr 30}P 9.227 -2.75 13.337 {n tyr 31}8.395 -2.1 12.554 {ca tyr 31}7.395 -2.739 11.662 {c tyr 31}7.928 -2.987 10.25 {o tyr 31}8.614 -2.092 9.71 {c tyr 31}P 7.928 -2.987 10.25 {n gly 32}7.807 -4.19 9.747 {ca gly 32}8.502 -4.713 8.547 {c gly 32}8.17 -3.866 7.326 {o gly 32}8.915 -3.906 6.323 {c gly 32}P 8.17 -3.866 7.326 {n asn 33}6.999 -3.265 7.354 {ca asn 33}6.443 -2.498 6.23 {ca thr 49}P 2.305 6.846 15.965 {c thr 49}3.632 6.458 15.35 {o thr 49}4.272 5.49 15.837 {c thr 49}P 3.632 6.458 15.35 {n leu 50}3.929 7.091 14.245 {ca leu 50}5.254 6.871 13.594 {c leu 50}6.344 7.685 14.309 {o leu 50}6.241 8.924 14.389 {c leu 50}P 6.344 7.685 14.309 {n ser 51}7.354 7.019 14.779 {ca ser 51}8.551 7.75 15.299 {c ser 51}9.442 8.219 14.143 {o ser 51}9.631 9.433 13.915 {c ser 51}P 9.442 8.219 14.143 {n his 52}9.876 7.301 13.347 {ca his 52}10.616 7.67 12.127 {c his 52}10.646 6.565 11.086 {o his 52}10.455 5.355 11.388 {c his 52}P 10.646 6.565 11.086 {n phe 53}10.934 6.978 9.893 {ca phe 53}11.191 6.078 8.794 {c phe 53}12.48 5.307 9.064 {o phe 53}13.352 5.819 9.814 {c phe 53}P 12.48 5.307 9.064 {n gly 54}12.494 4.044 8.656 {ca gly 54}13.666 3.161 8.786 @vectorlist {beta Hb} color=sea <1.81>{arg 21 hn} P U 9.68 -3.57 4.72 {gly 32 o} U 9.15 -3.81 5.84 <2.00>{leu 23 hn} P U 9.58 -0.34 9.67 {tyr 31 o} U 8.9 -1.57 9.7 <1.90>{cys 24 hn} P U 10.02 3.51 11.48 {his 52 o} U 10.32 4.8 11.41 <1.85>{gly 25 hn} P U 8.23 1.51 14.99 {lys 29 o} U 8.63 0.32 15.31 <1.78>{ser 26 hn} P U 5.52 4.78 16.89 {thr 49 o} U 4.65 5.28 16.15 <1.93>{asn 28 hn} P U 8.31 2.65 19.24 {gly 25 o} U 8.34 3.27 18.04 <1.89>{tyr 31 hn} P U 8.46 -1.1 12.58 {leu 23 o} U 8.9 0.06 12.12 <2.10>{ser 51 hn} P U 7.29 6.02 14.77 {cys 24 o} U 8.18 4.97 14.25 <2.19>{his 52 hn} P U 9.69 6.35 13.59 {cys 24 o} U 8.9 5.07 13.9 <2.30>{gly 54 hn} P U 11.66 3.68 8.24 {pro 22 o} U 11.23 2.19 7.84 @subgroup {helix} @vectorlist {main ch} color=pinktint {ca asn 33}P 6.443 -2.498 6.23 {c asn 33}5.224 -1.654 6.595 {o asn 33}4.743 -1.735 7.766 {c asn 33}P 5.224 -1.654 6.595 {n lys 34}4.844 -0.776 5.677 {ca lys 34}3.763 0.16 5.942 {c lys 34}2.431 -0.504 6.29 {o lys 34}1.665 0.017 7.13 {c lys 34}P 2.431 -0.504 6.29 {n cys 35}2.177 -1.597 5.643 {ca cys 35}0.93 -2.288 5.896 {c cys 35}0.933 -2.919 7.273 {o cys 35}-0.064 -2.731 7.995 {c cys 35}P 0.933 -2.919 7.273 {n asn 36}2.012 -3.516 7.722 {ca asn 36}2.015 -3.942 9.139 {c asn 36}1.86 -2.741 10.061 {o asn 36}1.187 -2.853 11.102 {c asn 36}P 1.86 -2.741 10.061 {n phe 37}2.493 -1.624 9.745 {ca phe 37}2.392 -0.47 10.625 {c phe 37}0.949 0.014 10.741 {o phe 37}0.478 0.344 11.859 {c phe 37}P 0.949 0.014 10.741 {n cys 38}0.334 0.191 9.599 {ca cys 38}-1.014 0.836 9.589 {c cys 38}-2.114 -0.086 10.122 {o cys 38}-3.011 0.424 10.856 {c cys 38}P -2.114 -0.086 10.122 {n asn 39}-1.856 -1.384 10.01 {ca asn 39}-2.63 -2.417 10.754 {c asn 39}-2.536 -2.292 12.277 {o asn 39}-3.57 -2.099 12.985 {c asn 39}P -2.536 -2.292 12.277 {n ala 40}-1.306 -2.043 12.75 {ca ala 40}-1.067 -1.747 14.186 {c ala 40}-1.588 -0.408 14.706 {o ala 40}-2.133 -0.373 15.849 {c ala 40}P -1.588 -0.408 14.706 {n val 41}-1.583 0.621 13.86 {ca val 41}-2.221 1.901 14.233 {c val 41}-3.731 1.704 14.524 {o val 41}-4.239 2.108 15.602 {c val 41}P -3.731 1.704 14.524 {n val 42}-4.362 0.967 13.629 {ca val 42}-5.773 0.628 13.797 {c val 42}-6.051 -0.244 15.01 {o val 42}-6.852 0.179 15.894 {c val 42}P -6.051 -0.244 15.01 {n glu 43}-5.311 -1.313 15.112 {ca glu 43}-5.381 -2.196 16.283 {c glu 43}-5.192 -1.484 17.609 {o glu 43}-5.868 -1.889 18.58 {c glu 43}P -5.192 -1.484 17.609 {n ser 44}-4.344 -0.454 17.659 {ca ser 44}-4.031 0.275 18.887 {c ser 44}-4.99 1.393 19.211 {o ser 44}-4.767 2.197 20.137 {c ser 44}P -4.99 1.393 19.211 {n asn 45}-6.005 1.494 18.369 {ca asn 45}-6.985 2.565 18.448 @vectorlist {helix Hb} color=pink <2.06>{phe 37 hn} P U 3.04 -1.58 8.91 {asn 33 o} U 4.23 -1.69 8.11 <1.86>{cys 38 hn} P U 0.79 -0.11 8.76 {lys 34 o} U 1.4 -0.02 7.62 <2.06>{asn 39 hn} P U -1.11 -1.66 9.4 {cys 35 o} U -0.38 -2.41 8.42 <2.15>{ala 40 hn} P U -0.54 -2.06 12.11 {asn 36 o} U 0.67 -2.61 11.41 <1.97>{val 41 hn} P U -1.14 0.51 12.97 {phe 37 o} U -0.01 0.4 12.19 <2.16>{val 42 hn} P U -3.86 0.64 12.83 {cys 38 o} U -3.27 0.49 11.45 <1.86>{glu 43 hn} P U -4.69 -1.52 14.36 {asn 39 o} U -3.9 -1.92 13.4 <2.02>{ser 44 hn} P U -3.9 -0.17 16.81 {ala 40 o} U -2.66 -0.31 16.14 <2.01>{asn 45 hn} P U -6.1 0.8 17.65 {val 42 o} U -6.63 0.37 16.42 <1.89>{gly 46 hn} P U -4.99 3.12 17.01 {val 41 o} U -4.46 2.41 16.02 @subgroup {loops} @vectorlist {Calpha} color= white {ca leu 1}P 1.048 15.759 17.962 {ca ala 2}2.514 13.661 15.12 {ca ala 3}5.758 14.999 13.53 {ca val 4}5.66 12.505 10.63 {ca ser 5}3.03 10.123 9.404 {ca val 6}1.991 7.63 6.781 {ca asp 7}-1.146 7.262 4.785 {ca cys 8}-3.232 4.802 6.856 {ca ser 9}-6.503 6.019 5.267 {ca glu 10}-7.513 2.726 3.742 {ca tyr 11}-6.819 0.582 6.79 {ca pro 12}-7.62 -1.968 8.384 {ca lys 13}-6.517 -4.692 5.883 {ca pro 14}-6.729 -8.531 6.268 {ca ala 15}-3.255 -9.161 4.88 {ca cys 16}0.023 -7.59 4.007 {ca thr 17}2.74 -8.589 1.753 {ca met 18}6.189 -9.507 2.993 {ca glu 19}8.414 -6.798 1.551 {ca tyr 20}10.947 -5.489 4.06 {ca asn 45}P -6.985 2.565 18.448 {ca gly 46}-4.608 5.216 17.1 {ca thr 47}-2.3 5.198 20.159 {ca leu 48}0.58 4.047 17.884 {ca thr 49}2.305 6.846 15.965 {ca gly 54}P 13.666 3.161 8.786 {ca lys 55}14.371 0.552 11.436 {ca cys 56}14.388 1.653 15.028 @vectorlist off {turn Hb} color=brown <2.53>{tyr 11 hn} P U -6.98 2.68 6.2 {cys 8 o} U -6. 3.86 7.08 <2.22>{thr 47 hn} P U -3.83 3.99 19.25 {ser 44 o} U -4.48 2.74 19.87 @subgroup dominant {SS} @vectorlist {SS} color= yellow {ca cys 16}P 0.023 -7.59 4.007 {cb cys 16}0.764 -7.065 5.274 {sg cys 16}-0.165 -5.926 6.292 {sg cys 35}-0.704 -4.424 5.031 {cb cys 35}0.714 -3.34 4.842 {ca cys 35}0.93 -2.288 5.896 {ca cys 8}P -3.232 4.802 6.856 {cb cys 8}-2.908 4.553 8.346 {sg cys 8}-1.179 4.11 8.78 {sg cys 38}-0.531 2.692 7.531 {cb cys 38}-1.369 1.267 8.164 {ca cys 38}-1.014 0.836 9.589 {ca cys 24}P 9.944 2.59 13.445 {cb cys 24}11.255 3.283 13.903 {sg cys 24}11.518 3.201 15.658 {sg cys 56}11.751 1.269 16.063 {cb cys 56}13.56 1.036 16.17 {ca cys 56}14.388 1.653 15.028 @group dominant {0} animate @vectorlist {dummy} @group dominant {1} animate @vectorlist {strand 1} color=sky {ca tyr 20}10.947 -5.489 4.06 {c tyr 20}11.37 -4.061 3.847 {n arg 21}10.479 -3.198 4.244 {ca arg 21}10.561 -1.759 4.048 {c arg 21}10.324 -1.02 5.359 {n pro 22}11.254 -1.114 6.32 {ca pro 22}10.998 -0.893 7.77 {c pro 22}10.624 0.504 8.231 {n leu 23}9.815 0.538 9.269 {ca leu 23}9.251 1.77 9.857 {c leu 23}9.399 1.638 11.357 {n cys 24}9.807 2.679 11.992 {ca cys 24}9.944 2.59 13.445 {c cys 24}8.753 3.279 14.147 {n gly 25}8.008 2.482 14.931 {ca gly 25}6.874 3.021 15.698 {c gly 25}7.28 3.81 16.928 {n ser 26}6.357 4.63 17.413 {ca ser 26}6.539 5.313 18.695 {c ser 26}6.586 4.372 19.887 {n asp 27}6.24 3.149 19.665 {ca asp 27}6.31 2.142 20.698 @group dominant {2} animate @vectorlist {b1} instance={strand 1} @vectorlist {strand 2} color=purple {ca asp 27}P 6.31 2.142 20.698 {c asp 27}7.67 1.42 20.727 {n asn 28}8.594 1.918 19.856 {ca asn 28}10.016 1.413 19.777 {c asn 28}10.06 -0.016 19.226 {n lys 29}9.084 -0.33 18.357 {ca lys 29}9.086 -1.483 17.486 {c lys 29}9.399 -1.125 16.039 {n thr 30}10.18 -1.97 15.418 {ca thr 30}10.333 -1.897 13.996 {c thr 30}9.227 -2.75 13.337 {n tyr 31}8.395 -2.1 12.554 {ca tyr 31}7.395 -2.739 11.662 {c tyr 31}7.928 -2.987 10.25 {n gly 32}7.807 -4.19 9.747 {ca gly 32}8.502 -4.713 8.547 {c gly 32}8.17 -3.866 7.326 {n asn 33}6.999 -3.265 7.354 {ca asn 33}6.443 -2.498 6.23 @group dominant {3} animate @vectorlist {b1} instance={strand 1} @vectorlist {b2} instance={strand 2} @vectorlist {crossover} color=magenta {ca asn 33}P 6.443 -2.498 6.23 {c asn 33}5.224 -1.654 6.595 {n lys 34}4.844 -0.776 5.677 {ca lys 34}3.763 0.16 5.942 {c lys 34}2.431 -0.504 6.29 {n cys 35}2.177 -1.597 5.643 {ca cys 35}0.93 -2.288 5.896 {c cys 35}0.933 -2.919 7.273 {n asn 36}2.012 -3.516 7.722 {ca asn 36}2.015 -3.942 9.139 {c asn 36}1.86 -2.741 10.061 {n phe 37}2.493 -1.624 9.745 {ca phe 37}2.392 -0.47 10.625 {c phe 37}0.949 0.014 10.741 {n cys 38}0.334 0.191 9.599 {ca cys 38}-1.014 0.836 9.589 {c cys 38}-2.114 -0.086 10.122 {n asn 39}-1.856 -1.384 10.01 {ca asn 39}-2.63 -2.417 10.754 {c asn 39}-2.536 -2.292 12.277 {n ala 40}-1.306 -2.043 12.75 {ca ala 40}-1.067 -1.747 14.186 {c ala 40}-1.588 -0.408 14.706 {n val 41}-1.583 0.621 13.86 {ca val 41}-2.221 1.901 14.233 {c val 41}-3.731 1.704 14.524 {n val 42}-4.362 0.967 13.629 {ca val 42}-5.773 0.628 13.797 {c val 42}-6.051 -0.244 15.01 {n glu 43}-5.311 -1.313 15.112 {ca glu 43}-5.381 -2.196 16.283 {c glu 43}-5.192 -1.484 17.609 {n ser 44}-4.344 -0.454 17.659 {ca ser 44}-4.031 0.275 18.887 {c ser 44}-4.99 1.393 19.211 {n asn 45}-6.005 1.494 18.369 {ca asn 45}-6.985 2.565 18.448 {ca gly 46}-4.608 5.216 17.1 {ca thr 47}-2.3 5.198 20.159 {ca leu 48}0.58 4.047 17.884 {ca thr 49}2.305 6.846 15.965 @group dominant {4} animate @vectorlist {b1} instance={strand 1} @vectorlist {b2} instance={strand 2} @vectorlist {crs} instance={crossover} @vectorlist {strand 3} color=hotpink {ca thr 49}P 2.305 6.846 15.965 {c thr 49}3.632 6.458 15.35 {n leu 50}3.929 7.091 14.245 {ca leu 50}5.254 6.871 13.594 {c leu 50}6.344 7.685 14.309 {n ser 51}7.354 7.019 14.779 {ca ser 51}8.551 7.75 15.299 {c ser 51}9.442 8.219 14.143 {n his 52}9.876 7.301 13.347 {ca his 52}10.616 7.67 12.127 {c his 52}10.646 6.565 11.086 {n phe 53}10.934 6.978 9.893 {ca phe 53}11.191 6.078 8.794 {c phe 53}12.48 5.307 9.064 {n gly 54}12.494 4.044 8.656 {ca gly 54}13.666 3.161 8.786 @kinemage 6 @caption Wheat germ agglutinin (file 3WGA) domain 1, of 4 similar domains: beta strands of N-centered overhand in greentint with seagreen H-bonds, short helix in pink, SS in yellow. @onewidth @zoom .7 @matrix .752481 -.171965 -.635768 -.486811 -.795404 -.361036 -.443607 .581172 -.682241 @2zoom 1.1 @2center -8.4 -9. 1.1 @2matrix .970244 -.181159 -.160648 -.241947 -.699695 -.672226 .009375 .691092 -.722706 @group {wh germ agglut} @subgroup {beta sheet} @vectorlist {hairpin} color=greentint {ca asn 15}-5.84 -1.823 -4.107 {c asn 15}-6.927 -2.849 -4.3 {o asn 15}-8.067 -2.529 -3.959 {c asn 15}P -6.927 -2.849 -4.3 {n leu 16}-6.654 -4.053 -4.833 {ca leu 16}-7.758 -5.052 -4.903 {c leu 16}-8.105 -5.386 -3.464 {o leu 16}-7.366 -5.249 -2.475 {c leu 16}P -8.105 -5.386 -3.464 {n cys 17}-9.382 -5.67 -3.335 {ca cys 17}-10.031 -6.025 -2.08 {c cys 17}-9.826 -7.529 -1.807 {o cys 17}-9.912 -8.344 -2.739 {c cys 17}P -9.826 -7.529 -1.807 {n cys 18}-9.55 -7.693 -0.548 {ca cys 18}-9.379 -9.12 -0.076 {c cys 18}-10.734 -9.532 0.478 {o cys 18}-11.061 -8.919 1.524 {c cys 18}P -10.734 -9.532 0.478 {n ser 19}-11.407 -10.495 -0.129 {ca ser 19}-12.7 -10.927 0.435 {c ser 19}-12.518 -11.526 1.819 {o ser 19}-11.475 -11.722 2.457 {c ser 19}P -12.518 -11.526 1.819 {n gln 20}-13.703 -11.865 2.332 {ca gln 20}-13.781 -12.492 3.67 {ca tyr 21}-12.353 -15.787 2.36 {c tyr 21}-10.855 -15.76 2.194 {o tyr 21}-10.27 -16.846 2.346 {c tyr 21}P -10.855 -15.76 2.194 {n gly 22}-10.263 -14.583 1.993 {ca gly 22}-8.821 -14.516 1.832 {c gly 22}-8.412 -14.517 0.368 {o gly 22}-7.231 -14.804 0.125 {c gly 22}P -8.412 -14.517 0.368 {n tyr 23}-9.231 -14.177 -0.587 {ca tyr 23}-8.947 -14.05 -1.99 {c tyr 23}-9.052 -12.552 -2.443 {o tyr 23}-10.01 -11.853 -2.053 {c tyr 23}P -9.052 -12.552 -2.443 {n cys 24}-8.165 -12.237 -3.386 {ca cys 24}-8.06 -10.924 -4.035 {c cys 24}-8.928 -10.742 -5.291 {o cys 24}-8.801 -11.517 -6.259 {c cys 24}P -8.928 -10.742 -5.291 {n gly 25}-9.728 -9.661 -5.343 {ca gly 25}-10.503 -9.41 -6.58 {c gly 25}-11.178 -8.047 -6.516 {o gly 25}-10.813 -7.235 -5.667 {c gly 25}P -11.178 -8.047 -6.516 {n met 26}-12.184 -7.94 -7.356 {ca met 26}-12.92 -6.654 -7.438 @vectorlist {strand 3} color=greentint {ca cys a 35}P -13.755 -7.064 2.848 {c cys a 35}-12.685 -6.879 3.91 {o cys a 35}-12.85 -6.293 4.976 {c cys a 35}P -12.685 -6.879 3.91 {n gln a 36}-11.491 -7.388 3.598 {ca gln a 36}-10.354 -7.353 4.468 {c gln a 36}-9.385 -6.193 4.378 {o gln a 36}-8.955 -5.846 5.517 {c gln a 36}P -9.385 -6.193 4.378 {n asp a 37}-8.978 -5.739 3.255 {ca asp a 37}-7.961 -4.652 3.109 {c asp a 37}-8.122 -4.29 1.654 {o asp a 37}-8.994 -5.044 1.158 {c asp a 37}P -8.122 -4.29 1.654 {n gly a 38}-7.495 -3.276 1.076 {ca gly a 38}-7.764 -2.908 -0.324 {c gly a 38}-8.893 -1.867 -0.384 {o gly a 38}-9.216 -1.373 0.679 {c gly a 38}P -8.893 -1.867 -0.384 {n ala a 39}-9.468 -1.574 -1.502 {ca ala a 39}-10.59 -0.633 -1.681 @vectorlist {beta Hb} color=sea <2.36>{cys 17 hn} P U -9.94 -5.64 -4.16 {gly 25 o} U -10.55 -6.76 -5.22 <2.21>{cys 18 hn} P U -9.47 -6.89 0.04 {asp 37 o} U -9.14 -5.6 0.82 <1.77>{ser 19 hn} P U -11.03 -10.91 -0.96 {tyr 23 o} U -10.32 -11.57 -1.72 <2.19>{gly 22 hn} P U -10.81 -13.74 1.95 {ser 19 o} U -11.27 -12.33 2.31 <1.95>{gly 25 hn} P U -9.8 -9.04 -4.56 {cys 17 o} U -9.88 -8.55 -3.29 <1.64>{gln 36 hn} P U -11.37 -7.82 2.71 {cys 18 o} U -11.15 -8.59 1.88 <2.01>{ala 39 hn} P U -9.09 -2.05 -2.3 {asn 15 o} U -8.37 -2.38 -3.46 @subgroup {helix} @vectorlist {main ch} color=pinktint {ca gly 27}-16.68 -6.461 -7.286 {c gly 27}-17.226 -6.524 -5.865 {o gly 27}-16.424 -6.395 -4.921 {c gly 27}P -17.226 -6.524 -5.865 {n gly 28}-18.529 -6.713 -5.765 {ca gly 28}-19.213 -6.826 -4.492 {c gly 28}-18.793 -8.084 -3.728 {o gly 28}-18.882 -8.115 -2.489 {c gly 28}P -18.793 -8.084 -3.728 {n asp 29}-18.287 -9.08 -4.426 {ca asp 29}-17.858 -10.356 -3.788 {c asp 29}-16.616 -10.161 -2.93 {o asp 29}-16.335 -10.967 -2.053 {c asp 29}P -16.616 -10.161 -2.93 {n tyr 30}-15.851 -9.129 -3.243 {ca tyr 30}-14.573 -8.894 -2.544 {c tyr 30}-14.567 -7.596 -1.73 {o tyr 30}-14.015 -7.638 -0.617 {c tyr 30}P -14.567 -7.596 -1.73 {n cys 31}-15.208 -6.607 -2.305 {ca cys 31}-15.199 -5.283 -1.649 {c cys 31}-16.359 -5.071 -0.719 {o cys 31}-16.212 -4.157 0.125 {c cys 31}P -16.359 -5.071 -0.719 {n gly 32}-17.414 -5.84 -0.875 {ca gly 32}-18.561 -5.706 0.009 @vectorlist {helix Hb} color=pink <2.34>{tyr 30 hn} P U -16.16 -8.51 -3.96 {gly 27 o} U -16.34 -7.03 -4.63 <1.94>{cys 31 hn} P U -15.69 -6.77 -3.17 {gly 27 o} U -16.2 -6.51 -4.4 <2.34>{gly 32 hn} P U -17.42 -6.52 -1.61 {gly 28 o} U -18.44 -7.64 -2.23 @subgroup {loops} @vectorlist {Calpha} color= white {ca pca 1}P -1.168 -16.401 -2.778 {ca arg 2}-3.667 -15.594 -0.009 {ca cys 3}-4.589 -12.292 1.675 {ca gly 4}-5.88 -11.064 5.02 {ca glu 5}-5.887 -13.458 7.975 {ca gln 6}-5.685 -16.424 5.599 {ca gly 7}-2.56 -14.939 4.008 {ca ser 8}-0.822 -13.617 7.1 {ca asn 9}-2.15 -10.07 6.682 {ca met 10}-0.933 -9.862 3.1 {ca glu 11}-2.436 -7.223 0.833 {ca cys 12}-3.529 -7.404 -2.809 {ca pro 13}-1.737 -5.34 -5.489 {ca asn 14}-3.414 -2.247 -6.977 {ca asn 15}-5.84 -1.823 -4.107 {ca gln 20}P -13.781 -12.492 3.67 {ca tyr 21}-12.353 -15.787 2.36 {ca met 26}P -12.92 -6.654 -7.438 {ca gly 27}-16.68 -6.461 -7.286 {ca gly 32}P -18.561 -5.706 0.009 {ca lys 33}-19.28 -7.177 3.485 {ca gly 34}-16.293 -9.013 4.944 {ca cys 35}-13.755 -7.064 2.848 {ca ala 39}P -10.59 -0.633 -1.681 {ca cys 40}-13.307 -1.991 0.676 {ca trp 41}-16.747 -0.476 0.049 @vectorlist off {other Hb} color=brown <2.05>{cys 3 hn} P U -5.43 -14.08 0.8 {gly 22 o} U -6.69 -14.59 0.33 <2.02>{gly 4 hn} P U -4.57 -10.44 3.47 {met 10 o} U -3.65 -9.67 2.71 <1.97>{gly 7 hn} P U -4.22 -14.35 5.26 {gly 4 o} U -4.19 -13.05 5.72 <2.87>{ser 8 hn} P U -2.46 -14.84 6.46 {glu 5 o} U -4.04 -15.29 7.63 <1.67>{asn 9 hn} P U -2.77 -12.1 6.73 {gly 4 o} U -3.76 -12.38 6.16 <2.61>{met 10 hn} P U -1.66 -11.13 4.57 {gly 7 o} U -0.97 -12.81 4.35 <2.10>{leu 16 hn} P U -5.74 -4.26 -5.17 {pro 13 o} U -4.52 -4.72 -5.84 <2.09>{cys 35 hn} P U -15.88 -7.2 3.25 {gly 32 o} U -16.77 -6.48 2.34 <1.99>{cys 40 hn} P U -11.2 -1.53 0.67 {gly 38 o} U -9.81 -1.42 0.68 <2.00>{trp 41 hn} P U -15.65 -2.24 0.11 {cys 31 o} U -16.04 -3.58 0.12 @subgroup dominant {SS} @vectorlist {SS} color=yellow {ca cys 3}P -4.589 -12.292 1.675 {cb cys 3}-5.186 -11.338 0.654 {sg cys 3}-6.891 -11.415 0.15 {sg cys 18}-7.934 -10.621 1.67 {cb cys 18}-8.376 -8.998 1.066 {ca cys 18}-9.379 -9.12 -0.076 {ca cys 12}P -3.529 -7.404 -2.809 {cb cys 12}-5.016 -7.41 -3.099 {sg cys 12}-5.968 -8.722 -2.289 {sg cys 24}-5.365 -10.399 -3.3 {cb cys 24}-6.622 -10.649 -4.518 {ca cys 24}-8.06 -10.924 -4.035 @vectorlist {SSb} color=yellow {ca cys 17}P -10.031 -6.025 -2.08 {cb cys 17}-11.541 -5.884 -2.2 {sg cys 17}-11.947 -4.16 -2.574 {sg cys 31}-13.594 -4.218 -3.709 {cb cys 31}-15.018 -4.193 -2.697 {ca cys 31}-15.199 -5.283 -1.649 {ca cys 35}P -13.755 -7.064 2.848 {cb cys 35}-13.981 -5.8 2.016 {sg cys 35}-12.45 -5.16 1.242 {sg cys 40}-11.951 -3.621 2.542 {cb cys 40}-13.183 -2.369 2.136 {ca cys 40}-13.307 -1.991 0.676 @subgroup dominant off {C-C hairpin} @vectorlist {Hp mc} instance={hairpin} color=red @vectorlist {Hp end} color=red {ca gln 20}P -13.781 -12.492 3.67 {ca tyr 21}-12.353 -15.787 2.36 @vectorlist {Hp SS} instance={SS} color=gold @vectorlist {Hp Hb} color=gold <2.36>{cys 17 hn} P U -9.94 -5.64 -4.16 {gly 25 o} U -10.55 -6.76 -5.22 <1.77>{ser 19 hn} P U -11.03 -10.91 -0.96 {tyr 23 o} U -10.32 -11.57 -1.72 <2.19>{gly 22 hn} P U -10.81 -13.74 1.95 {ser 19 o} U -11.27 -12.33 2.31 <1.95>{gly 25 hn} P U -9.8 -9.04 -4.56 {cys 17 o} U -9.88 -8.55 -3.29 @kinemage 7 @caption Hirudin, residues 1-49: beta strand main chain in greentint, loop Calphas in white, SS in yellow, and thrombin-binding N-terminus in skyblue. View2 shows the beta sheet and View3 the core. @onewidth @matrix .561926 -.82411 -.071278 -.607648 -.469721 .640411 -.56125 -.316552 -.764718 @2zoom 1.2 @2matrix -.191487 -.535801 .822344 -.521669 -.654145 -.547682 .831381 -.533866 -.15425 @3zoom 1.5 @3matrix -.781852 .145621 .60622 .452721 .801134 .391442 -.428661 .580499 -.692293 @group {hirudin} @subgroup {beta sheet} @vectorlist {strand 1} color=greentint {ca ser 9}P 3.886 -1.977 5.356 {c ser 9}3.176 -3.302 5.056 {o ser 9}2.967 -4.108 5.942 {c ser 9}P 3.176 -3.302 5.056 {n gly 10}2.818 -3.492 3.806 {ca gly 10}2.128 -4.76 3.41 {c gly 10}0.685 -4.488 2.966 {o gly 10}-0.039 -5.401 2.623 {c gly 10}P 0.685 -4.488 2.966 {n gln 11}0.297 -3.242 2.979 {ca gln 11}-1.1 -2.909 2.559 {c gln 11}-1.185 -2.817 1.029 {o gln 11}-0.215 -3.059 0.34 {c gln 11}P -1.185 -2.817 1.029 {n asn 12}-2.344 -2.467 0.526 {ca asn 12}-2.493 -2.378 -0.961 @vectorlist {hairpin} color=greentint {ca asn 26}P 0.429 -6.57 -4.911 {c asn 26}0.907 -6.546 -3.445 {o asn 26}0.361 -7.234 -2.607 {c asn 26}P 0.907 -6.546 -3.445 {n lys 27}1.914 -5.766 -3.168 {ca lys 27}2.422 -5.697 -1.768 {c lys 27}3.227 -4.41 -1.565 {o lys 27}4.348 -4.296 -2.02 {c lys 27}P 3.227 -4.41 -1.565 {n cys 28}2.636 -3.467 -0.884 {ca cys 28}3.348 -2.178 -0.646 {c cys 28}4.286 -2.298 0.561 {o cys 28}4.016 -3.035 1.489 {c cys 28}P 4.286 -2.298 0.561 {n ile 29}5.369 -1.564 0.513 {ca ile 29}6.35 -1.596 1.644 {ca gln 38}P 6.883 1.091 -3.251 {c gln 38}5.829 0.031 -3.597 {o gln 38}5.693 -0.959 -2.905 {c gln 38}P 5.829 0.031 -3.597 {n cys 39}5.105 0.258 -4.66 {ca cys 39}4.049 -0.726 -5.047 {c cys 39}4.69 -1.944 -5.737 {o cys 39}4.73 -2.029 -6.948 {c cys 39}P 4.69 -1.944 -5.737 {n val 40}5.181 -2.861 -4.938 {ca val 40}5.823 -4.084 -5.516 {c val 40}4.807 -5.239 -5.544 {o val 40}3.804 -5.197 -4.866 {c val 40}P 4.807 -5.239 -5.544 {n thr 41}5.09 -6.246 -6.327 {ca thr 41}4.14 -7.401 -6.412 @vectorlist {beta Hb} color=sea <1.95>{gly 10 hn} P U 3.02 -2.77 3.14 {cys 28 o} U 3.72 -2.96 1.99 <2.20>{cys 28 hn} P U 1.71 -3.64 -0.54 {gln 11 o} U 0.36 -3.23 0.08 <1.77>{lys 27 hn} P U 2.32 -5.23 -3.91 {val 40 o} U 3.36 -5.21 -4.58 <2.62>{ile 29 hn} P U 5.51 -0.99 -0.3 {gln 38 o} U 5.64 -0.97 -2.12 <2.61>{val 40 hn} P U 5.11 -2.71 -3.95 {lys 27 o} U 4.58 -3.82 -2.6 @subgroup {loops} @vectorlist {Calpha} color= white {ca tyr 3}P -9.645 4.196 0.674 {ca thr 4}-7.32 5.855 3.207 {ca asp 5}-3.668 6.699 3.889 {ca cys 6}-1.606 3.575 4.562 {ca thr 7}-0.188 3.086 8.062 {ca glu 8}1.587 -0.282 7.882 {ca ser 9}3.886 -1.977 5.356 {ca asn 12}P -2.493 -2.378 -0.961 {ca leu 13}-5.788 -0.475 -1.279 {ca cys 14}-4.293 2.639 0.315 {ca leu 15}-2.461 5.771 -0.851 {ca cys 16}0.87 4.03 -1.428 {ca glu 17}2.734 5.786 -4.251 {ca gly 18}2.017 9.46 -3.617 {ca ser 19}-1.751 9.977 -3.61 {ca asn 20}-2.331 7.082 -6.024 {ca val 21}-3.595 3.723 -4.756 {ca cys 22}-1.941 0.33 -5.366 {ca gly 23}-3.91 -2.727 -6.534 {ca gln 24}-5.029 -5.78 -4.541 {ca gly 25}-2.705 -8.69 -5.349 {ca asn 26}0.429 -6.57 -4.911 {ca ile 29}P 6.35 -1.596 1.644 {ca leu 30}6.14 1.542 3.804 {ca gly 31}8.87 3.137 5.988 {ca ser 32}12.217 1.592 5.072 {ca asp 33}14.967 4.189 5.6 {ca gly 34}13.982 6.702 2.907 {ca glu 35}11.667 4.226 1.17 {ca lys 36}8.256 5.598 2.159 {ca asn 37}6.367 3.731 -0.566 {ca gln 38}6.883 1.091 -3.251 {ca thr 41}P 4.14 -7.401 -6.412 {ca gly 42}3.269 -10.087 -3.831 {ca glu 43}0.349 -10.408 -1.381 {ca gly 44}-0.828 -7.305 0.489 {ca thr 45}-3.836 -6.795 2.781 {ca pro 46}-6.986 -4.592 2.349 {ca lys 47}-6.18 -1.743 4.758 {ca pro 48}-9.179 -2.127 7.17 {ca gln 49}-11.21 0.927 8.194 @vectorlist off {other Hb} color=brown <2.82>{gln 11 hn} P U 0.95 -2.55 3.27 {glu 8 o} U 1.23 -1.49 4.92 <1.79>{cys 14 hn} P U -3.8 0.98 -1.03 {asn 12 o} U -3.37 0.04 -1.74 <2.14>{leu 15 hn} P U -3.69 5.04 0.82 {thr 4 o} U -4.77 5.1 1.87 <2.04>{cys 16 hn} P U -1.2 4.06 -2.15 {cys 14 o} U -2.43 3.48 -1.74 <2.14>{asn 20 hn} P U -0.73 8.33 -5.19 {glu 17 o} U 0.61 7.66 -5.15 <2.73>{cys 22 hn} P U -2.67 1.64 -3.76 {cys 14 o} U -2.88 2.75 -2.22 <2.33>{asn 26 hn} P U -1.75 -6.49 -4.71 {gly 23 o} U -2.52 -5.25 -5.46 <2.56>{glu 35 hn} P U 13.26 4.32 2.68 {ser 32 o} U 13.91 2.86 3.5 <2.17>{thr 45 hn} P U -2.08 -5.74 1.99 {gly 10 o} U -0.65 -5.5 2.43 @subgroup dominant {SS} @vectorlist {SSa} color= yellow {ca cys 6}P -1.606 3.575 4.562 {cb cys 6}-0.46 3.099 3.676 {sg cys 6}-0.685 3.224 1.887 {sg cys 14}-1.866 1.65 1.435 {cb cys 14}-3.547 2.299 1.602 {ca cys 14}-4.293 2.639 0.315 @vectorlist {SS} color= yellow {ca cys 16}P 0.87 4.03 -1.428 {cb cys 16}0.997 2.64 -2.052 {sg cys 16}0.481 1.227 -1.045 {sg cys 28}1.511 -0.331 -1.816 {cb cys 28}2.318 -1.082 -0.38 {ca cys 28}3.348 -2.178 -0.646 {ca cys 22}P -1.941 0.33 -5.366 {cb cys 22}-1.173 -0.451 -4.275 {sg cys 22}0.531 -0.995 -4.623 {sg cys 39}1.524 0.636 -5.28 {cb cys 39}3.051 -0.046 -5.999 {ca cys 39}4.049 -1.944 -5.737 @subgroup dominant {inh site} @vectorlist {1-3} color=sky {ca val 1}P -13.798 4.788 -4.661 {ca val 2}-11.375 6.184 -2.074 {ca tyr 3}-9.645 4.196 0.674 @subgroup dominant off {C-C hairpin} @vectorlist {mc} instance={hairpin} color=red @vectorlist {Hp end} color=red {ca ile 29}P 6.35 -1.596 1.644 {ca leu 30}6.14 1.542 3.804 {ca gly 31}8.87 3.137 5.988 {ca ser 32}12.217 1.592 5.072 {ca asp 33}14.967 4.189 5.6 {ca gly 34}13.982 6.702 2.907 {ca glu 35}11.667 4.226 1.17 {ca lys 36}8.256 5.598 2.159 {ca asn 37}6.367 3.731 -0.566 {ca gln 38}6.883 1.091 -3.251 @vectorlist {Hp SS} instance={SS} color=gold @vectorlist {Hp Hb} color=gold <1.77>{lys 27 hn} P U 2.32 -5.23 -3.91 {val 40 o} U 3.36 -5.21 -4.58 <2.62>{ile 29 hn} P U 5.51 -0.99 -0.3 {gln 38 o} U 5.64 -0.97 -2.12 <2.61>{val 40 hn} P U 5.11 -2.71 -3.95 {lys 27 o} U 4.58 -3.82 -2.6 @subgroup dominant off {core sc} @vectorlist {Leu} color=gold {ca leu 30}P 6.14 1.542 3.804 {cb leu 30}5.03 1.801 4.823 {cg leu 30}3.658 1.744 4.125 {cd1 leu 30}2.543 1.864 5.178 {cg leu 30}P 3.658 1.744 4.125 {cd2 leu 30}3.536 2.904 3.125 @vectorlist {Gln} color=pink {ca gln 11}P -1.1 -2.909 2.559 {cb gln 11}-1.504 -1.58 3.191 {cg gln 11}-2.007 -1.849 4.619 {cd gln 11}-1.723 -0.641 5.522 {oe1 gln 11}-0.939 0.227 5.2 {cd gln 11}P -1.723 -0.641 5.522 {ne2 gln 11}-2.341 -0.554 6.667 @vectorlist {Asn} color=cyan {ca asn 12}P -2.493 -2.378 -0.961 {cb asn 12}-2.974 -3.731 -1.493 {cg asn 12}-1.777 -4.644 -1.78 {od1 asn 12}-0.632 -4.258 -1.654 {cg asn 12}P -1.777 -4.644 -1.78 {nd2 asn 12}-2.002 -5.868 -2.17 {ca asn 26}P 0.429 -6.57 -4.911 {cb asn 26}0.474 -5.154 -5.523 {cg asn 26}1.115 -5.214 -6.914 {od1 asn 26}1.062 -6.219 -7.594 {cg asn 26}P 1.115 -5.214 -6.914 {nd2 asn 26}1.73 -4.157 -7.372 {ca asn 37}P 6.367 3.731 -0.566 {cb asn 37}5.268 4.688 -1.009 {cg asn 37}4.1 4.58 -0.036 {od1 asn 37}3.78 5.511 0.676 {cg asn 37}P 4.1 4.58 -0.036 {nd2 asn 37}3.434 3.465 0.022 @kinemage 8 @caption Rubredoxin, a small metal-rich protein: Calpha backbone and Fe ligands (yellow Cys, red Fe). @onewidth @zoom .8 @matrix -.952287 -.302807 -.038175 -.066166 .08272 .994374 -.297946 .949455 -.098809 @2zoom .85 @2matrix -.261538 -.146646 -.953988 -.898381 -.324354 .296152 -.35286 .934499 -.046914 @3zoom 1.2 @3zslab 70 @3center 14.2 26.2 26.3 @3matrix -.827056 .38515 -.409436 -.537048 -.756507 .373196 -.166005 .528541 .832519 @group {rubredoxin} @subgroup {mainchain} @vectorlist off {mc} color= white {n met 1}P 19.56 27.73 6.05 {ca met 1}19.49 27.16 7.39 {c met 1}18.31 27.78 8.2 {o met 1}18.11 29. 8.35 {c met 1}P 18.31 27.78 8.2 {n lys 2}17.46 26.83 8.59 {ca lys 2}16.26 27.17 9.36 {c lys 2}16.61 27.45 10.83 {o lys 2}17.46 26.8 11.48 {c lys 2}P 16.61 27.45 10.83 {n lys 3}15.83 28.36 11.36 {ca lys 3}15.73 28.51 12.82 {c lys 3}14.87 27.42 13.48 {o lys 3}13.98 26.81 12.87 {c lys 3}P 14.87 27.42 13.48 {n tyr 4}15.21 27.1 14.7 {ca tyr 4}14.48 26.12 15.53 {c tyr 4}14.06 26.79 16.83 {o tyr 4}14.85 27.52 17.47 {c tyr 4}P 14.06 26.79 16.83 {n thr 5}12.92 26.4 17.32 {ca thr 5}12.47 26.98 18.6 {c thr 5}12.39 25.91 19.68 {o thr 5}11.9 24.79 19.41 {c thr 5}P 12.39 25.91 19.68 {n cys 6}12.8 26.26 20.88 {ca cys 6}12.57 25.39 22.04 {c cys 6}11.07 25.49 22.41 {o cys 6}10.58 26.57 22.79 {c cys 6}P 11.07 25.49 22.41 {n thr 7}10.35 24.39 22.32 {ca thr 7}8.88 24.44 22.55 {c thr 7}8.5 24.51 24.05 {o thr 7}7.32 24.82 24.36 {c thr 7}P 8.5 24.51 24.05 {n val 8}9.5 24.33 24.88 {ca val 8}9.32 24.48 26.32 {c val 8}9.43 25.94 26.8 {o val 8}8.52 26.35 27.53 {c val 8}P 9.43 25.94 26.8 {n cys 9}10.42 26.7 26.35 {ca cys 9}10.63 28.07 26.84 {c cys 9}10.55 29.15 25.72 {o cys 9}10.37 30.32 26.06 {c cys 9}P 10.55 29.15 25.72 {n gly 10}10.58 28.81 24.44 {ca gly 10}10.51 29.84 23.4 {c gly 10}11.88 30.34 22.89 {o gly 10}11.91 31.12 21.93 {c gly 10}P 11.88 30.34 22.89 {n tyr 11}12.99 29.91 23.48 {ca tyr 11}14.31 30.21 22.91 {c tyr 11}14.39 29.8 21.43 {o tyr 11}13.89 28.75 20.99 {c tyr 11}P 14.39 29.8 21.43 {n ile 12}14.98 30.68 20.66 {ca ile 12}15.16 30.41 19.23 {c ile 12}16.65 30.19 18.91 {o ile 12}17.53 30.99 19.27 {c ile 12}P 16.65 30.19 18.91 {n tyr 13}16.92 29.02 18.38 {ca tyr 13}18.27 28.75 17.86 {c tyr 13}18.34 29.35 16.44 {o tyr 13}17.57 28.98 15.54 {c tyr 13}P 18.34 29.35 16.44 {n asp 14}19.26 30.28 16.28 {ca asp 14}19.55 30.89 15. {c asp 14}20.92 30.48 14.5 {o asp 14}21.94 30.76 15.16 {c asp 14}P 20.92 30.48 14.5 {n pro 15}20.9 29.67 13.45 {ca pro 15}22.14 29.09 12.94 {c pro 15}23.17 30.15 12.53 {o pro 15}24.37 29.87 12.64 {c pro 15}P 23.17 30.15 12.53 {n glu 16}22.77 31.38 12.25 {ca glu 16}23.75 32.45 11.99 {c glu 16}24.6 32.87 13.16 {o glu 16}25.75 33.33 13.04 {c glu 16}P 24.6 32.87 13.16 {n asp 17}23.99 32.74 14.31 {ca asp 17}24.61 33.11 15.56 {c asp 17}25.3 31.93 16.28 {o asp 17}26.17 32.13 17.15 {c asp 17}P 25.3 31.93 16.28 {n gly 18}24.75 30.74 16.07 {ca gly 18}25.14 29.54 16.85 {c gly 18}24.77 29.63 18.35 {o gly 18}23.9 30.42 18.78 {c gly 18}P 24.77 29.63 18.35 {n asp 19}25.55 28.92 19.13 {ca asp 19}25.54 29.02 20.58 {c asp 19}26.98 28.84 21.07 {o asp 19}27.34 27.79 21.6 {c asp 19}P 26.98 28.84 21.07 {n pro 20}27.84 29.83 20.75 {ca pro 20}29.31 29.64 20.86 {c pro 20}29.83 29.33 22.26 {o pro 20}30.78 28.56 22.45 {c pro 20}P 29.83 29.33 22.26 {n asp 21}29.18 29.9 23.26 {ca asp 21}29.56 29.59 24.64 {c asp 21}29.3 28.16 25.18 {o asp 21}30.06 27.66 26.03 {c asp 21}P 29.3 28.16 25.18 {n asp 22}28.53 27.45 24.4 {ca asp 22}28.36 26.02 24.56 {c asp 22}28.96 25.17 23.45 {o asp 22}28.65 24. 23.25 {c asp 22}P 28.96 25.17 23.45 {n gly 23}29.84 25.79 22.7 {ca gly 23}30.61 25.08 21.69 {c gly 23}29.95 24.87 20.33 {o gly 23}30.43 24.11 19.49 {c gly 23}P 29.95 24.87 20.33 {n val 24}28.87 25.59 20.07 {ca val 24}28.14 25.48 18.8 {c val 24}28.41 26.73 17.98 {o val 24}27.98 27.85 18.31 {c val 24}P 28.41 26.73 17.98 {n asn 25}29.29 26.56 17.03 {ca asn 25}29.78 27.74 16.3 {c asn 25}28.72 28.32 15.36 {o asn 25}27.83 27.59 14.87 {c asn 25}P 28.72 28.32 15.36 {n pro 26}28.82 29.63 15.04 {ca pro 26}27.98 30.23 13.96 {c pro 26}28.11 29.41 12.68 {o pro 26}29.16 28.85 12.32 {c pro 26}P 28.11 29.41 12.68 {n gly 27}26.98 29.24 12.03 {ca gly 27}26.86 28.37 10.85 {c gly 27}26.55 26.88 11.03 {o gly 27}26.56 26.11 10.06 {c gly 27}P 26.55 26.88 11.03 {n thr 28}26.27 26.49 12.25 {ca thr 28}25.98 25.07 12.49 {c thr 28}24.46 24.87 12.35 {o thr 28}23.66 25.55 13.01 {c thr 28}P 24.46 24.87 12.35 {n asp 29}24.11 24.04 11.39 {ca asp 29}22.69 23.66 11.2 {c asp 29}22.29 22.92 12.48 {o asp 29}23.09 22.18 13.08 {c asp 29}P 22.29 22.92 12.48 {n phe 30}21.03 23.05 12.84 {ca phe 30}20.5 22.34 14.01 {c phe 30}20.78 20.83 14.04 {o phe 30}21.15 20.29 15.09 {c phe 30}P 20.78 20.83 14.04 {n lys 31}20.6 20.17 12.91 {ca lys 31}20.83 18.72 12.88 {c lys 31}22.31 18.32 13.14 {o lys 31}22.59 17.24 13.68 {c lys 31}P 22.31 18.32 13.14 {n asp 32}23.24 19.25 12.96 {ca asp 32}24.65 18.99 13.27 {c asp 32}25.12 19.45 14.63 {o asp 32}26.2 19.07 15.07 {c asp 32}P 25.12 19.45 14.63 {n ile 33}24.23 20.02 15.42 {ca ile 33}24.53 20.26 16.82 {c ile 33}24.65 18.93 17.55 {o ile 33}23.8 18.04 17.35 {c ile 33}P 24.65 18.93 17.55 {n pro 34}25.71 18.71 18.34 {ca pro 34}25.86 17.45 19.08 {c pro 34}24.61 17.14 19.92 {o pro 34}23.97 18.03 20.53 {c pro 34}P 24.61 17.14 19.92 {n asp 35}24.21 15.89 19.84 {ca asp 35}22.92 15.48 20.4 {c asp 35}22.78 15.53 21.93 {o asp 35}21.67 15.29 22.43 {c asp 35}P 22.78 15.53 21.93 {n asp 36}23.84 15.84 22.64 {ca asp 36}23.72 16.06 24.08 {c asp 36}23.58 17.55 24.43 {o asp 36}23.6 17.9 25.62 {c asp 36}P 23.58 17.55 24.43 {n trp 37}23.54 18.44 23.45 {ca trp 37}23.32 19.88 23.68 {c trp 37}21.9 20.12 24.23 {o trp 37}20.95 19.39 23.89 {c trp 37}P 21.9 20.12 24.23 {n val 38}21.8 21.1 25.09 {ca val 38}20.5 21.45 25.67 {c val 38}20.23 22.95 25.52 {o val 38}21.12 23.78 25.27 {c val 38}P 20.23 22.95 25.52 {n cys 39}18.94 23.28 25.52 {ca cys 39}18.49 24.68 25.45 {c cys 39}19.21 25.51 26.53 {o cys 39}19.16 25.2 27.73 {c cys 39}P 19.21 25.51 26.53 {n pro 40}19.92 26.56 26.07 {ca pro 40}20.7 27.45 26.96 {c pro 40}19.83 28.12 28.05 {o pro 40}20.33 28.58 29.09 {c pro 40}P 19.83 28.12 28.05 {n leu 41}18.57 28.36 27.77 {ca leu 41}17.71 29.08 28.72 {c leu 41}17.04 28.1 29.71 {o leu 41}16.93 28.31 30.93 {c leu 41}P 17.04 28.1 29.71 {n cys 42}16.5 26.99 29.22 {ca cys 42}15.72 26.1 30.11 {c cys 42}16.31 24.7 30.36 {o cys 42}15.68 23.91 31.09 {c cys 42}P 16.31 24.7 30.36 {n gly 43}17.34 24.32 29.61 {ca gly 43}18.02 23.05 29.86 {c gly 43}17.38 21.77 29.29 {o gly 43}17.94 20.69 29.52 {c gly 43}P 17.38 21.77 29.29 {n val 44}16.31 21.84 28.5 {ca val 44}15.73 20.66 27.85 {c val 44}16.55 20.28 26.6 {o val 44}17.26 21.11 25.97 {c val 44}P 16.55 20.28 26.6 {n gly 45}16.43 19.01 26.25 {ca gly 45}17.14 18.44 25.09 {c gly 45}16.58 18.92 23.72 {o gly 45}15.51 19.52 23.52 {c gly 45}P 16.58 18.92 23.72 {n lys 46}17.33 18.52 22.69 {ca lys 46}16.96 18.82 21.29 {c lys 46}15.59 18.29 20.81 {o lys 46}14.97 18.88 19.9 {c lys 46}P 15.59 18.29 20.81 {n asp 47}15.16 17.18 21.42 {ca asp 47}13.9 16.54 21.07 {c asp 47}12.67 17.41 21.42 {o asp 47}11.57 17.18 20.9 {c asp 47}P 12.67 17.41 21.42 {n glu 48}12.84 18.5 22.18 {ca glu 48}11.73 19.46 22.37 {c glu 48}11.81 20.69 21.5 {o glu 48}11.02 21.63 21.69 {c glu 48}P 11.81 20.69 21.5 {n phe 49}12.69 20.69 20.53 {ca phe 49}12.76 21.78 19.54 {c phe 49}11.92 21.39 18.31 {o phe 49}11.87 20.23 17.88 {c phe 49}P 11.92 21.39 18.31 {n glu 50}11.46 22.43 17.63 {ca glu 50}10.78 22.32 16.31 {c glu 50}11.35 23.38 15.34 {o glu 50}11.64 24.52 15.75 {c glu 50}P 11.35 23.38 15.34 {n glu 51}11.42 23.01 14.07 {ca glu 51}11.75 23.89 12.95 {c glu 51}10.69 25. 12.89 {o glu 51}9.47 24.86 13.11 {c glu 51}P 10.69 25. 12.89 {n val 52}11.28 26.16 12.71 {ca val 52}10.52 27.37 12.39 {c val 52}10.34 27.36 10.82 {o val 52}11.31 27.62 10.06 {c val 52}P 10.34 27.36 10.82 {n glu 53}9.18 26.96 10.27 {ca glu 53}8.74 27.09 8.82 {c glu 53}7.78 28.33 8.94 {o glu 53}6.97 28.49 9.89 {c glu 53}P 7.78 28.33 8.94 {n glu 54}7.9 29.12 7.88 {ca glu 54}7.04 30.3 7.7 {c glu 54}6.61 30.51 6.23 {o glu 54}7.25 29.93 5.3 {c glu 54}P 6.61 30.51 6.23 {oxt glu 54}5.69 31.33 5.94 @vectorlist {Calpha} color= white {ca met 1}P 19.49 27.16 7.39 {ca lys 2}16.26 27.17 9.36 {ca lys 3}15.73 28.51 12.82 {ca tyr 4}14.48 26.12 15.53 {ca thr 5}12.47 26.98 18.6 {ca cys 6}12.57 25.39 22.04 {ca thr 7}8.88 24.44 22.55 {ca val 8}9.32 24.48 26.32 {ca cys 9}10.63 28.07 26.84 {ca gly 10}10.51 29.84 23.4 {ca tyr 11}14.31 30.21 22.91 {ca ile 12}15.16 30.41 19.23 {ca tyr 13}18.27 28.75 17.86 {ca asp 14}19.55 30.89 15. {ca pro 15}22.14 29.09 12.94 {ca glu 16}23.75 32.45 11.99 {ca asp 17}24.61 33.11 15.56 {ca gly 18}25.14 29.54 16.85 {ca asp 19}25.54 29.02 20.58 {ca pro 20}29.31 29.64 20.86 {ca asp 21}29.56 29.59 24.64 {ca asp 22}28.36 26.02 24.56 {ca gly 23}30.61 25.08 21.69 {ca val 24}28.14 25.48 18.8 {ca asn 25}29.78 27.74 16.3 {ca pro 26}27.98 30.23 13.96 {ca gly 27}26.86 28.37 10.85 {ca thr 28}25.98 25.07 12.49 {ca asp 29}22.69 23.66 11.2 {ca phe 30}20.5 22.34 14.01 {ca lys 31}20.83 18.72 12.88 {ca asp 32}24.65 18.99 13.27 {ca ile 33}24.53 20.26 16.82 {ca pro 34}25.86 17.45 19.08 {ca asp 35}22.92 15.48 20.4 {ca asp 36}23.72 16.06 24.08 {ca trp 37}23.32 19.88 23.68 {ca val 38}20.5 21.45 25.67 {ca cys 39}18.49 24.68 25.45 {ca pro 40}20.7 27.45 26.96 {ca leu 41}17.71 29.08 28.72 {ca cys 42}15.72 26.1 30.11 {ca gly 43}18.02 23.05 29.86 {ca val 44}15.73 20.66 27.85 {ca gly 45}17.14 18.44 25.09 {ca lys 46}16.96 18.82 21.29 {ca asp 47}13.9 16.54 21.07 {ca glu 48}11.73 19.46 22.37 {ca phe 49}12.76 21.78 19.54 {ca glu 50}10.78 22.32 16.31 {ca glu 51}11.75 23.89 12.95 {ca val 52}10.52 27.37 12.39 {ca glu 53}8.74 27.09 8.82 {ca glu 54}7.04 30.3 7.7 @vectorlist {Hbonds} color=brown <2.16>{tyr 4 hn} P U 16.02 27.56 15.07 {tyr 13 o} U 17.1 28.55 15.4 <1.77>{thr 5 hn} P U 12.38 25.72 16.82 {glu 50 o} U 11.86 24.88 16.07 <1.73>{cys 6 hn} P U 13.27 27.13 20.99 {tyr 11 o} U 13.71 28.27 20.99 <1.96>{thr 7 hn} P U 10.82 23.53 22.1 {glu 48 o} U 10.96 22.2 21.81 <1.90>{gly 10 hn} P U 10.65 27.84 24.19 {cys 6 o} U 10.6 26.95 23.21 <1.80>{tyr 13 hn} P U 16.2 28.33 18.34 {tyr 4 o} U 15.25 27.76 17.73 <2.14>{asp 17 hn} P U 23.06 32.37 14.32 {asp 14 o} U 22.28 31.24 14.91 <2.12>{gly 18 hn} P U 24.05 30.67 15.36 {asp 14 o} U 22.57 30.73 15.22 <1.89>{asp 19 hn} P U 26.18 28.28 18.69 {val 24 o} U 27.44 27.98 18.43 <2.19>{asp 22 hn} P U 28.04 27.92 23.67 {asp 19 o} U 27.55 27.83 22.22 <2.00>{gly 23 hn} P U 29.98 26.77 22.83 {pro 20 o} U 30.54 28.02 22.57 <2.14>{val 24 hn} P U 28.55 26.23 20.77 {asp 19 o} U 27.7 27.32 21.35 <1.83>{gly 27 hn} P U 26.18 29.73 12.37 {pro 15 o} U 24.91 29.83 12.56 <2.49>{thr 28 hn} P U 26.26 27.16 12.99 {asn 25 o} U 27.36 27.46 14.31 <2.09>{asp 32 hn} P U 22.97 20.14 12.6 {asp 29 o} U 23.05 21.57 12.94 <2.19>{ile 33 hn} P U 23.34 20.29 15.05 {phe 30 o} U 21.81 20.29 15.08 <2.01>{trp 37 hn} P U 23.67 18.11 22.52 {pro 34 o} U 23.88 18.05 21.13 <1.80>{cys 39 hn} P U 18.26 22.55 25.57 {val 44 o} U 17.56 21.54 25.85 <1.91>{gly 43 hn} P U 17.65 24.91 28.87 {cys 39 o} U 18.71 25.11 28.07 <2.18>{glu 48 hn} P U 13.73 18.66 22.62 {gly 45 o} U 14.97 19.26 23.25 <2.03>{phe 49 hn} P U 13.32 19.92 20.48 {lys 46 o} U 14.48 19.19 20.07 <2.02>{glu 50 hn} P U 11.59 23.33 18.05 {thr 5 o} U 11.81 24.35 19. <1.81>{val 52 hn} P U 12.27 26.2 12.8 {lys 3 o} U 13.47 26.63 12.85 @group {Fe, ligands} @vectorlist {Cys} color=yellow {ca cys 6}P 12.57 25.39 22.04 {cb cys 6}13.45 25.86 23.19 {sg cys 6}13.12 24.88 24.66 {ca cys 9}P 10.63 28.07 26.84 {cb cys 9}11.94 28.26 27.63 {sg cys 9}13.41 28.28 26.51 {ca cys 39}P 18.49 24.68 25.45 {cb cys 39}16.98 24.72 25.66 {sg cys 39}16.41 26.45 25.65 {ca cys 42}P 15.72 26.1 30.11 {cb cys 42}14.25 25.94 29.67 {sg cys 42}14.03 24.91 28.15 @vectorlist {Fe} color=red {sg cys 6}P 13.12 24.88 24.66 {Fe} 14.21 26.15 26.28 {sg cys 9} 13.41 28.28 26.51 {sg cys 39}P 16.41 26.45 25.65 {Fe} 14.21 26.15 26.28 {sg cys 42}14.03 24.91 28.15 @kinemage 9 @caption Ferredoxin (P. aerogenes): Calpha backbone, two Fe4S4 clusters (red), and their Cys ligands (yellow). @onewidth @zoom .95 @matrix .767305 .596672 .235003 -.608754 .562483 .559492 .201649 -.57236 .794821 @group {ferredoxin} @vectorlist {Calpha} color= white {ca ala 1}P 18.608 -1.306 15.701 {ca tyr 2}20.387 1.903 14.595 {ca val 3}21.935 2.186 11.095 {ca ile 4}24.816 4.428 10.287 {ca asn 5}24.187 5.953 6.929 {ca asp 6}26.195 7.425 4.114 {ca ser 7}26.94 10.819 5.921 {ca cys 8}29.492 9.056 7.969 {ca ile 9}32.983 10.77 8.114 {ca ala 10}34.683 7.769 10.071 {ca cys 11}35.553 10.272 12.799 {ca gly 12}34.775 7.248 14.752 {ca ala 13}33.938 8.683 18.22 {ca cys 14}30.908 6.693 18.579 {ca lys 15}32.522 3.213 19.197 {ca pro 16}33.133 4.168 22.681 {ca glu 17}29.882 5.697 23.618 {ca cys 18}27.959 2.593 22.783 {ca pro 19}27.343 0.597 25.921 {ca val 20}27.547 -2.88 24.35 {ca asn 21}30.544 -2.299 21.906 {ca ile 22}28.619 -3.311 18.949 {ca ile 23}29.989 -0.861 16.406 {ca gln 24}32.952 -1.034 14.154 {ca gly 25}34.945 -0.661 10.728 {ca ser 26}35.525 1.706 7.213 {ca ile 27}32.461 4.005 7.016 {ca tyr 28}31.24 2.688 10.543 {ca ala 29}28.838 -0.162 11.205 {ca ile 30}26.586 -1.521 13.787 {ca asp 31}26.171 -5.153 14.051 {ca ala 32}22.2 -5.04 14.63 {ca asp 33}21.16 -8.037 16.516 {ca ser 34}23.235 -6.814 19.524 {ca cys 35}22.228 -2.994 19.358 {ca ile 36}19.841 -1.956 22.012 {ca asp 37}18.318 1.231 20.248 {ca cys 38}19.896 3.315 23. {ca gly 39}20.372 6.553 20.874 {ca ser 40}23.809 6.742 22.165 {ca cys 41}25.805 6.81 18.965 {ca ala 42}23.296 9.302 17.555 {ca ser 43}23.836 11.465 20.528 {ca val 44}27.398 11.929 19.594 {ca cys 45}27.615 12.012 15.724 {ca pro 46}28.79 15.481 14.37 {ca val 47}27.026 14.734 10.976 {ca gly 48}24.05 12.869 12.067 {ca ala 49}24.541 9.558 10.291 {ca pro 50}23.601 6.999 13.122 {ca asn 51}19.817 6.678 12.665 {ca pro 52}17.213 4.307 13.898 {ca glu 53}16.276 1.88 11.665 {ca asp 54}17.964 -0.914 9.673 @vectorlist {beta Hb} color=brown <1.85>{val 3 hn} P U 20.93 3.31 12.67 {asn 51 o} U 19.85 4.02 12.53 <1.81>{asn 5 hn} P U 24.24 6.62 9.07 {ala 49 o} U 23.58 7.34 9.89 <1.61>{asn 51 hn} P U 21.68 5.75 11.93 {val 3 o} U 21.96 4.9 11.24 <1.57>{gln 24 hn} P U 30.77 -0.69 13.97 {ala 29 o} U 29.76 -0.47 13.58 <2.14>{asp 31 hn} P U 27.32 -3.8 15.36 {ile 22 o} U 28.34 -3.22 16.29 @subgroup {sidechain} @vectorlist {Cys} color=yellow {ca cys 8}P 29.492 9.056 7.969 {cb cys 8}29.638 7.576 8.484 {sg cys 8}30.767 6.852 9.74 {fe1 fes 1}30.535 7.886 11.642 {ca cys 11}P 35.553 10.272 12.799 {cb cys 11}34.616 11.431 13.268 {sg cys 11}33.27 10.97 14.503 {fe2 fes 1}31.762 9.524 13.595 {ca cys 14}P 30.908 6.693 18.579 {cb cys 14}29.812 6.452 17.551 {sg cys 14}30.364 5.564 15.917 {fe3 fes 1}30.328 7.308 14.228 {ca cys 45}P 27.615 12.012 15.724 {cb cys 45}26.8 11.302 14.602 {sg cys 45}27.795 11.065 13.311 {fe4 fes 1}29.104 9.577 13.205 {ca cys 35}P 22.228 -2.994 19.358 {cb cys 35}21.962 -2.208 18.083 {sg cys 35}21.379 -0.585 18.201 {fe2 fes 2}23.03 0.627 19.142 {ca cys 38}P 19.896 3.315 23. {cb cys 38}21.111 2.741 23.717 {sg cys 38}22.448 3.239 23.185 {fe3 fes 2}23.394 2.329 21.268 {ca cys 41}P 25.805 6.81 18.965 {cb cys 41}25.896 5.613 17.874 {sg cys 41}24.135 5.093 17.63 {fe4 fes 2}24.129 2.929 18.791 {ca cys 18}P 27.959 2.593 22.783 {cb cys 18}28.164 2.118 21.374 {sg cys 18}27.166 0.502 21.043 {fe1 fes 2}25.417 0.955 20.244 @subgroup dominant {Fe4S4} @vectorlist {FeS} color=red {fe1 fes 1}P 30.535 7.886 11.642 {s2 fes 1}30.715 10.272 11.819 {fe2 fes 1}31.762 9.524 13.595 {s1 fes 1}32.144 7.244 13.138 {fe3 fes 1}30.328 7.308 14.228 {s3 fes 1}28.71 7.561 12.803 {fe4 fes 1}29.104 9.577 13.205 {s2 fes 1}30.715 10.272 11.819 {s3 fes 1}P 28.71 7.561 12.803 {fe1 fes 1}30.535 7.886 11.642 {s1 fes 1}32.144 7.244 13.138 {fe4 fes 1}P 29.104 9.577 13.205 {S4 FeS 1}30.27 9.336 15.26 {fe2 fes 1}31.762 9.524 13.595 {fe3 fes 1}P 30.328 7.308 14.228 {S4 FeS 1}30.27 9.336 15.26 {fe1 fes 2}P 25.417 0.955 20.244 {s1 fes 2}23.821 0.049 20.972 {fe2 fes 2}23.03 0.627 19.142 {s2 fes 2}24.999 1.167 18.02 {fe4 fes 2}24.129 2.929 18.791 {s3 fes 2}25.091 3.307 20.791 {fe3 fes 2}23.394 2.329 21.268 {s3 fes 2}P 25.091 3.307 20.791 {fe1 fes 2}25.417 0.955 20.244 {s2 fes 2}24.999 1.167 18.02 {s1 fes 2}P 23.821 0.049 20.972 {fe3 fes 2}23.394 2.329 21.268 {S4 FeS 2}22.002 2.677 19.52 {fe4 fes 2}24.129 2.929 18.791 {fe2 fes 2}P 23.03 0.627 19.142 {S4 FeS 2}22.002 2.677 19.52 @kinemage 10 @caption Cytochrome C3: Calphas (white), four heme groups (shades of pink), and Cys and His ligands (yellowtint and cyan). @onewidth @multibin 3 @zoom .8 @matrix .296558 .478234 -.826647 -.25658 .873659 .413384 .919902 .089509 .381797 @2matrix -.309252 .803362 .508893 .219869 .581026 -.783623 -.925214 -.130447 -.356319 @group {Cyt C3} @vectorlist {Calpha} color= white {ca ala 1}P 41.676 63.465 31.165 {ca pro 2}38.362 61.654 31.592 {ca lys 3}37.57 59.819 34.826 {ca ala 4}36.424 56.192 35.165 {ca pro 5}32.891 56.469 36.557 {ca ala 6}31.538 54.611 39.585 {ca asp 7}30.637 50.935 39.602 {ca gly 8}26.99 49.972 39.122 {ca leu 9}26.482 51.506 35.657 {ca lys 10}23.467 50.072 33.839 {ca met 11}23.597 49.156 30.175 {ca asp 12}19.88 49.227 29.437 {ca lys 13}19.242 49.786 25.74 {ca thr 14}17.64 46.32 25.576 {ca lys 15}15.308 44.068 27.532 {ca gln 16}18.341 42.177 28.802 {ca pro 17}20.16 44.86 30.816 {ca val 18}23.71 44.458 32.113 {ca val 19}25.618 46.08 34.988 {ca phe 20}29.113 47.264 34.097 {ca asn 21}31.737 47.796 36.843 {ca his 22}34.936 49.722 36.06 {ca ser 23}36.696 48.476 39.198 {ca thr 24}36.709 44.914 37.851 {ca his 25}38.226 45.983 34.521 {ca lys 26}41.195 47.898 35.988 {ca ala 27}43.64 45.615 34.2 {ca val 28}42.216 46.709 30.816 {ca lys 29}43.325 50.022 29.254 {ca cys 30}40.572 52.665 28.867 {ca gly 31}41.211 52.792 25.12 {ca asp 32}40.567 49.086 24.648 {ca cys 33}36.845 49.814 25.188 {ca his 34}36.533 53.564 24.723 {ca his 35}38.321 53.044 21.384 {ca pro 36}39.758 55.518 18.879 {ca val 37}37.363 56.955 16.358 {ca asn 38}38.899 59.371 13.852 {ca gly 39}42.181 58.979 15.775 {ca lys 40}40.968 59.851 19.27 {ca glu 41}39.554 57.626 22.016 {ca asn 42}35.807 58.257 22.256 {ca tyr 43}34.101 58.301 25.62 {ca gln 44}30.496 58.564 24.412 {ca lys 45}27.925 55.876 25.255 {ca cys 46}28.455 52.953 22.927 {ca ala 47}24.947 53.341 21.482 {ca thr 48}25.166 57.097 20.763 {ca ala 49}23.494 57.897 17.426 {ca gly 50}25.952 57.25 14.594 {ca cys 51}27.758 54.78 16.885 {ca his 52}26.522 51.218 17.656 {ca asp 53}22.889 52.29 17.206 {ca asn 54}21.46 49.369 15.188 {ca met 55}19.185 47.578 17.625 {ca asp 56}18.641 44.633 15.297 {ca lys 57}20.431 41.803 17.103 {ca lys 58}20.993 40.069 13.767 {ca asp 59}23.153 42.776 12.181 {ca lys 60}26.875 41.928 12.009 {ca ser 61}28.077 45.3 10.693 {ca ala 62}30.032 47.512 13.119 {ca lys 63}26.82 49.482 13.812 {ca gly 64}25.123 46.495 15.481 {ca tyr 65}24.931 46.923 19.263 {ca tyr 66}24.397 43.203 19.974 {ca his 67}27.307 42.444 17.634 {ca ala 68}29.664 44.914 19.376 {ca met 69}28.85 43.344 22.741 {ca his 70}28.942 39.651 21.839 {ca asp 71}30.951 38.764 18.715 {ca lys 72}34.42 37.264 18.212 {ca gly 73}36.871 38.463 15.53 {ca thr 74}35.854 42.103 16.003 {ca lys 75}38.338 44.963 15.582 {ca phe 76}38.259 45.717 19.329 {ca lys 77}37.514 42.788 21.73 {ca ser 78}33.833 42.447 22.679 {ca cys 79}32.62 41.809 26.223 {ca val 80}32.101 38.112 25.386 {ca gly 81}35.148 37.933 23.108 {ca cys 82}37.517 39.144 25.871 {ca his 83}35.781 37.071 28.509 {ca leu 84}36.167 33.935 26.391 {ca glu 85}39.92 34.52 26.263 {ca thr 86}39.971 35.237 29.956 {ca ala 87}38.188 32.054 31.097 {ca gly 88}40.478 29.823 29.038 {ca ala 89}39.682 26.168 29.736 {ca asp 90}37.998 26.827 33.093 {ca ala 91}34.389 25.646 32.747 {ca ala 92}33.268 27.501 35.856 {ca lys 93}34.715 30.821 34.634 {ca lys 94}33.272 30.218 31.142 {ca lys 95}29.832 29.971 32.746 {ca glu 96}30.297 33.026 34.987 {ca leu 97}31.863 35.271 32.311 {ca thr 98}30.329 34.014 29.05 {ca gly 99}27.078 32.214 29.894 {ca cys 100}23.975 33.348 28.034 {ca lys 101}21.908 32.598 31.193 {ca gly 102}23.01 32.394 34.823 {ca ser 103}26.188 34.373 34.109 {ca lys 104}27.506 37.604 35.639 {ca cys 105}26.044 39.429 32.682 {ca his 106}22.624 37.832 32.377 {ca ser 107}21.076 36.117 35.448 @subgroup off {sidechain} @vectorlist {Cys} color=yellowtint {ca cys 30}P 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31.163 {cac hem 4} 28.676 40.098 29.441 @vectorlist {His} color=cyan {ca his 22}P 34.936 49.722 36.06 {cb his 22}35.066 51.257 35.978 {cg his 22}34.552 51.827 34.692 {nd1 his 22}33.258 52.182 34.473 {ce1 his 22}33.132 52.608 33.222 {ne2 his 22}34.329 52.651 32.66 {cg his 22}P 34.552 51.827 34.692 {cd2 his 22}35.214 52.053 33.535 {ne2 his 22}34.329 52.651 32.66 {ca his 25}P 38.226 45.983 34.521 {cb his 25}37.319 46.465 33.38 {cg his 25}36.15 45.543 33.266 {nd1 his 25}35.06 45.547 34.106 {ce1 his 25}34.231 44.621 33.723 {ne2 his 25}34.758 43.926 32.716 {cg his 25}P 36.15 45.543 33.266 {cd2 his 25}35.958 44.543 32.354 {ne2 his 25}34.758 43.926 32.716 {ca his 34}P 36.533 53.564 24.723 {cb his 34}36.755 54.533 25.913 {cg his 34}35.745 54.229 27. {nd1 his 34}34.4 54.437 26.933 {ce1 his 34}33.882 54.103 28.101 {ne2 his 34}34.814 53.648 28.925 {cg his 34}P 35.745 54.229 27. {cd2 his 34}36.029 53.803 28.274 {ne2 his 34}34.814 53.648 28.925 {ca his 35}P 38.321 53.044 21.384 {cb his 35}38.037 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83}34.174 40.419 30.748 {cg his 83}P 34.089 38.446 29.793 {cd2 his 83}34.894 39.521 30.002 {ne2 his 83}34.174 40.419 30.748 {ca his 106}P 22.624 37.832 32.377 {cb his 106}22.313 37.284 30.944 {cg his 106}22.636 38.17 29.797 {nd1 his 106}22.062 39.389 29.577 {ce1 his 106}22.556 39.915 28.435 {ne2 his 106}23.33 39.008 27.817 {cg his 106}P 22.636 38.17 29.797 {cd2 his 106}23.367 37.912 28.681 {ne2 his 106}23.33 39.008 27.817 @subgroup {het groups} @vectorlist {heme 1} color=pinktint {fe hem 1} P 34.538 53.144 30.711 {n a hem 1} 33.616 54.887 31.031 {c1a hem 1} 32.263 55.144 30.973 {n a hem 1} P 33.616 54.887 31.031 {c4a hem 1} 34.216 56.127 31.245 {c3a hem 1} 33.199 57.169 31.298 {cha hem 1} P 31.294 54.186 30.774 {c1a hem 1} 32.263 55.144 30.973 {c2a hem 1} 32.02 56.564 31.186 {c3a hem 1} 33.199 57.169 31.298 {cma hem 1} 33.53 58.667 31.447 {chb hem 1} P 35.57 56.355 31.297 {c4a hem 1} 34.216 56.127 31.245 {c2a hem 1} P 32.02 56.564 31.186 {caa hem 1} 30.612 57.164 31.162 {cba hem 1} 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30.576 {c1b hem 3} 31.623 43.057 30.986 {n b hem 3} P 32.931 42.966 30.576 {c4b hem 3} 33.006 43.66 29.385 {c3b hem 3} 31.673 44.166 29.05 {chb hem 3} P 31.15 42.517 32.158 {c1b hem 3} 31.623 43.057 30.986 {c2b hem 3} 30.85 43.789 30.017 {c3b hem 3} 31.673 44.166 29.05 {cab hem 3} 31.371 44.908 27.712 {cbb hem 3} 30.746 46.121 27.83 {chc hem 3} P 34.165 43.832 28.645 {c4b hem 3} 33.006 43.66 29.385 {c2b hem 3} P 30.85 43.789 30.017 {cmb hem 3} 29.332 44.064 30.165 {fe hem 3} P 34.457 42.151 31.595 {n c hem 3} 35.705 42.602 30.096 {c1c hem 3} 35.426 43.325 28.953 {n c hem 3} P 35.705 42.602 30.096 {c4c hem 3} 37.015 42.162 29.954 {c3c hem 3} 37.54 42.642 28.706 {chc hem 3} P 34.165 43.832 28.645 {c1c hem 3} 35.426 43.325 28.953 {c2c hem 3} 36.582 43.321 28.082 {c3c hem 3} 37.54 42.642 28.706 {cac hem 3} 38.988 42.336 28.216 {cbc hem 3} 39.44 43.198 27.243 {chd hem 3} P 37.743 41.527 30.934 {c4c hem 3} 37.015 42.162 29.954 {c2c hem 3} P 36.582 43.321 28.082 {cmc hem 3} 36.623 44.074 26.738 {fe hem 3} P 34.457 42.151 31.595 {n d hem 3} 35.992 41.336 32.609 {c1d hem 3} 37.291 41.235 32.191 {n d hem 3} P 35.992 41.336 32.609 {c4d hem 3} 35.951 40.875 33.912 {c3d hem 3} 37.27 40.448 34.289 {chd hem 3} P 37.743 41.527 30.934 {c1d hem 3} 37.291 41.235 32.191 {c2d hem 3} 38.069 40.619 33.263 {c3d hem 3} 37.27 40.448 34.289 {cad hem 3} 37.545 39.784 35.668 {cbd hem 3} 37.535 38.227 35.498 {cgd hem 3} 37.442 37.477 36.79 {o1d hem 3} 38.54 37.21 37.337 {cha hem 3} P 34.822 40.72 34.661 {c4d hem 3} 35.951 40.875 33.912 {c2d hem 3} P 38.069 40.619 33.263 {cmd hem 3} 39.579 40.335 33.143 {cgd hem 3} P 37.442 37.477 36.79 {o2d hem 3} 36.35 37.058 37.258 @vectorlist {heme 4} color=magenta {fe hem 4} P 24.191 39.364 26.12 {n a hem 4} 22.418 39.682 25.174 {c1a hem 4} 21.682 40.867 25.13 {n a hem 4} P 22.418 39.682 25.174 {c4a hem 4} 21.6 38.721 24.615 {c3a hem 4} 20.39 39.35 24.103 {cha hem 4} P 22.15 42.086 25.629 {c1a hem 4} 21.682 40.867 25.13 {c2a hem 4} 20.398 40.605 24.518 {c3a hem 4} 20.39 39.35 24.103 {cma hem 4} 19.284 38.548 23.377 {chb hem 4} P 21.94 37.409 24.391 {c4a hem 4} 21.6 38.721 24.615 {c2a hem 4} P 20.398 40.605 24.518 {caa hem 4} 19.357 41.704 24.144 {cba hem 4} 19.297 41.934 22.595 {cga hem 4} 18.16 42.823 22.137 {o1a hem 4} 17.009 42.493 22.507 {cga hem 4} P 18.16 42.823 22.137 {o2a hem 4} 18.465 43.888 21.567 {fe hem 4} P 24.191 39.364 26.12 {n b hem 4} 24. 37.426 25.728 {c1b hem 4} 23.079 36.821 24.891 {n b hem 4} P 24. 37.426 25.728 {c4b hem 4} 24.923 36.42 26.022 {c3b hem 4} 24.656 35.268 25.223 {chb hem 4} P 21.94 37.409 24.391 {c1b hem 4} 23.079 36.821 24.891 {c2b hem 4} 23.527 35.48 24.539 {c3b hem 4} 24.656 35.268 25.223 {cab hem 4} 25.54 33.99 25.202 {cbb hem 4} 26.234 33.828 24.044 {chc hem 4} P 25.995 36.619 26.892 {c4b hem 4} 24.923 36.42 26.022 {c2b hem 4} P 23.527 35.48 24.539 {cmb hem 4} 22.756 34.534 23.614 {fe hem 4} P 24.191 39.364 26.12 {n c hem 4} 25.942 39.083 27.012 {c1c hem 4} 26.495 37.845 27.354 {n c hem 4} P 25.942 39.083 27.012 {c4c hem 4} 26.671 40.027 27.698 {c3c hem 4} 27.684 39.36 28.503 {chc hem 4} P 25.995 36.619 26.892 {c1c hem 4} 26.495 37.845 27.354 {c2c hem 4} 27.452 38.03 28.396 {c3c hem 4} 27.684 39.36 28.503 {cac hem 4} 28.676 40.098 29.441 {cbc hem 4} 30.031 39.908 29.319 {chd hem 4} P 26.563 41.383 27.535 {c4c hem 4} 26.671 40.027 27.698 {c2c hem 4} P 27.452 38.03 28.396 {cmc hem 4} 28.273 36.877 29.009 {fe hem 4} P 24.191 39.364 26.12 {n d hem 4} 24.32 41.331 26.518 {c1d hem 4} 25.431 41.988 27.029 {n d hem 4} P 24.32 41.331 26.518 {c4d hem 4} 23.424 42.322 26.163 {c3d hem 4} 24.03 43.63 26.395 {chd hem 4} P 26.563 41.383 27.535 {c1d hem 4} 25.431 41.988 27.029 {c2d hem 4} 25.231 43.432 26.946 {c3d hem 4} 24.03 43.63 26.395 {cad hem 4} 23.286 44.956 26.165 {cbd hem 4} 22.71 45.509 27.496 {cgd hem 4} 21.707 46.614 27.272 {o1d hem 4} 22.163 47.721 26.905 {cha hem 4} P 22.15 42.086 25.629 {c4d hem 4} 23.424 42.322 26.163 {c2d hem 4} P 25.231 43.432 26.946 {cmd hem 4} 26.278 44.484 27.358 {cgd hem 4} P 21.707 46.614 27.272 {o2d hem 4} 20.506 46.32 27.303 @kinemage 11 @caption Human metallothionein domain 2 (file 1MHU): Calphas (white), Cys (yellow), and bound Cd (green). @onewidth @zoom .9 @center 4.7 3.8 11.8 @matrix .68993 -.647188 .32426 -.424367 .001283 .905489 -.586438 -.76233 -.27376 @2matrix -.419567 -.76479 -.488938 .626992 .145326 -.76535 .656387 -.627676 .418544 @group {mth dom 2} @vectorlist {Calpha} color= white {ca lys 31} P 1.453 0. 0. {ca ser 32}3.802 0.292 2.954 {ca cys 33}4.089 3.835 4.253 {ca cys 34}7.281 3.16 6.172 {ca ser 35}9.399 0.194 7.192 {ca cys 36}8.653 1.022 10.809 {ca cys 37}4.874 1.244 10.836 {ca pro 38}2.496 -1.569 9.859 {ca val 39}-0.411 -0.271 7.812 {ca gly 40}-3.463 1.952 8.073 {ca cys 41}-1.495 3.899 10.654 {ca ala 42}-3.48 7.036 11.395 {ca lys 43}-0.094 8.597 12.046 {ca cys 44}0.663 7.716 8.443 {ca ala 45}-2.791 7.887 6.904 {ca gln 46}-2.526 11.501 5.808 {ca gly 47}0.862 10.666 4.341 {ca cys 48}3.881 9.877 6.483 {ca ile 49}4.163 11.887 9.677 {ca cys 50}6.61 9.279 10.914 {ca lys 51}10.04 10.79 11.441 {ca gly 52}11.126 8.63 14.353 {ca ala 53}13.152 5.922 12.653 {ca ser 54}12.672 2.869 10.468 {ca asp 55}13.075 0.002 12.906 {ca lys 56}11.64 1.946 15.819 {ca cys 57}9.848 5.275 16.013 {ca ser 58}8.054 7.254 18.694 {ca cys 59}5.283 8.972 16.771 {ca cys 60}3.281 5.825 16.128 {ca ala 61}4.174 3.841 19.226 @vectorlist off {Hbonds} color=brown <2.46>{cys 36 hn} P U 8.05 1.54 8.83 {cys 34 o} U 7.13 1.11 7.44 <1.65>{cys 44 hn} P U -0.83 7.44 9.94 {cys 41 o} U -1.39 6.46 9.68 <2.41>{ala 45 hn} P U -1.74 8.44 8.67 {ala 42 o} U -2.29 8.95 10.18 <3.01>{gly 47 hn} P U -0.78 9.75 5.34 {cys 44 o} U -0.39 7.8 6.04 <2.56>{ile 49 hn} P U 2.94 10.41 8.75 {lys 43 o} U 2.11 9.48 10.05 @subgroup {sidechain} @vectorlist {Cys} color=yellow {ca cys 33}P 4.089 3.835 4.253 {cb cys 33}3.152 4.496 5.266 {sg cys 33}3.385 6.311 5.244 {ca cys 34}P 7.281 3.16 6.172 {cb cys 34}7.468 4.183 7.294 {sg cys 34}5.911 4.367 8.239 {ca cys 36}P 8.653 1.022 10.809 {cb cys 36}9.239 2.336 11.327 {sg cys 36}8.008 3.204 12.367 {ca cys 37}P 4.874 1.244 10.836 {cb cys 37}4.128 2.559 10.602 {sg cys 37}4.662 3.808 11.827 {ca cys 41}P -1.495 3.899 10.654 {cb cys 41}0.024 3.866 10.837 {sg cys 41}0.511 4.953 12.226 {ca cys 44}P 0.663 7.716 8.443 {cb cys 44}1.673 6.567 8.409 {sg cys 44}3.169 7.02 9.359 {ca cys 48}P 3.881 9.877 6.483 {cb cys 48}4.979 9.311 5.58 {sg cys 48}6.291 8.541 6.597 {ca cys 50}P 6.61 9.279 10.914 {cb cys 50}6.442 7.779 10.663 {sg cys 50}7.598 6.833 11.72 {ca cys 57}P 9.848 5.275 16.013 {cb cys 57}8.882 5.628 14.881 {sg cys 57}7.17 5.191 15.359 {ca cys 59}P 5.283 8.972 16.771 {cb cys 59}5.711 9.92 15.649 {sg cys 59}7.199 9.266 14.809 {ca cys 60}P 3.281 5.825 16.128 {cb cys 60}3.392 5.396 14.664 {sg cys 60}3.643 6.863 13.6 @group {metals} @vectorlist {Cd} color=green {Cd 101}P 6.089 7.03 13.926 6.089 7.03 13.926 P U 5.989 7.03 13.926 U 6.189 7.03 13.926 P U 6.089 6.93 13.926 U 6.089 7.13 13.926 P U 6.089 7.03 13.826 U 6.089 7.03 14.026 {Cd 105}P 4.887 6.44 7.398 4.887 6.44 7.398 P U 4.787 6.44 7.398 U 4.987 6.44 7.398 P U 4.887 6.34 7.398 U 4.887 6.54 7.398 P U 4.887 6.44 7.298 U 4.887 6.44 7.498 {Cd 106}P 2.923 5.625 11.331 2.923 5.625 11.331 P U 2.823 5.625 11.331 U 3.023 5.625 11.331 P U 2.923 5.525 11.331 U 2.923 5.725 11.331 P U 2.923 5.625 11.231 U 2.923 5.625 11.431 {Cd 107}P 6.936 4.543 10.531 6.936 4.543 10.531 P U 6.836 4.543 10.531 U 7.036 4.543 10.531 P U 6.936 4.443 10.531 U 6.936 4.643 10.531 P U 6.936 4.543 10.431 U 6.936 4.543 10.631 @vectorlist {lig bonds} color=sea {sg cys 41}P U 0.965 5.079 12.058 {Cd 106}U 2.469 5.499 11.499 {Cd 106}P U 3.262 5.271 11.428 {sg cys 37}U 4.323 4.162 11.73 {sg cys 60}P U 3.509 6.632 13.177 {Cd 106}U 3.057 5.856 11.754 {Cd 106}P U 2.974 5.912 10.925 {sg cys 44}U 3.118 6.733 9.765 {sg cys 44}P U 3.491 6.911 8.992 {Cd 105}U 4.565 6.549 7.765 {Cd 105}P U 5.152 6.836 7.247 {sg cys 48}U 6.026 8.145 6.748 {sg cys 34}P U 5.703 4.788 8.068 {Cd 105}U 5.095 6.019 7.569 {Cd 105}P U 4.601 6.415 6.988 {sg cys 33}U 3.671 6.336 5.654 {sg cys 34}P U 6.115 4.402 8.694 {Cd 107}U 6.732 4.508 10.076 {Cd 107}P U 7.06 4.973 10.754 {sg cys 50}U 7.474 6.403 11.497 {sg cys 36}P U 7.795 3.47 12.002 {Cd 107}U 7.149 4.277 10.896 {Cd 107}P U 6.518 4.408 10.769 {sg cys 37}U 5.08 3.943 11.589 {sg cys 50}P U 7.316 6.87 12.132 {Cd 101}U 6.371 6.993 13.514 {Cd 101}P U 6.299 7.452 14.093 {sg cys 59}U 6.989 8.844 14.642 {sg cys 57}P U 6.96 5.549 15.08 {Cd 101}U 6.299 6.672 14.205 {Cd 101}P U 5.595 6.996 13.86 {sg cys 60}U 4.137 6.897 13.666 @kinemage 12 @caption Immunoglobulin-binding domain of Streptococcal protein G, a small protein with no disulfides or bound metals. Beta strands are in greentint and helix in pink. @onewidth @zoom 1.2 @matrix .039019 .99869 .033102 .219269 -.040877 .974808 .974884 -.030778 -.220577 @2matrix -.009806 .961015 -.276322 -.947962 .079009 .308424 .318232 .264968 .910231 @3matrix .212005 -.026191 .976917 -.154872 .986108 .060047 -.964919 -.164027 .205005 @group {1GB1} @subgroup {beta sheet} @vectorlist {main ch} color=greentint {n met 1}P -14.152 0.961 4.712 {ca met 1}-13.296 0.028 3.924 {c met 1}-11.822 0.338 4.193 {o met 1}-11.358 1.432 3.941 {c met 1}P -11.822 0.338 4.193 {n thr 2}-11.121 -0.642 4.703 {ca thr 2}-9.669 -0.447 4.998 {c thr 2}-8.861 -1.586 4.373 {o thr 2}-9.036 -2.736 4.724 {c thr 2}P -8.861 -1.586 4.373 {n tyr 3}-7.99 -1.247 3.462 {ca tyr 3}-7.173 -2.314 2.811 {c tyr 3}-5.864 -2.502 3.578 {o tyr 3}-5.487 -1.663 4.367 {c tyr 3}P -5.864 -2.502 3.578 {n lys 4}-5.204 -3.598 3.323 {ca lys 4}-3.922 -3.881 4.044 {c lys 4}-2.734 -3.794 3.085 {o lys 4}-2.647 -4.537 2.142 {c lys 4}P -2.734 -3.794 3.085 {n leu 5}-1.839 -2.896 3.36 {ca leu 5}-0.651 -2.752 2.466 {c leu 5}0.458 -3.716 2.906 {o leu 5}0.605 -4. 4.076 {c leu 5}P 0.458 -3.716 2.906 {n ile 6}1.201 -4.204 1.943 {ca ile 6}2.338 -5.105 2.255 {c ile 6}3.607 -4.526 1.623 {o ile 6}3.809 -4.624 0.429 {c ile 6}P 3.607 -4.526 1.623 {n leu 7}4.435 -3.938 2.439 {ca leu 7}5.682 -3.321 1.9 {c leu 7}6.752 -4.379 1.64 {o leu 7}7.236 -5.013 2.556 {c leu 7}P 6.752 -4.379 1.64 {n asn 8}7.093 -4.546 0.387 {ca asn 8}8.137 -5.541 0.03 {c asn 8}9.434 -4.805 -0.331 {o asn 8}10.174 -5.212 -1.205 {c asn 8}P 9.434 -4.805 -0.331 {n gly 9}9.692 -3.742 0.37 {ca gly 9}10.92 -2.963 0.07 {c gly 9}12.144 -3.871 0.156 {o gly 9}12.21 -4.757 0.986 {c gly 9}P 12.144 -3.871 0.156 {n lys 10}13.089 -3.629 -0.701 {ca lys 10}14.315 -4.474 -0.703 {ca thr 11}P 16.093 -3.026 2.321 {c thr 11}15.087 -2.749 3.444 {o thr 11}15.468 -2.437 4.554 {c thr 11}P 15.087 -2.749 3.444 {n leu 12}13.821 -2.868 3.139 {ca leu 12}12.799 -2.608 4.198 {c leu 12}11.475 -3.31 3.872 {o leu 12}11.027 -3.305 2.748 {c leu 12}P 11.475 -3.31 3.872 {n lys 13}10.887 -3.91 4.872 {ca lys 13}9.579 -4.606 4.659 {c lys 13}8.617 -4.221 5.786 {o lys 13}9.031 -4.01 6.909 {c lys 13}P 8.617 -4.221 5.786 {n gly 14}7.359 -4.135 5.47 {ca gly 14}6.374 -3.757 6.521 {c gly 14}4.946 -3.999 6.036 {o gly 14}4.726 -4.686 5.059 {c gly 14}P 4.946 -3.999 6.036 {n glu 15}4.004 -3.421 6.731 {ca glu 15}2.583 -3.604 6.342 {c glu 15}1.686 -2.742 7.236 {o glu 15}1.813 -2.755 8.443 {c glu 15}P 1.686 -2.742 7.236 {n thr 16}0.804 -2.006 6.625 {ca thr 16}-0.108 -1.143 7.43 {c thr 16}-1.458 -1.016 6.723 {o thr 16}-1.538 -1.132 5.516 {c thr 16}P -1.458 -1.016 6.723 {n thr 17}-2.49 -0.784 7.492 {ca thr 17}-3.848 -0.651 6.886 {c thr 17}-4.288 0.816 6.882 {o thr 17}-4.083 1.527 7.846 {c thr 17}P -4.288 0.816 6.882 {n thr 18}-4.883 1.233 5.79 {ca thr 18}-5.35 2.653 5.692 {c thr 18}-6.842 2.699 5.34 {o thr 18}-7.367 1.793 4.713 {c thr 18}P -6.842 2.699 5.34 {n glu 19}-7.489 3.756 5.753 {ca glu 19}-8.945 3.892 5.458 {c glu 19}-9.15 4.702 4.173 {o glu 19}-8.734 5.84 4.084 {c glu 19}P -9.15 4.702 4.173 {n ala 20}-9.786 4.095 3.208 {ca ala 20}-10.035 4.811 1.92 {ca gly 41}P 8.449 1.498 -7.716 {c gly 41}7.216 0.864 -8.362 {o gly 41}6.495 1.512 -9.095 {c gly 41}P 7.216 0.864 -8.362 {n glu 42}7.001 -0.392 -8.074 {ca glu 42}5.817 -1.093 -8.656 {c glu 42}4.72 -1.21 -7.601 {o glu 42}4.996 -1.524 -6.461 {c glu 42}P 4.72 -1.21 -7.601 {n trp 43}3.501 -0.969 -8.009 {ca trp 43}2.365 -1.045 -7.038 {c trp 43}1.324 -2.064 -7.504 {o trp 43}0.97 -2.104 -8.667 {c trp 43}P 1.324 -2.064 -7.504 {n thr 44}0.86 -2.864 -6.577 {ca thr 44}-0.167 -3.897 -6.929 {c thr 44}-1.417 -3.736 -6.051 {o thr 44}-1.392 -3.062 -5.04 {c thr 44}P -1.417 -3.736 -6.051 {n tyr 45}-2.483 -4.363 -6.468 {ca tyr 45}-3.762 -4.276 -5.696 {c tyr 45}-4.399 -5.669 -5.627 {o tyr 45}-4.573 -6.322 -6.638 {c tyr 45}P -4.399 -5.669 -5.627 {n asp 46}-4.731 -6.09 -4.433 {ca asp 46}-5.366 -7.437 -4.268 {c asp 46}-6.852 -7.281 -3.913 {o asp 46}-7.242 -7.435 -2.773 {c asp 46}P -6.852 -7.281 -3.913 {n asp 47}-7.649 -6.981 -4.9 {ca asp 47}-9.109 -6.81 -4.634 {ca thr 49}P -8.885 -9.951 -0.032 {c thr 49}-8.669 -8.546 0.543 {o thr 49}-8.332 -8.391 1.7 {c thr 49}P -8.669 -8.546 0.543 {n lys 50}-8.863 -7.553 -0.281 {ca lys 50}-8.673 -6.154 0.203 {c lys 50}-7.292 -6.011 0.844 {o lys 50}-7.177 -5.682 2.009 {c lys 50}P -7.292 -6.011 0.844 {n thr 51}-6.281 -6.263 0.065 {ca thr 51}-4.889 -6.162 0.598 {c thr 51}-3.986 -5.468 -0.44 {o thr 51}-3.756 -5.993 -1.51 {c thr 51}P -3.986 -5.468 -0.44 {n phe 52}-3.492 -4.302 -0.099 {ca phe 52}-2.612 -3.587 -1.056 {c phe 52}-1.21 -4.186 -0.984 {o phe 52}-0.873 -4.856 -0.027 {c phe 52}P -1.21 -4.186 -0.984 {n thr 53}-0.418 -3.943 -1.981 {ca thr 53}0.96 -4.492 -1.948 {c thr 53}1.862 -3.707 -2.896 {o thr 53}1.48 -3.394 -4.002 {c thr 53}P 1.862 -3.707 -2.896 {n val 54}3.04 -3.402 -2.431 {ca val 54}3.999 -2.641 -3.279 {c val 54}5.385 -3.272 -3.142 {o val 54}5.709 -3.833 -2.113 {c val 54}P 5.385 -3.272 -3.142 {n thr 55}6.17 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o} U -5.34 -0.99 4.57 <2.22>{ala 20 hn} P U -10.09 3.16 3.37 {met 1 o} U -10.98 1.95 3.77 <2.44>{glu 42 hn} P U 7.65 -0.85 -7.46 {thr 55 o} U 8.18 -2.14 -6.48 <1.79>{thr 44 hn} P U 1.21 -2.76 -5.65 {thr 53 o} U 1.4 -3.2 -4.5 <2.34>{asp 46 hn} P U -4.55 -5.49 -3.66 {thr 51 o} U -3.99 -5.84 -2.15 <2.28>{thr 49 hn} P U -8.06 -9.41 -2. {asp 46 o} U -7.49 -8.03 -2.54 <2.24>{thr 51 hn} P U -6.48 -6.52 -0.88 {asp 46 o} U -7.01 -7.16 -2.21 <1.83>{phe 52 hn} P U -3.72 -3.92 0.8 {lys 4 o} U -2.97 -4.35 1.74 <2.41>{thr 53 hn} P U -0.76 -3.39 -2.74 {thr 44 o} U -1.2 -3.16 -4.35 <2.21>{val 54 hn} P U 3.27 -3.69 -1.5 {ile 6 o} U 3.65 -4.35 -0.15 <2.06>{thr 55 hn} P U 5.83 -2.69 -4.98 {glu 42 o} U 5.25 -1.87 -6.02 @subgroup {helix} @vectorlist {main ch} color=pinktint {ca asp 22}P -12.201 3.975 -3.121 {c asp 22}-10.767 3.482 -3.375 {o asp 22}-9.865 3.757 -2.608 {c asp 22}P -10.767 3.482 -3.375 {n ala 23}-10.594 2.767 -4.455 {ca ala 23}-9.237 2.226 -4.777 {c ala 23}-8.287 3.342 -5.231 {o ala 23}-7.095 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