@text
"PROTEIN TOURIST #3: PROTEIN-DNA INTERACTIONS IN THE LAMBDA REPRESSOR / OPERATOR COMPLEX"  W. Olson, H. Berman, and J. Richardson

		Contents of file ProTour3.kin:
Kin.1 - Overview schematic, with  Lambda repressor Calphas and virtual-bond DNA
Kin.2 - DNA, for consensus half-operator sequence, with bases color-coded
Kin.3 - Detail of sequence-specific interactions with bases in one major groove
Kin.4 - Non-specific interactions with phosphate backbone

	Kinemage 1 shows the entire complex in schematic form, with Calphas for the N-terminal domains of the protein dimer (which interact mainly at their C-terminal helices); the helix-turn-helix motifs are highlighted.  The DNA backbone is represented by virtual bonds from P to C4' to P, the sugars with a virtual bond from C4' to C1', and each base pair with a line from C1' to C1'.  
	In the startup view, the DNA double-helix is angled so that you look down the major grooves in which the repressor mainly binds.  There is a nearly-exact twofold between the two subunits of the lambda repressor dimer and between the two halves of the operator site on the DNA, but for subunit B the N-terminal tail is shown wrapped around the DNA (it includes 3 lysines) while residues 1-5 of subunit A were disordered in the crystal.  Subunit B binds to the half of the DNA that has the consensus operator sequence, while the other half has a non-consensus sequence with 3 changes. 
	Choose View2 (on the "Graphics" pulldown menu), which has the axis of the double helix vertical and the dimer twofold horizontal in the plane of the screen.  Stereo is very helpful here (choose "stereo on" under the "Other" pulldown menu).  If you are not used to using it, try the following procedure: with your head about 2-3 feet from the screen, relax the focus of your eyes and stare through the screen toward infinity; let the two images drift toward each other, and then when they overlap, focus on them.  Now you should see the shape of the DNA and the relationship with the protein more clearly.  The DNA is nearly standard B-form, but it is bent slightly around the protein.  View3 looks down the double helix from one end, with the repressor sitting on top.

	Kinemage 2 shows the full structure of the DNA for the consensus half-operator sequence (TATCACCGC).  To read out the sequence, turn off strand 1 and read down strand 2 according to the base color code: G seagreen, C yellow, A pink, T skyblue.  Phosphates and sugars are white for strand 1 and bluetint for strand 2, and the base-pair hydrogen bonds are gray.  This is within the range of standard B-form DNA conformation, with just a slight bend that pulls the ends in closer to the protein (can be seen in View2 by the non-roundness in end view).  

	Kinemage 3 shows a closeup of lambda repressor (LRP) subunit B bound to the DNA, emphasizing sequence-specific interactions with base pairs.  Only those bases that make specific interactions are color-coded.  Turn off one strand at a time to see how the contacts are distributed in the DNA sequence.  The base-pair Hbonds can be turned on (gray), while the protein-nucleic acid Hbonds are shown in purple.  Interacting atoms have color-coded markers: red for O, blue for N, and green for methyl C.  Gln 44, Ser 45, and Asn 55 of both LRP subunits, and Thr 2 and Lys 4 of subunit B, make specific Hbonds with bases in the major groove.  Stereo is helpful for all of these views.
	View2 (under "Graphics") is a closeup of the Gln 44 interaction, showing the Hbond network to Gln 33 and a phosphate O that helps determine the nature and orientation of hydrogen bonds to Adenine 4 on strand 2 of the DNA.  View3 shows the double sidechain interaction of Asn 55 and Lys 4 with G 14 of strand 1, and also the Hbond between Thr 2 and G 10.  View4 looks deep into the interface, to show how the methyl groups of Thymidines 5 and 15 (green atom-marks) fit snugly in between hydrophobic sidechains and up against the helix backbone at Gly 46 and Gly 48.
	Overall, on DNA strand 1, there are specific contacts with bases  G 16 n7 (from Ser 45), T 15 methyl, and G 14 n7 and o6 (Ans 55 and Lys 4).  On strand 2, there are base-specific contacts to A 4 n7and n6 (from Gln 44 and its backup network), to T 5 methyl, and to G 10 n7 (Thr 2 og).

	Kinemage 4 shows the non-specific interactions with the phosphate backbone, again for subunit B of LRP and the consensus half-operator.  There are strong interactions with five of the phosphates (highlighted in hotpink), and also some Hbonds made by sidechains in the N-terminal arm.  View2 is a closeup of the hetwork of Hbonds to the phosphates of T 3 and A 4 of strand 2.
	The other important kind of non-specific binding involves the helix dipoles of the helix-turn-helix motif.  View3 (choose under "Graphics") looks down helix 2 from the N-terminal end and View4 down helix 3, both showing that they point toward the phosphate backbone, as well as each making a hydrogen bond from one of the peptide NH's in the first helical turn.

	Coordinates from Brookhaven Data Bank file: 1LRD.
    Reference:  S.R. Jordan and C.O. Pabo (1988) Science 242: 893 - Crystal structure of lambda repressor-operator complex at 2.5 A resolution 
@kinemage 1 
@caption 
Lambda repressor-DNA complex, with Calphas for LRP dimer (yellowtint and gold) and P-C4'-C1' schematic for DNA double helix (white and bluetint).  The helix-turn-helix motifs are emphasized in yellow or orange.
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{c4* g 1 11}12.088 2.433 6.126
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{lys A 25}32.006 -18.101 22.858
{lys A 26}32.166 -14.507 24.112
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{leu A 29}36.121 -14.472 20.47
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{asn B 61}10.6 -12.727 -3.579
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{lys B 67}11.518 -20.424 -9.557
{ile B 68}8.165 -19.248 -11.016
{leu B 69}9.785 -17.943 -14.23
{lys B 70}11.962 -21.07 -14.429
{val B 71}15.056 -18.857 -14.441
{ser B 72}17.971 -17.97 -12.15
{val B 73}18.137 -14.658 -10.252
{glu B 74}21.664 -13.641 -11.386
{glu B 75}19.718 -13.098 -14.606
{phe B 76}17.615 -10.294 -13.136
{ser B 77}19.639 -9.456 -10.018
{pro B 78}23.389 -9.971 -9.699
{ser B 79}23.525 -8.123 -6.343
{ile B 80}20.69 -10.081 -4.724
{ala B 81}22.162 -13.29 -6.138
{arg B 82}25.515 -12.349 -4.559
{glu B 83}23.586 -11.559 -1.345
{ile B 84}21.998 -15.036 -1.294
{tyr B 85}25.42 -16.623 -2.006
{glu B 86}26.719 -14.665 0.992
{met B 87}23.969 -15.998 3.305
{tyr B 88}24.466 -19.578 2.086
{glu B 89}28.158 -19.51 3.083
{ala B 90}26.807 -19.324 6.662
{val B 91}25.058 -22.684 6.257
{ser B 92}27.897 -24.299 4.342
@vectorlist {hlx-t-hlx} color=yellow
{ser B 32}P -0.463 -13.297 -15.94
{gln B 33}0.382 -11.085 -12.942
{glu B 34}-3.066 -12.404 -11.95
{ser B 35}-1.681 -15.971 -11.665
{val B 36}1.97 -15.173 -10.879
{ala B 37}0.391 -13.407 -7.864
{asp B 38}-1.641 -16.355 -6.497
{lys B 39}1.514 -18.499 -6.662
{met B 40}3.155 -15.943 -4.337
{gly B 41}0.26 -15.153 -2.012
{met B 42}-0.3 -11.517 -3.055
{gly B 43}-2.536 -9.525 -5.397
{gln B 44}-1.924 -8.288 -8.919
{ser B 45}-0.917 -4.852 -7.534
{gly B 46}1.75 -6.315 -5.26
{val B 47}3.194 -8.198 -8.246
{gly B 48}2.547 -5.058 -10.298
{ala B 49}4.666 -2.955 -7.91
{leu B 50}7.514 -5.436 -8.229
{phe B 51}7.579 -5.532 -12.036
{asn B 52}7.386 -1.711 -12.258
{gly B 53}9.952 -0.337 -9.756
@kinemage 2
@caption 
Lambda operator DNA, consensus half-sequence
@onewidth 
@zoom 1.2
@matrix 
-.857547 -.449924 -.249362 .327825 -.104436 -.938948 .396414 -.886939 .237055 
@2zoom 1.4
@2matrix <end>
-.808591 .363461 -.462684 .471764 .870427 -.140697 .351596 -.332044 -.875287 
@group {DNA str 1} 
@vectorlist {backbone} color= white 
{o1p g 1 11}P 11.974 7.044 5.807
{p g 1 11}13.191 6.267 6.189
{o2p g 1 11}14.481 6.329 5.454
{o3* G 1 10} P 12.984 5.896 7.716
{p g 1 11}13.191 6.267 6.189
{o5* g 1 11}12.652 4.694 5.796
{c5* g 1 11}12.944 3.553 6.616
{c4* g 1 11}12.088 2.433 6.126
{c3* g 1 11}11.57 2.515 4.69
{o3* g 1 11}11.406 1.175 4.206
{o3* g 1 11}P 11.406 1.175 4.206
{p c 1 12}12.21 0.667 3.043
{o1p c 1 12}11.606 1.402 1.92
{p c 1 12}P 12.21 0.667 3.043
{o2p c 1 12}13.676 0.35 3.174
{p c 1 12}P 12.21 0.667 3.043
{o5* c 1 12}11.552 -0.948 3.032
{c5* c 1 12}11.977 -1.526 4.285
{c4* c 1 12}11.246 -2.797 4.513
{c3* c 1 12}10.863 -3.58 3.237
{o3* c 1 12}10.604 -4.955 3.59
{o3* c 1 12}P 10.604 -4.955 3.59
{p g 1 13}10.567 -6.329 2.792
{o1p g 1 13}10.557 -5.91 1.419
{p g 1 13}P 10.567 -6.329 2.792
{o2p g 1 13}11.419 -7.415 3.305
{p g 1 13}P 10.567 -6.329 2.792
{o5* g 1 13}9.202 -6.975 3.271
{c5* g 1 13}8.299 -5.903 2.844
{c4* g 1 13}6.901 -6.528 2.992
{c3* g 1 13}6.41 -7.058 1.63
{o3* g 1 13}5.243 -7.855 1.772
{o3* g 1 13}P 5.243 -7.855 1.772
{p g 1 14}4.914 -8.837 0.564
{o1p g 1 14}6.261 -9.023 0.074
{p g 1 14}P 4.914 -8.837 0.564
{o2p g 1 14}3.593 -9.373 0.849
{p g 1 14}P 4.914 -8.837 0.564
{o5* g 1 14}4.398 -7.889 -0.65
{c5* g 1 14}3.112 -7.387 -0.992
{c4* g 1 14}2.238 -6.996 0.16
{c3* g 1 14}0.8 -6.755 -0.296
{o3* g 1 14}0.028 -7.868 -0.536
{o3* g 1 14}P 0.028 -7.868 -0.536
{p t 1 15}-1.398 -7.999 -0.906
{o1p t 1 15}-1.15 -7.82 -2.331
{p t 1 15}P -1.398 -7.999 -0.906
{o2p t 1 15}-1.968 -9.38 -0.604
{p t 1 15}P -1.398 -7.999 -0.906
{o5* t 1 15}-2.284 -7.003 -0.239
{c5* t 1 15}-3.002 -6.913 1.014
{c4* t 1 15}-4.12 -5.931 0.866
{c3* t 1 15}-5.139 -6.199 -0.234
{o3* t 1 15}-6.468 -5.992 0.268
{o3* t 1 15}P -6.468 -5.992 0.268
{p g 1 16}-7.591 -6.879 -0.536
{o1p g 1 16}-7.113 -7.992 -1.248
{p g 1 16}P -7.591 -6.879 -0.536
{o2p g 1 16}-8.598 -7.023 0.598
{p g 1 16}P -7.591 -6.879 -0.536
{o5* g 1 16}-8.2 -5.649 -1.436
{c5* g 1 16}-8.623 -4.625 -0.513
{c4* g 1 16}-9.11 -3.457 -1.299
{c3* g 1 16}-10.017 -3.697 -2.502
{o3* g 1 16}-11.076 -2.728 -2.542
{o3* g 1 16}P -11.076 -2.728 -2.542
{p a 1 17}-12.254 -2.763 -3.642
{o1p a 1 17}-11.859 -3.945 -4.428
{p a 1 17}P -12.254 -2.763 -3.642
{o2p a 1 17}-13.527 -2.453 -2.98
{p a 1 17}P -12.254 -2.763 -3.642
{o5* a 1 17}-11.927 -1.388 -4.422
{c5* a 1 17}-11.932 -0.199 -3.607
{c4* a 1 17}-11.48 0.852 -4.616
{c3* a 1 17}-12.275 0.838 -5.927
{o3* a 1 17}-12.575 2.158 -6.343
{o3* a 1 17}P -12.575 2.158 -6.343
{p t 1 18}-13.562 2.811 -7.38
{o1p t 1 18}-14.641 1.869 -7.596
{p t 1 18}P -13.562 2.811 -7.38
{o2p t 1 18}-13.823 4.192 -6.896
{p t 1 18}P -13.562 2.811 -7.38
{o5* t 1 18}-12.775 2.763 -8.776
{c5* t 1 18}-12.208 4.096 -8.81
{c4* t 1 18}-10.999 4.02 -9.677
{c3* t 1 18}-11.168 4.199 -11.198
{o3* t 1 18}-10.871 5.587 -11.546
{o3* t 1 18}P -10.871 5.587 -11.546
{p a 1 19}-11.125 6.233 -12.976
{o1p a 1 19}-12.293 5.395 -13.386
{p a 1 19}P -11.125 6.233 -12.976
{o2p a 1 19}-11.542 7.58 -12.412
{p a 1 19}P -11.125 6.233 -12.976
{o5* a 1 19}-9.743 5.986 -13.603
{c5* a 1 19}-8.545 6.659 -13.107
{c4* a 1 19}-7.521 6.405 -14.179
{c3* a 1 19}-8.021 6.666 -15.609
{o3* a 1 19}-6.873 6.961 -16.418
@vector {sugars} color=white
{c4* g 1 11}P 12.088 2.433 6.126
{o4* g 1 11}10.938 2.206 6.901
{c1* g 1 11}9.76 2.144 6.075
{c3* g 1 11}P 11.57 2.515 4.69
{c2* g 1 11}10.154 3.106 4.941
{c1* g 1 11}9.76 2.144 6.075
{c4* c 1 12}P 11.246 -2.797 4.513
{o4* c 1 12}10.021 -2.584 5.186
{c1* c 1 12}8.926 -2.673 4.251
{c3* c 1 12}P 10.863 -3.58 3.237
{c2* c 1 12}9.593 -2.804 2.878
{c1* c 1 12}8.926 -2.673 4.251
{c4* g 1 13}P 6.901 -6.528 2.992
{o4* g 1 13}6.011 -5.456 3.294
{c1* g 1 13}5.406 -5.003 2.08
{c3* g 1 13}P 6.41 -7.058 1.63
{c2* g 1 13}6.113 -5.731 0.929
{c1* g 1 13}5.406 -5.003 2.08
{c4* g 1 14}P 2.238 -6.996 0.16
{o4* g 1 14}2.632 -5.731 0.667
{c1* g 1 14}1.516 -4.831 0.747
{c3* g 1 14}P 0.8 -6.755 -0.296
{c2* g 1 14}0.309 -5.621 0.57
{c1* g 1 14}1.516 -4.831 0.747
{c4* t 1 15}P -4.12 -5.931 0.866
{o4* t 1 15}-3.751 -4.597 0.758
{c1* t 1 15}-4.339 -3.951 -0.399
{c3* t 1 15}P -5.139 -6.199 -0.234
{c2* t 1 15}-4.764 -5.147 -1.259
{c1* t 1 15}-4.339 -3.951 -0.399
{c4* g 1 16}P -9.11 -3.457 -1.299
{o4* g 1 16}-8.063 -2.653 -1.727
{c1* g 1 16}-8.232 -2.295 -3.123
{c3* g 1 16}P -10.017 -3.697 -2.502
{c2* g 1 16}-9.053 -3.477 -3.647
{c1* g 1 16}-8.232 -2.295 -3.123
{c4* a 1 17}P -11.48 0.852 -4.616
{o4* a 1 17}-10.145 0.625 -4.975
{c1* a 1 17}-9.974 0.694 -6.417
{c3* a 1 17}P -12.275 0.838 -5.927
{c2* a 1 17}-11.326 0.117 -6.873
{c1* a 1 17}-9.974 0.694 -6.417
{c4* t 1 18}P -10.999 4.02 -9.677
{o4* t 1 18}-10.447 2.728 -9.597
{c1* t 1 18}-9.3 2.845 -10.497
{c3* t 1 18}P -11.168 4.199 -11.198
{c2* t 1 18}-10.037 3.312 -11.751
{c1* t 1 18}-9.3 2.845 -10.497
{c4* a 1 19}P -7.521 6.405 -14.179
{o4* a 1 19}-6.99 5.099 -14.236
{c1* a 1 19}-7.424 4.405 -15.432
{c3* a 1 19}P -8.021 6.666 -15.609
{c2* a 1 19}-8.573 5.264 -15.945
{c1* a 1 19}-7.424 4.405 -15.432
@subgroup {bases}
@vectorlist {G} color=sea
{c1* g 1 11}P 9.76 2.144 6.075
{n9 g 1 11}8.576 2.625 6.77
{c8 g 1 11}8.071 3.903 6.73
{n7 g 1 11}6.994 4.068 7.448
{c5 g 1 11}6.776 2.811 8.001
{c6 g 1 11}5.756 2.364 8.879
{o6 g 1 11}4.808 3.024 9.323
{c6 g 1 11}P 5.756 2.364 8.879
{n1 g 1 11}5.832 1.031 9.204
{c2 g 1 11}6.816 0.234 8.702
{n2 g 1 11}6.695 -1.045 9.141
{c2 g 1 11}P 6.816 0.234 8.702
{n3 g 1 11}7.807 0.612 7.904
{c4 g 1 11}7.726 1.91 7.579
{c5 g 1 11}6.776 2.811 8.001
{c4 g 1 11}7.726 1.91 7.579
{n9 g 1 11}8.576 2.625 6.77
{c1* g 1 13}P 5.406 -5.003 2.08
{n9 g 1 13}5.45 -3.573 1.807
{c8 g 1 13}6.311 -2.872 1.009
{n7 g 1 13}6.02 -1.594 0.94
{c5 g 1 13}4.884 -1.45 1.727
{c6 g 1 13}4.089 -0.33 2.069
{o6 g 1 13}4.246 0.845 1.675
{c6 g 1 13}P 4.089 -0.33 2.069
{n1 g 1 13}3.022 -0.612 2.906
{c2 g 1 13}2.766 -1.855 3.374
{n2 g 1 13}1.697 -2. 4.166
{c2 g 1 13}P 2.766 -1.855 3.374
{n3 g 1 13}3.488 -2.927 3.1
{c4 g 1 13}4.524 -2.659 2.268
{c5 g 1 13}4.884 -1.45 1.727
{n9 g 1 13}P 5.45 -3.573 1.807
{c4 g 1 13}4.524 -2.659 2.268
{c1* g 1 14}P 1.516 -4.831 0.747
{n9 g 1 14}1.768 -3.567 0.091
{c8 g 1 14}2.824 -3.285 -0.752
{n7 g 1 14}2.887 -2.048 -1.134
{c5 g 1 14}1.838 -1.429 -0.473
{c6 g 1 14}1.385 -0.089 -0.484
{o6 g 1 14}1.881 0.873 -1.111
{c6 g 1 14}P 1.385 -0.089 -0.484
{n1 g 1 14}0.275 0.151 0.291
{c2 g 1 14}-0.317 -0.838 0.997
{n2 g 1 14}-1.38 -0.467 1.715
{c2 g 1 14}P -0.317 -0.838 0.997
{n3 g 1 14}0.064 -2.123 1.049
{c4 g 1 14}1.158 -2.35 0.291
{c5 g 1 14}1.838 -1.429 -0.473
{n9 g 1 14}P 1.768 -3.567 0.091
{c4 g 1 14}1.158 -2.35 0.291
{c1* g 1 16}P -8.232 -2.295 -3.123
{n9 g 1 16}-6.898 -2.391 -3.75
{c8 g 1 16}-6.233 -3.546 -4.006
{n7 g 1 16}-5.058 -3.354 -4.559
{c5 g 1 16}-4.968 -1.959 -4.667
{c6 g 1 16}-3.922 -1.154 -5.163
{o6 g 1 16}-2.843 -1.539 -5.642
{c6 g 1 16}P -3.922 -1.154 -5.163
{n1 g 1 16}-4.188 0.186 -5.118
{c2 g 1 16}-5.358 0.667 -4.61
{n2 g 1 16}-5.428 2.007 -4.627
{c2 g 1 16}P -5.358 0.667 -4.61
{n3 g 1 16}-6.359 -0.041 -4.132
{c4 g 1 16}-6.1 -1.361 -4.183
{n9 g 1 16}-6.898 -2.391 -3.75
{c5 g 1 16}P -4.968 -1.959 -4.667
{c4 g 1 16}-6.1 -1.361 -4.183
@vectorlist {C} color=yellow
{c1* c 1 12}P 8.926 -2.673 4.251
{n1 c 1 12}8.041 -1.498 4.32
{c2 c 1 12}6.878 -1.656 5.049
{o2 c 1 12}6.679 -2.763 5.579
{c2 c 1 12}P 6.878 -1.656 5.049
{n3 c 1 12}6.018 -0.618 5.157
{c4 c 1 12}6.241 0.584 4.576
{n4 c 1 12}5.388 1.587 4.696
{c4 c 1 12}P 6.241 0.584 4.576
{c5 c 1 12}7.423 0.735 3.83
{c6 c 1 12}8.272 -0.302 3.738
{n1 c 1 12}P 8.041 -1.498 4.32
{c6 c 1 12}8.272 -0.302 3.738
@vectorlist {A} color=pink
{c1* a 1 17}P -9.974 0.694 -6.417
{n9 a 1 17}-8.894 -0.227 -6.816
{c8 a 1 17}-8.887 -1.594 -6.719
{n7 a 1 17}-7.772 -2.13 -7.169
{c5 a 1 17}-7.007 -1.065 -7.608
{c6 a 1 17}-5.72 -0.996 -8.161
{n6 a 1 17}-4.924 -2.027 -8.423
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{c2 a 1 17}-6.031 1.354 -8.212
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{n7 a 1 19}-9.365 1.471 -14.412
{c5 a 1 19}-8.135 0.9 -14.76
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{c6 a 1 19}P -7.678 -0.426 -14.737
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{c4 a 1 19}-7.259 1.876 -15.17
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{n9 a 1 19}P -7.94 3.065 -15.09
{c4 a 1 19}-7.259 1.876 -15.17
@vectorlist {T} color=sky
{c1* t 1 15}P -4.339 -3.951 -0.399
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{c4 t 1 18}P -8.015 -1.086 -11.187
{c5 t 1 18}-9.305 -0.873 -10.645
{c5m t 1 18}-10.237 -1.993 -10.315
{n1 t 1 18}P -8.874 1.45 -10.742
{c6 t 1 18}-9.696 0.399 -10.457
{c5 t 1 18}-9.305 -0.873 -10.645
@group {DNA str 2} 
@vectorlist {backbone} color=bluetint
{o5* t 2 3}P -0.73 -7.456 -17.518
{c5* t 2 3}0.152 -6.57 -18.287
{c4* t 2 3}-0.239 -5.161 -17.809
{c3* t 2 3}0.263 -4.769 -16.441
{o3* t 2 3}1.563 -4.309 -16.264
{o3* t 2 3}P 1.563 -4.309 -16.264
{p a 2 4}2.483 -3.292 -16.863
{o1p a 2 4}3.528 -3.835 -15.769
{p a 2 4}P 2.483 -3.292 -16.863
{o2p a 2 4}3.104 -3.099 -18.116
{p a 2 4}P 2.483 -3.292 -16.863
{o5* a 2 4}1.512 -2.165 -16.304
{c5* a 2 4}1.709 -0.941 -17.079
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{c3* a 2 4}1.959 0.605 -15.051
{o3* a 2 4}2.228 1.993 -15.164
{o3* a 2 4}P 2.228 1.993 -15.164
{p t 2 5}2.865 3.285 -14.714
{o1p t 2 5}4.074 2.708 -14.008
{p t 2 5}P 2.865 3.285 -14.714
{o2p t 2 5}2.796 4.556 -15.427
{p t 2 5}P 2.865 3.285 -14.714
{o5* t 2 5}1.786 3.56 -13.461
{c5* t 2 5}0.64 4.357 -13.939
{c4* t 2 5}-0.074 4.625 -12.594
{c3* t 2 5}0.936 4.762 -11.483
{o3* t 2 5}1.143 5.992 -10.856
{o3* t 2 5}P 1.143 5.992 -10.856
{p c 2 6}0.932 7.449 -10.224
{o1p c 2 6}1.487 7.429 -8.964
{p c 2 6}P 0.932 7.449 -10.224
{o2p c 2 6}1.236 8.446 -11.352
{p c 2 6}P 0.932 7.449 -10.224
{o5* c 2 6}-0.806 7.442 -10.406
{c5* c 2 6}-1.249 6.666 -9.249
{c4* c 2 6}-2.553 7.236 -8.731
{c3* c 2 6}-2.366 7.985 -7.386
{o3* c 2 6}-3.562 8.569 -6.873
{o3* c 2 6}P -3.562 8.569 -6.873
{p a 2 7}-3.077 9.683 -5.75
{o1p a 2 7}-1.567 9.593 -5.534
{p a 2 7}P -3.077 9.683 -5.75
{o2p a 2 7}-3.708 11.002 -6.189
{p a 2 7}P -3.077 9.683 -5.75
{o5* a 2 7}-3.729 9.208 -4.36
{c5* a 2 7}-5.119 8.851 -4.627
{c4* a 2 7}-5.605 8.288 -3.294
{c3* a 2 7}-4.938 8.92 -2.069
{o3* a 2 7}-5.775 8.844 -0.923
{o3* a 2 7}P -5.775 8.844 -0.923
{p c 2 8}-5.593 9.525 0.547
{o1p c 2 8}-4.309 10.171 0.359
{p c 2 8}P -5.593 9.525 0.547
{o2p c 2 8}-7.029 9.435 1.026
{p c 2 8}P -5.593 9.525 0.547
{o5* c 2 8}-5.216 8.178 1.493
{c5* c 2 8}-6.116 7.044 1.271
{c4* c 2 8}-5.38 5.827 1.801
{c3* c 2 8}-4.615 6.102 3.106
{o3* c 2 8}-5.429 5.766 4.217
{o3* c 2 8}P -5.429 5.766 4.217
{p c 2 9}-5.014 5.766 5.733
{o1p c 2 9}-4.342 7.037 5.858
{p c 2 9}P -5.014 5.766 5.733
{o2p c 2 9}-6.465 5.34 6.098
{p c 2 9}P -5.014 5.766 5.733
{o5* c 2 9}-4.242 4.501 6.172
{c5* c 2 9}-4.856 3.223 5.79
{c4* c 2 9}-3.833 2.206 6.286
{c3* c 2 9}-3.057 2.708 7.488
{o3* c 2 9}-2.962 1.691 8.503
{o3* c 2 9}P -2.962 1.691 8.503
{p g 2 10}-4.03 1.67 9.751
{o1p g 2 10}-3.035 1.952 10.794
{p g 2 10}P -4.03 1.67 9.751
{o2p g 2 10}-5.354 2.11 9.437
{p g 2 10}P -4.03 1.67 9.751
{o5* g 2 10}-4.221 -0.027 9.5
{c5* g 2 10}-3.383 -0.687 10.463
{c4* g 2 10}-2.9 -1.986 9.802
{c3* g 2 10}-2.093 -2.831 10.794
{o3* g 2 10}-2.733 -3.958 11.255
{o3* g 2 10}P -2.733 -3.958 11.255
{p c 2 11}-2.214 -4.639 12.572
{o1p c 2 11}-2.85 -4.144 13.831
{p c 2 11}P -2.214 -4.639 12.572
{o2p c 2 11}-2.456 -6.123 12.19
{p c 2 11}P -2.214 -4.639 12.572
{o5* c 2 11}-0.573 -4.481 12.497
{c5* c 2 11}-0.165 -5.518 11.557
{c4* c 2 11}1.328 -5.546 11.557
{c3* c 2 11}1.921 -5.663 12.976
{o3* c 2 11}2.988 -6.611 12.908
@vectorlist {sugars} color=white
{c4* t 2 3}P -0.239 -5.161 -17.809
{o4* t 2 3}-1.643 -5.264 -17.484
{c1* t 2 3}-1.976 -4.061 -16.766
{c3* t 2 3}P 0.263 -4.769 -16.441
{c2* t 2 3}-0.815 -3.951 -15.803
{c1* t 2 3}-1.976 -4.061 -16.766
{c4* a 2 4}P 1.102 0.131 -16.196
{o4* a 2 4}-0.132 -0.268 -15.655
{c1* a 2 4}-0.24 0.11 -14.287
{c3* a 2 4}P 1.959 0.605 -15.051
{c2* a 2 4}1.159 0.241 -13.802
{c1* a 2 4}-0.24 0.11 -14.287
{c4* t 2 5}P -0.074 4.625 -12.594
{o4* t 2 5}-0.852 3.45 -12.309
{c1* t 2 5}-0.659 3.113 -10.942
{c3* t 2 5}P 0.936 4.762 -11.483
{c2* t 2 5}0.788 3.512 -10.64
{c1* t 2 5}-0.659 3.113 -10.942
{c4* c 2 6}P -2.553 7.236 -8.731
{o4* c 2 6}-3.406 6.164 -8.315
{c1* c 2 6}-2.975 5.738 -7.044
{c3* c 2 6}P -2.366 7.985 -7.386
{c2* c 2 6}-1.967 6.769 -6.542
{c1* c 2 6}-2.975 5.738 -7.044
{c4* a 2 7}P -5.605 8.288 -3.294
{o4* a 2 7}-5.307 6.899 -3.214
{c1* a 2 7}-4.24 6.666 -2.314
{c3* a 2 7}P -4.938 8.92 -2.069
{c2* a 2 7}-3.682 8.033 -1.926
{c1* a 2 7}-4.24 6.666 -2.314
{c4* c 2 8}P -5.38 5.827 1.801
{o4* c 2 8}-4.338 5.436 0.918
{c1* c 2 8}-3.579 4.46 1.715
{c3* c 2 8}P -4.615 6.102 3.106
{c2* c 2 8}-3.353 5.25 2.986
{c1* c 2 8}-3.579 4.46 1.715
{c4* c 2 9}P -3.833 2.206 6.286
{o4* c 2 9}-2.88 1.876 5.306
{c1* c 2 9}-1.556 1.979 5.824
{c3* c 2 9}P -3.057 2.708 7.488
{c2* c 2 9}-1.708 3.079 6.873
{c1* c 2 9}-1.556 1.979 5.824
{c4* g 2 10}P -2.9 -1.986 9.802
{o4* g 2 10}-1.952 -1.622 8.776
{c1* g 2 10}-0.673 -1.649 9.483
{c3* g 2 10}P -2.093 -2.831 10.794
{c2* g 2 10}-0.692 -2.934 10.172
{c1* g 2 10}-0.673 -1.649 9.483
{c4* c 2 11}P 1.328 -5.546 11.557
{o4* c 2 11}1.999 -4.508 10.942
{c1* c 2 11}2.913 -3.848 11.848
{c3* c 2 11}P 1.921 -5.663 12.976
{c2* c 2 11}2.335 -4.213 13.227
{c1* c 2 11}2.913 -3.848 11.848
@subgroup {bases}
@vectorlist {G} color=sea
{c1* g 2 10}P -0.673 -1.649 9.483
{n9 g 2 10}0.345 -0.852 8.953
{c8 g 2 10}0.347 0.536 8.981
{n7 g 2 10}1.353 1.086 8.372
{c5 g 2 10}2.072 -0.007 7.881
{c6 g 2 10}3.266 -0.055 7.135
{o6 g 2 10}3.936 0.893 6.742
{c6 g 2 10}P 3.266 -0.055 7.135
{n1 g 2 10}3.701 -1.326 6.856
{c2 g 2 10}3.023 -2.426 7.249
{n2 g 2 10}3.599 -3.567 6.89
{c2 g 2 10}P 3.023 -2.426 7.249
{n3 g 2 10}1.887 -2.433 7.944
{c4 g 2 10}1.474 -1.182 8.235
{n9 g 2 10}P 0.345 -0.852 8.953
{c4 g 2 10}1.474 -1.182 8.235
{c5 g 2 10}2.072 -0.007 7.881
@vectorlist {C} color=yellow
{c1* c 2 6}P -2.975 5.738 -7.044
{n1 c 2 6}-2.337 4.405 -6.987
{c2 c 2 6}-3.19 3.415 -6.497
{o2 c 2 6}-4.369 3.69 -6.223
{c2 c 2 6}P -3.19 3.415 -6.497
{n3 c 2 6}-2.674 2.165 -6.36
{c4 c 2 6}-1.389 1.876 -6.668
{n4 c 2 6}-0.994 0.605 -6.497
{c4 c 2 6}P -1.389 1.876 -6.668
{c5 c 2 6}-0.533 2.886 -7.152
{n1 c 2 6}P -2.337 4.405 -6.987
{c6 c 2 6}-1.042 4.123 -7.277
{c5 c 2 6}-0.533 2.886 -7.152
{c1* c 2 8}P -3.579 4.46 1.715
{n1 c 2 8}-2.302 4.254 1.026
{c2 c 2 8}-1.913 2.934 0.861
{o2 c 2 8}-2.567 2. 1.328
{c2 c 2 8}P -1.913 2.934 0.861
{n3 c 2 8}-0.748 2.708 0.194
{c4 c 2 8}-0.003 3.718 -0.319
{n4 c 2 8}1.127 3.381 -0.952
{n1 c 2 8}P -2.302 4.254 1.026
{c6 c 2 8}-1.578 5.285 0.49
{c5 c 2 8}-0.418 5.072 -0.177
{c4 c 2 8}-0.003 3.718 -0.319
{c1* c 2 9}P -1.556 1.979 5.824
{n1 c 2 9}-0.481 2.275 4.855
{c2 c 2 9}0.245 1.203 4.365
{o2 c 2 9}-0.001 0.041 4.673
{c2 c 2 9}P 0.245 1.203 4.365
{n3 c 2 9}1.272 1.457 3.51
{c4 c 2 9}1.615 2.708 3.117
{n4 c 2 9}2.648 2.838 2.28
{c4 c 2 9}P 1.615 2.708 3.117
{c5 c 2 9}0.892 3.807 3.624
{n1 c 2 9}P -0.481 2.275 4.855
{c6 c 2 9}-0.112 3.539 4.462
{c5 c 2 9}0.892 3.807 3.624
{c1* c 2 11}P 2.913 -3.848 11.848
{n1 c 2 11}2.994 -2.385 11.677
{c2 c 2 11}4.099 -1.89 11.004
{o2 c 2 11}4.955 -2.625 10.537
{c2 c 2 11}P 4.099 -1.89 11.004
{n3 c 2 11}4.213 -0.543 10.856
{c4 c 2 11}3.29 0.33 11.335
{n4 c 2 11}3.451 1.649 11.113
{c4 c 2 11}P 3.29 0.33 11.335
{c5 c 2 11}2.18 -0.172 12.036
{n1 c 2 11}P 2.994 -2.385 11.677
{c6 c 2 11}2.086 -1.498 12.167
{c5 c 2 11}2.18 -0.172 12.036
@vectorlist {A} color=pink
{c1* a 2 4}P -0.24 0.11 -14.287
{n9 a 2 4}-1.086 -0.852 -13.592
{c8 a 2 4}-0.84 -2.158 -13.295
{n7 a 2 4}-1.849 -2.769 -12.714
{c5 a 2 4}-2.828 -1.773 -12.611
{c6 a 2 4}-4.126 -1.794 -12.064
{n6 a 2 4}-4.698 -2.845 -11.5
{c6 a 2 4}P -4.126 -1.794 -12.064
{n1 a 2 4}-4.811 -0.625 -12.138
{c2 a 2 4}-4.265 0.495 -12.691
{n3 a 2 4}-3.046 0.55 -13.233
{c4 a 2 4}-2.376 -0.605 -13.147
{n9 a 2 4}P -1.086 -0.852 -13.592
{c4 a 2 4}-2.376 -0.605 -13.147
{c5 a 2 4}-2.828 -1.773 -12.611
{c1* a 2 7}P -4.24 6.666 -2.314
{n9 a 2 7}-3.151 5.814 -2.764
{c8 a 2 7}-1.97 6.157 -3.374
{n7 a 2 7}-1.189 5.127 -3.636
{c5 a 2 7}-1.904 4.034 -3.146
{c6 a 2 7}-1.612 2.653 -3.094
{n6 a 2 7}-0.515 2.068 -3.55
{c6 a 2 7}P -1.612 2.653 -3.094
{n1 a 2 7}-2.583 1.869 -2.53
{c2 a 2 7}-3.744 2.385 -2.04
{n3 a 2 7}-4.074 3.683 -2.069
{c4 a 2 7}-3.104 4.439 -2.61
{c5 a 2 7}-1.904 4.034 -3.146
{n9 a 2 7}P -3.151 5.814 -2.764
{c4 a 2 7}-3.104 4.439 -2.61
@vectorlist {T} color=sky
{c1* t 2 3}P -1.976 -4.061 -16.766
{n1 t 2 3}-3.198 -4.329 -15.968
{c2 t 2 3}-4.001 -3.237 -15.706
{o2 t 2 3}-3.709 -2.123 -16.133
{c2 t 2 3}P -4.001 -3.237 -15.706
{n3 t 2 3}-5.119 -3.477 -14.982
{c4 t 2 3}-5.434 -4.714 -14.538
{o4 t 2 3}-6.491 -4.886 -13.865
{c4 t 2 3}P -5.434 -4.714 -14.538
{c5 t 2 3}-4.596 -5.821 -14.828
{c5m t 2 3}-4.981 -7.181 -14.304
{n1 t 2 3}P -3.198 -4.329 -15.968
{c6 t 2 3}-3.494 -5.58 -15.529
{c5 t 2 3}-4.596 -5.821 -14.828
{c1* t 2 5}P -0.659 3.113 -10.942
{n1 t 2 5}-0.985 1.766 -10.509
{c2 t 2 5}-2.311 1.581 -10.093
{o2 t 2 5}-3.067 2.543 -10.178
{c2 t 2 5}P -2.311 1.581 -10.093
{n3 t 2 5}-2.715 0.364 -9.642
{c4 t 2 5}-1.859 -0.694 -9.557
{o4 t 2 5}-2.296 -1.8 -9.118
{c4 t 2 5}P -1.859 -0.694 -9.557
{c5 t 2 5}-0.501 -0.502 -9.927
{c5m t 2 5}0.471 -1.642 -9.842
{n1 t 2 5}P -0.985 1.766 -10.509
{c6 t 2 5}-0.125 0.701 -10.406
{c5 t 2 5}-0.501 -0.502 -9.927
@group dominant {bp Hbonds}
@vectorlist {Hb} color=gray
{o4 t 2 3}P U -6.88 -4.193 -13.958
{n6 a 1 19}U -8.027 -2.15 -14.234
{n1 a 1 19}P U -6.067 -1.361 -15.114
{n3 t 2 3}U -5.445 -2.748 -15.027
{n6 a 2 4}P U -5.48 -2.676 -11.488
{o4 t 1 18}U -6.739 -2.402 -11.467
{n1 a 2 4}P U -5.558 -0.432 -11.927
{n3 t 1 18}U -6.461 -0.2 -11.671
{n3 t 2 5}P U -3.44 0.335 -9.305
{n1 a 1 17}U -4.552 0.29 -8.788
{n6 a 1 17}P U -4.153 -1.96 -8.627
{o4 t 2 5}U -3.067 -1.867 -8.914
{o2 c 2 6}P U -4.701 3.162 -5.722
{n2 g 1 16}U -5.096 2.535 -5.128
{n3 c 2 6}P U -3.109 1.596 -6.003
{n1 g 1 16}U -3.753 0.755 -5.475
{o6 g 1 16}P U -2.343 -0.959 -5.873
{n4 c 2 6}U -1.494 0.025 -6.266
{n6 a 2 7}P U -0.532 1.277 -3.433
{o4 t 1 15}U -0.564 -0.178 -3.217
{n1 a 2 7}P U -2.568 1.084 -2.379
{n3 t 1 15}U -2.542 -0.328 -2.106
{n4 c 2 8}P U 1.357 2.616 -1.
{o6 g 1 14}U 1.651 1.638 -1.063
{n3 c 2 8}P U -0.451 1.966 0.222
{n1 g 1 14}U -0.022 0.893 0.263
{o2 c 2 8}P U -2.224 1.286 1.44
{n2 g 1 14}U -1.723 0.247 1.603
{n4 c 2 9}P U 3.135 2.231 2.096
{o6 g 1 13}U 3.759 1.452 1.859
{n3 c 2 9}P U 1.776 0.861 3.336
{n1 g 1 13}U 2.518 -0.016 3.08
{n2 g 1 13}P U 1.194 -1.396 4.316
{o2 c 2 9}U 0.502 -0.563 4.523
{n4 c 1 12}P U 4.942 1.374 5.325
{o6 g 2 10}U 4.382 1.106 6.113
{n3 c 1 12}P U 5.392 -0.809 5.616
{n1 g 2 10}U 4.327 -1.135 6.397
{o2 c 1 12}P U 5.963 -2.95 5.884
{n2 g 2 10}U 4.315 -3.38 6.585
{o6 g 1 11}P U 4.396 2.606 9.867
{n4 c 2 11}U 3.863 2.067 10.569
{n1 g 1 11}P U 5.369 0.581 9.676
{n3 c 2 11}U 4.676 -0.093 10.384
{n2 g 1 11}P U 6.186 -1.507 9.55
{o2 c 2 11}U 5.464 -2.163 10.128
@kinemage 3
@caption
Lambda repressor - specific contacts to base pairs, in the consensus half of the operator sequence.  Bases are shown in full, and those that make contacts are color-coded (G green, C yellow, A pink, T skyblue).  The phosphate-sugar backbone is represented by virtual bonds through P, C4', and C1', with the virtual sugars, and the base-pair Hbonds, turned off.
@onewidth
@multibins 3
@zoom 1.3
@center 2.5 -1.3 -4.5
@matrix 
-.67054 .190179 -.717083 .664873 -.274757 -.694587 -.329121 -.942518 .057789 
@2zoom 2.5
@2zslab 260
@2center -1.5 -5.5 -12.3
@2matrix <Q Q>
-.753077 .253509 -.607131 .582204 -.173043 -.794414 -.306453 -.95173 -.017279 
@3zoom 1.5
@3center 4.7 .8 -2.1
@3matrix <T2, K4>
.923039 -.167726 -.346217 .249139 -.425118 .870174 -.293133 -.889462 -.350615 
@4zoom 2.2
@4center -.1 -3.8 -3.0
@4matrix <c5m>
.817953 -.099118 .566682 -.570183 -.270573 .77568 .076447 -.957584 -.277831 
@group {DNA str 1}
@subgroup {sugar-phos}
@vectorlist {virt. bb} color=white
{p g 1 11}P 13.191 6.267 6.189
{c4* g 1 11}12.088 2.433 6.126
{p c 1 12}12.21 0.667 3.043
{c4* c 1 12}11.246 -2.797 4.513
{p g 1 13}10.567 -6.329 2.792
{c4* g 1 13}6.901 -6.528 2.992
{p g 1 14}4.914 -8.837 0.564
{c4* g 1 14}2.238 -6.996 0.16
{p t 1 15}-1.398 -7.999 -0.906
{c4* t 1 15}-4.12 -5.931 0.866
{p g 1 16}-7.591 -6.879 -0.536
{c4* g 1 16}-9.11 -3.457 -1.299
{p a 1 17}-12.254 -2.763 -3.642
{c4* a 1 17}-11.48 0.852 -4.616
{p t 1 18}-13.562 2.811 -7.38
{c4* t 1 18}-10.999 4.02 -9.677
{p a 1 19}-11.125 6.233 -12.976
{c4* a 1 19}-7.521 6.405 -14.179
{p t 1 20}-7.048 7.807 -17.769
@vectorlist off {virt sugar} color=white
{c4* g 1 11}P 12.088 2.433 6.126
{c1* g 1 11}9.76 2.144 6.075
{c4* c 1 12}P 11.246 -2.797 4.513
{c1* c 1 12}8.926 -2.673 4.251
{c4* g 1 13}P 6.901 -6.528 2.992
{c1* g 1 13}5.406 -5.003 2.08
{c4* g 1 14}P 2.238 -6.996 0.16
{c1* g 1 14}1.516 -4.831 0.747
{c4* t 1 15}P -4.12 -5.931 0.866
{c1* t 1 15}-4.339 -3.951 -0.399
{c4* g 1 16}P -9.11 -3.457 -1.299
{c1* g 1 16}-8.232 -2.295 -3.123
{c4* a 1 17}P -11.48 0.852 -4.616
{c1* a 1 17}-9.974 0.694 -6.417
{c4* t 1 18}P -10.999 4.02 -9.677
{c1* t 1 18}-9.3 2.845 -10.497
{c4* a 1 19}P -7.521 6.405 -14.179
{c1* a 1 19}-7.424 4.405 -15.432
@subgroup dominant {no-con base}
@vectorlist {non-contct} color=gray
{c1* g 1 11}P 9.76 2.144 6.075
{n9 g 1 11}8.576 2.625 6.77
{c8 g 1 11}8.071 3.903 6.73
{n7 g 1 11}6.994 4.068 7.448
{c5 g 1 11}6.776 2.811 8.001
{c6 g 1 11}5.756 2.364 8.879
{o6 g 1 11}4.808 3.024 9.323
{c6 g 1 11}P 5.756 2.364 8.879
{n1 g 1 11}5.832 1.031 9.204
{c2 g 1 11}6.816 0.234 8.702
{n2 g 1 11}6.695 -1.045 9.141
{c2 g 1 11}P 6.816 0.234 8.702
{n3 g 1 11}7.807 0.612 7.904
{c4 g 1 11}7.726 1.91 7.579
{c5 g 1 11}6.776 2.811 8.001
{c4 g 1 11}7.726 1.91 7.579
{n9 g 1 11}8.576 2.625 6.77
{c1* c 1 12}P 8.926 -2.673 4.251
{n1 c 1 12}8.041 -1.498 4.32
{c2 c 1 12}6.878 -1.656 5.049
{o2 c 1 12}6.679 -2.763 5.579
{c2 c 1 12}P 6.878 -1.656 5.049
{n3 c 1 12}6.018 -0.618 5.157
{c4 c 1 12}6.241 0.584 4.576
{n4 c 1 12}5.388 1.587 4.696
{c4 c 1 12}P 6.241 0.584 4.576
{c5 c 1 12}7.423 0.735 3.83
{c6 c 1 12}8.272 -0.302 3.738
{n1 c 1 12}P 8.041 -1.498 4.32
{c6 c 1 12}8.272 -0.302 3.738
{c1* g 1 13}P 5.406 -5.003 2.08
{n9 g 1 13}5.45 -3.573 1.807
{c8 g 1 13}6.311 -2.872 1.009
{n7 g 1 13}6.02 -1.594 0.94
{c5 g 1 13}4.884 -1.45 1.727
{c6 g 1 13}4.089 -0.33 2.069
{o6 g 1 13}4.246 0.845 1.675
{c6 g 1 13}P 4.089 -0.33 2.069
{n1 g 1 13}3.022 -0.612 2.906
{c2 g 1 13}2.766 -1.855 3.374
{n2 g 1 13}1.697 -2. 4.166
{c2 g 1 13}P 2.766 -1.855 3.374
{n3 g 1 13}3.488 -2.927 3.1
{c4 g 1 13}4.524 -2.659 2.268
{c5 g 1 13}4.884 -1.45 1.727
{n9 g 1 13}P 5.45 -3.573 1.807
{c4 g 1 13}4.524 -2.659 2.268
{c1* a 1 17}P -9.974 0.694 -6.417
{n9 a 1 17}-8.894 -0.227 -6.816
{c8 a 1 17}-8.887 -1.594 -6.719
{n7 a 1 17}-7.772 -2.13 -7.169
{c5 a 1 17}-7.007 -1.065 -7.608
{c6 a 1 17}-5.72 -0.996 -8.161
{n6 a 1 17}-4.924 -2.027 -8.423
{c6 a 1 17}P -5.72 -0.996 -8.161
{n1 a 1 17}-5.277 0.261 -8.451
{c2 a 1 17}-6.031 1.354 -8.212
{n3 a 1 17}-7.249 1.347 -7.682
{c4 a 1 17}-7.685 0.11 -7.391
{c5 a 1 17}-7.007 -1.065 -7.608
{n9 a 1 17}P -8.894 -0.227 -6.816
{c4 a 1 17}-7.685 0.11 -7.391
{c5 a 1 17}-7.007 -1.065 -7.608
{c1* t 1 18}P -9.3 2.845 -10.497
{n1 t 1 18}-8.874 1.45 -10.742
{c2 t 1 18}-7.594 1.278 -11.221
{o2 t 1 18}-6.867 2.261 -11.437
{c2 t 1 18}P -7.594 1.278 -11.221
{n3 t 1 18}-7.208 -0.007 -11.46
{c4 t 1 18}-8.015 -1.086 -11.187
{o4 t 1 18}-7.521 -2.233 -11.455
{c4 t 1 18}P -8.015 -1.086 -11.187
{c5 t 1 18}-9.305 -0.873 -10.645
{c5m t 1 18}-10.237 -1.993 -10.315
{n1 t 1 18}P -8.874 1.45 -10.742
{c6 t 1 18}-9.696 0.399 -10.457
{c5 t 1 18}-9.305 -0.873 -10.645
{c1* a 1 19}P -7.424 4.405 -15.432
{n9 a 1 19}-7.94 3.065 -15.09
{c8 a 1 19}-9.197 2.742 -14.64
{n7 a 1 19}-9.365 1.471 -14.412
{c5 a 1 19}-8.135 0.9 -14.76
{c6 a 1 19}-7.678 -0.426 -14.737
{n6 a 1 19}-8.416 -1.457 -14.327
{c6 a 1 19}P -7.678 -0.426 -14.737
{n1 a 1 19}-6.393 -0.632 -15.159
{c2 a 1 19}-5.615 0.399 -15.552
{n3 a 1 19}-5.99 1.691 -15.575
{c4 a 1 19}-7.259 1.876 -15.17
{c5 a 1 19}-8.135 0.9 -14.76
{n9 a 1 19}P -7.94 3.065 -15.09
{c4 a 1 19}-7.259 1.876 -15.17
@subgroup dominant {contct bases}
@vector {G contact} color=sea
{c1* g 1 14}P 1.516 -4.831 0.747
{n9 g 1 14}1.768 -3.567 0.091
{c8 g 1 14}2.824 -3.285 -0.752
{n7 g 1 14}2.887 -2.048 -1.134
{c5 g 1 14}1.838 -1.429 -0.473
{c6 g 1 14}1.385 -0.089 -0.484
{o6 g 1 14}1.881 0.873 -1.111
{c6 g 1 14}P 1.385 -0.089 -0.484
{n1 g 1 14}0.275 0.151 0.291
{c2 g 1 14}-0.317 -0.838 0.997
{n2 g 1 14}-1.38 -0.467 1.715
{c2 g 1 14}P -0.317 -0.838 0.997
{n3 g 1 14}0.064 -2.123 1.049
{c4 g 1 14}1.158 -2.35 0.291
{c5 g 1 14}1.838 -1.429 -0.473
{n9 g 1 14}P 1.768 -3.567 0.091
{c4 g 1 14}1.158 -2.35 0.291
{c1* g 1 16}P -8.232 -2.295 -3.123
{n9 g 1 16}-6.898 -2.391 -3.75
{c8 g 1 16}-6.233 -3.546 -4.006
{n7 g 1 16}-5.058 -3.354 -4.559
{c5 g 1 16}-4.968 -1.959 -4.667
{c6 g 1 16}-3.922 -1.154 -5.163
{o6 g 1 16}-2.843 -1.539 -5.642
{c6 g 1 16}P -3.922 -1.154 -5.163
{n1 g 1 16}-4.188 0.186 -5.118
{c2 g 1 16}-5.358 0.667 -4.61
{n2 g 1 16}-5.428 2.007 -4.627
{c2 g 1 16}P -5.358 0.667 -4.61
{n3 g 1 16}-6.359 -0.041 -4.132
{c4 g 1 16}-6.1 -1.361 -4.183
{n9 g 1 16}-6.898 -2.391 -3.75
{c5 g 1 16}P -4.968 -1.959 -4.667
{c4 g 1 16}-6.1 -1.361 -4.183
@vectorlist {T contact} color=sky
{c1* t 1 15}P -4.339 -3.951 -0.399
{n1 t 1 15}-3.321 -3.168 -1.134
{c2 t 1 15}-3.476 -1.807 -1.271
{o2 t 1 15}-4.447 -1.209 -0.798
{c2 t 1 15}P -3.476 -1.807 -1.271
{n3 t 1 15}-2.527 -1.113 -1.955
{c4 t 1 15}-1.434 -1.697 -2.496
{o4 t 1 15}-0.581 -0.969 -3.1
{c4 t 1 15}P -1.434 -1.697 -2.496
{c5 t 1 15}-1.279 -3.092 -2.359
{c5m t 1 15}-0.084 -3.793 -2.941
{n1 t 1 15}P -3.321 -3.168 -1.134
{c6 t 1 15}-2.203 -3.738 -1.67
{c5 t 1 15}P -1.279 -3.092 -2.359
{c6 t 1 15}-2.203 -3.738 -1.67
@group {DNA str 2} 
@subgroup {sugar-phos}
@vectorlist {virt. bb} color=bluetint
{p t 2 3}P -0.737 -9.14 -17.626
{c4* t 2 3}-0.239 -5.161 -17.809
{o3* t 2 3}1.563 -4.309 -16.264
{p a 2 4}2.483 -3.292 -16.863
{o1p a 2 4}3.528 -3.835 -15.769
{o2p a 2 4}P 3.104 -3.099 -18.116
{p a 2 4}2.483 -3.292 -16.863
{o5* a 2 4}1.512 -2.165 -16.304
{c4* a 2 4}1.102 0.131 -16.196
{p t 2 5}2.865 3.285 -14.714
{c4* t 2 5}-0.074 4.625 -12.594
{p c 2 6}0.932 7.449 -10.224
{c4* c 2 6}-2.553 7.236 -8.731
{p a 2 7}-3.077 9.683 -5.75
{c4* a 2 7}-5.605 8.288 -3.294
{p c 2 8}-5.593 9.525 0.547
{c4* c 2 8}-5.38 5.827 1.801
{p c 2 9}-5.014 5.766 5.733
{c4* c 2 9}-3.833 2.206 6.286
{p g 2 10}-4.03 1.67 9.751
{c4* g 2 10}-2.9 -1.986 9.802
{p c 2 11}-2.214 -4.639 12.572
{c4* c 2 11}1.328 -5.546 11.557
{p c 2 12}3.501 -7.834 13.694
@vectorlist off {virt sugar} color=bluetint
{c4* t 2 3}P -0.239 -5.161 -17.809
{c1* t 2 3}-1.976 -4.061 -16.766
{c4* a 2 4}P 1.102 0.131 -16.196
{c1* a 2 4}-0.24 0.11 -14.287
{c4* t 2 5}P -0.074 4.625 -12.594
{c1* t 2 5}-0.659 3.113 -10.942
{c4* c 2 6}P -2.553 7.236 -8.731
{c1* c 2 6}-2.975 5.738 -7.044
{c4* a 2 7}P -5.605 8.288 -3.294
{c1* a 2 7}-4.24 6.666 -2.314
{c4* c 2 8}P -5.38 5.827 1.801
{c1* c 2 8}-3.579 4.46 1.715
{c4* c 2 9}P -3.833 2.206 6.286
{c1* c 2 9}-1.556 1.979 5.824
{c4* g 2 10}P -2.9 -1.986 9.802
{c1* g 2 10}-0.673 -1.649 9.483
{c4* c 2 11}P 1.328 -5.546 11.557
{c1* c 2 11}2.913 -3.848 11.848
@subgroup dominant {no-con base}
@vectorlist {non-contact} color=gray
{c1* c 2 6}P -2.975 5.738 -7.044
{n1 c 2 6}-2.337 4.405 -6.987
{c2 c 2 6}-3.19 3.415 -6.497
{o2 c 2 6}-4.369 3.69 -6.223
{c2 c 2 6}P -3.19 3.415 -6.497
{n3 c 2 6}-2.674 2.165 -6.36
{c4 c 2 6}-1.389 1.876 -6.668
{n4 c 2 6}-0.994 0.605 -6.497
{c4 c 2 6}P -1.389 1.876 -6.668
{c5 c 2 6}-0.533 2.886 -7.152
{n1 c 2 6}P -2.337 4.405 -6.987
{c6 c 2 6}-1.042 4.123 -7.277
{c5 c 2 6}-0.533 2.886 -7.152
{c1* a 2 7}P -4.24 6.666 -2.314
{n9 a 2 7}-3.151 5.814 -2.764
{c8 a 2 7}-1.97 6.157 -3.374
{n7 a 2 7}-1.189 5.127 -3.636
{c5 a 2 7}-1.904 4.034 -3.146
{c6 a 2 7}-1.612 2.653 -3.094
{n6 a 2 7}-0.515 2.068 -3.55
{c6 a 2 7}P -1.612 2.653 -3.094
{n1 a 2 7}-2.583 1.869 -2.53
{c2 a 2 7}-3.744 2.385 -2.04
{n3 a 2 7}-4.074 3.683 -2.069
{c4 a 2 7}-3.104 4.439 -2.61
{c5 a 2 7}-1.904 4.034 -3.146
{n9 a 2 7}P -3.151 5.814 -2.764
{c4 a 2 7}-3.104 4.439 -2.61
{c1* c 2 8}P -3.579 4.46 1.715
{n1 c 2 8}-2.302 4.254 1.026
{c2 c 2 8}-1.913 2.934 0.861
{o2 c 2 8}-2.567 2. 1.328
{c2 c 2 8}P -1.913 2.934 0.861
{n3 c 2 8}-0.748 2.708 0.194
{c4 c 2 8}-0.003 3.718 -0.319
{n4 c 2 8}1.127 3.381 -0.952
{n1 c 2 8}P -2.302 4.254 1.026
{c6 c 2 8}-1.578 5.285 0.49
{c5 c 2 8}-0.418 5.072 -0.177
{c4 c 2 8}-0.003 3.718 -0.319
{c1* c 2 9}P -1.556 1.979 5.824
{n1 c 2 9}-0.481 2.275 4.855
{c2 c 2 9}0.245 1.203 4.365
{o2 c 2 9}-0.001 0.041 4.673
{c2 c 2 9}P 0.245 1.203 4.365
{n3 c 2 9}1.272 1.457 3.51
{c4 c 2 9}1.615 2.708 3.117
{n4 c 2 9}2.648 2.838 2.28
{c4 c 2 9}P 1.615 2.708 3.117
{c5 c 2 9}0.892 3.807 3.624
{n1 c 2 9}P -0.481 2.275 4.855
{c6 c 2 9}-0.112 3.539 4.462
{c5 c 2 9}0.892 3.807 3.624
{c1* c 2 11}P 2.913 -3.848 11.848
{n1 c 2 11}2.994 -2.385 11.677
{c2 c 2 11}4.099 -1.89 11.004
{o2 c 2 11}4.955 -2.625 10.537
{c2 c 2 11}P 4.099 -1.89 11.004
{n3 c 2 11}4.213 -0.543 10.856
{c4 c 2 11}3.29 0.33 11.335
{n4 c 2 11}3.451 1.649 11.113
{c4 c 2 11}P 3.29 0.33 11.335
{c5 c 2 11}2.18 -0.172 12.036
{n1 c 2 11}P 2.994 -2.385 11.677
{c6 c 2 11}2.086 -1.498 12.167
{c5 c 2 11}2.18 -0.172 12.036
@subgroup dominant {contct bases}
@vector {G contact} color=sea
{c1* g 2 10}P -0.673 -1.649 9.483
{n9 g 2 10}0.345 -0.852 8.953
{c8 g 2 10}0.347 0.536 8.981
{n7 g 2 10}1.353 1.086 8.372
{c5 g 2 10}2.072 -0.007 7.881
{c6 g 2 10}3.266 -0.055 7.135
{o6 g 2 10}3.936 0.893 6.742
{c6 g 2 10}P 3.266 -0.055 7.135
{n1 g 2 10}3.701 -1.326 6.856
{c2 g 2 10}3.023 -2.426 7.249
{n2 g 2 10}3.599 -3.567 6.89
{c2 g 2 10}P 3.023 -2.426 7.249
{n3 g 2 10}1.887 -2.433 7.944
{c4 g 2 10}1.474 -1.182 8.235
{n9 g 2 10}P 0.345 -0.852 8.953
{c4 g 2 10}1.474 -1.182 8.235
{c5 g 2 10}2.072 -0.007 7.881
@vectorlist {A contact} color=pink
{c1* a 2 4}P -0.24 0.11 -14.287
{n9 a 2 4}-1.086 -0.852 -13.592
{c8 a 2 4}-0.84 -2.158 -13.295
{n7 a 2 4}-1.849 -2.769 -12.714
{c5 a 2 4}-2.828 -1.773 -12.611
{c6 a 2 4}-4.126 -1.794 -12.064
{n6 a 2 4}-4.698 -2.845 -11.5
{c6 a 2 4}P -4.126 -1.794 -12.064
{n1 a 2 4}-4.811 -0.625 -12.138
{c2 a 2 4}-4.265 0.495 -12.691
{n3 a 2 4}-3.046 0.55 -13.233
{c4 a 2 4}-2.376 -0.605 -13.147
{n9 a 2 4}P -1.086 -0.852 -13.592
{c4 a 2 4}-2.376 -0.605 -13.147
{c5 a 2 4}-2.828 -1.773 -12.611
@vectorlist {T contact} color=sky
{c1* t 2 3}P -1.976 -4.061 -16.766
{n1 t 2 3}-3.198 -4.329 -15.968
{c2 t 2 3}-4.001 -3.237 -15.706
{o2 t 2 3}-3.709 -2.123 -16.133
{c2 t 2 3}P -4.001 -3.237 -15.706
{n3 t 2 3}-5.119 -3.477 -14.982
{c4 t 2 3}-5.434 -4.714 -14.538
{o4 t 2 3}-6.491 -4.886 -13.865
{c4 t 2 3}P -5.434 -4.714 -14.538
{c5 t 2 3}-4.596 -5.821 -14.828
{c5m t 2 3}-4.981 -7.181 -14.304
{n1 t 2 3}P -3.198 -4.329 -15.968
{c6 t 2 3}-3.494 -5.58 -15.529
{c5 t 2 3}-4.596 -5.821 -14.828
{c1* t 2 5}P -0.659 3.113 -10.942
{n1 t 2 5}-0.985 1.766 -10.509
{c2 t 2 5}-2.311 1.581 -10.093
{o2 t 2 5}-3.067 2.543 -10.178
{c2 t 2 5}P -2.311 1.581 -10.093
{n3 t 2 5}-2.715 0.364 -9.642
{c4 t 2 5}-1.859 -0.694 -9.557
{o4 t 2 5}-2.296 -1.8 -9.118
{c4 t 2 5}P -1.859 -0.694 -9.557
{c5 t 2 5}-0.501 -0.502 -9.927
{c5m t 2 5}0.471 -1.642 -9.842
{n1 t 2 5}P -0.985 1.766 -10.509
{c6 t 2 5}-0.125 0.701 -10.406
{c5 t 2 5}-0.501 -0.502 -9.927
@group off {basepair Hb}
@vectorlist {Hbonds} color=gray
{o4 t 2 3}P U -6.88 -4.193 -13.958
{n6 a 1 19}U -8.027 -2.15 -14.234
{n1 a 1 19}P U -6.067 -1.361 -15.114
{n3 t 2 3}U -5.445 -2.748 -15.027
{n6 a 2 4}P U -5.48 -2.676 -11.488
{o4 t 1 18}U -6.739 -2.402 -11.467
{n1 a 2 4}P U -5.558 -0.432 -11.927
{n3 t 1 18}U -6.461 -0.2 -11.671
{n3 t 2 5}P U -3.44 0.335 -9.305
{n1 a 1 17}U -4.552 0.29 -8.788
{n6 a 1 17}P U -4.153 -1.96 -8.627
{o4 t 2 5}U -3.067 -1.867 -8.914
{o2 c 2 6}P U -4.701 3.162 -5.722
{n2 g 1 16}U -5.096 2.535 -5.128
{n3 c 2 6}P U -3.109 1.596 -6.003
{n1 g 1 16}U -3.753 0.755 -5.475
{o6 g 1 16}P U -2.343 -0.959 -5.873
{n4 c 2 6}U -1.494 0.025 -6.266
{n6 a 2 7}P U -0.532 1.277 -3.433
{o4 t 1 15}U -0.564 -0.178 -3.217
{n1 a 2 7}P U -2.568 1.084 -2.379
{n3 t 1 15}U -2.542 -0.328 -2.106
{n4 c 2 8}P U 1.357 2.616 -1.
{o6 g 1 14}U 1.651 1.638 -1.063
{n3 c 2 8}P U -0.451 1.966 0.222
{n1 g 1 14}U -0.022 0.893 0.263
{o2 c 2 8}P U -2.224 1.286 1.44
{n2 g 1 14}U -1.723 0.247 1.603
{n4 c 2 9}P U 3.135 2.231 2.096
{o6 g 1 13}U 3.759 1.452 1.859
{n3 c 2 9}P U 1.776 0.861 3.336
{n1 g 1 13}U 2.518 -0.016 3.08
{n2 g 1 13}P U 1.194 -1.396 4.316
{o2 c 2 9}U 0.502 -0.563 4.523
{n4 c 1 12}P U 4.942 1.374 5.325
{o6 g 2 10}U 4.382 1.106 6.113
{n3 c 1 12}P U 5.392 -0.809 5.616
{n1 g 2 10}U 4.327 -1.135 6.397
{o2 c 1 12}P U 5.963 -2.95 5.884
{n2 g 2 10}U 4.315 -3.38 6.585
{o6 g 1 11}P U 4.396 2.606 9.867
{n4 c 2 11}U 3.863 2.067 10.569
{n1 g 1 11}P U 5.369 0.581 9.676
{n3 c 2 11}U 4.676 -0.093 10.384
{n2 g 1 11}P U 6.186 -1.507 9.55
{o2 c 2 11}U 5.464 -2.163 10.128
@group {LRP sub B} 
@vectorlist {main ch} color=yellowtint
{ser B 1}P 4.538 4.776 9.386
{thr B 2}3.128 5.037 5.858
{lys B 3}5.989 6.453 3.869
{lys B 4}7.501 4.68 0.832
{lys B 5}11.182 5.078 -0.04
{pro B 6}12.365 5.669 -3.602
{leu B 7}14.211 2.824 -5.345
{thr B 8}17.924 2.763 -6.075
{gln B 9}19.233 2.989 -9.637
{glu B 10}20.342 -0.66 -9.437
{gln B 11}17.076 -1.773 -7.745
{leu B 12}15.168 -0.11 -10.583
{glu B 13}17.307 -1.924 -13.164
{asp B 14}16.785 -5.374 -11.603
{ala B 15}13.045 -4.618 -11.797
{arg B 16}13.284 -3.67 -15.495
{arg B 17}15.316 -6.851 -16.071
{leu B 18}12.563 -8.789 -14.184
{lys B 19}9.659 -7.477 -16.299
{ala B 20}11.752 -8.033 -19.433
{ile B 21}12.101 -11.696 -18.436
{tyr B 22}8.398 -11.999 -17.564
{glu B 23}7.623 -10.432 -20.937
{lys B 24}9.656 -12.919 -22.983
{lys B 25}8.435 -15.998 -21.051
{lys B 26}4.812 -15.008 -20.43
{asn B 27}3.295 -16.878 -23.371
{glu B 28}5.68 -19.86 -23.268
{leu B 29}4.916 -20.369 -19.541
{gly B 30}1.43 -18.925 -20.065
{leu B 31}0.964 -16.562 -17.142
{ser B 32}-0.463 -13.297 -15.94
{gln B 33}0.382 -11.085 -12.942
{glu B 34}-3.066 -12.404 -11.95
{ser B 35}-1.681 -15.971 -11.665
{val B 36}1.97 -15.173 -10.879
{ala B 37}0.391 -13.407 -7.864
{asp B 38}-1.641 -16.355 -6.497
{lys B 39}1.514 -18.499 -6.662
{met B 40}3.155 -15.943 -4.337
{gly B 41}0.26 -15.153 -2.012
{met B 42}-0.3 -11.517 -3.055
{gly B 43}-2.536 -9.525 -5.397
{gln B 44}-1.924 -8.288 -8.919
{ser B 45}-0.917 -4.852 -7.534
{gly B 46}1.75 -6.315 -5.26
{val B 47}3.194 -8.198 -8.246
{gly B 48}2.547 -5.058 -10.298
{ala B 49}4.666 -2.955 -7.91
{leu B 50}7.514 -5.436 -8.229
{phe B 51}7.579 -5.532 -12.036
{asn B 52}7.386 -1.711 -12.258
{gly B 53}9.952 -0.337 -9.756
{ile B 54}7.446 0.818 -7.118
{asn B 55}8.444 -1.745 -4.422
{ala B 56}11.938 -3.312 -4.206
{leu B 57}12.531 -7.058 -4.434
{asn B 58}14.134 -8.975 -1.579
@vectorlist {side ch} color=gold
{ca thr B 2}P 3.128 5.037 5.858
{cb thr B 2}1.765 5.518 6.48
{og1 thr B 2}1.147 4.268 6.947
{cb thr B 2}P 1.765 5.518 6.48
{cg2 thr B 2}0.858 6.425 5.665
{ca lys B 4}P 7.501 4.68 0.832
{cb lys B 4}6.469 4.35 -0.194
{cg lys B 4}5.214 3.69 0.405
{cd lys B 4}5.07 2.254 -0.103
{ce lys B 4}4.934 2.24 -1.624
{nz lys B 4}4.677 0.838 -2.08
{ca gln B 33}P 0.382 -11.085 -12.942
{cb gln B 33}0.479 -9.566 -12.868
{cg gln B 33}1.424 -9.002 -13.911
{cd gln B 33}1.636 -7.518 -13.808
{oe1 gln B 33}0.913 -6.817 -13.113
{cd gln B 33}P 1.636 -7.518 -13.808
{ne2 gln B 33}2.654 -7.071 -14.549
{ca gln B 44}P -1.924 -8.288 -8.919
{cb gln B 44}-2.957 -8.143 -10.041
{cg gln B 44}-2.376 -7.573 -11.289
{cd gln B 44}-2.508 -6.116 -11.551
{oe1 gln B 44}-3.49 -5.477 -11.181
{cd gln B 44}P -2.508 -6.116 -11.551
{ne2 gln B 44}-1.527 -5.559 -12.281
{ca ser B 45}P -0.917 -4.852 -7.534
{cb ser B 45}-1.789 -3.883 -6.816
{og ser B 45}-2.667 -4.398 -5.853
{ca ala B 49}P 4.666 -2.955 -7.91
{cb ala B 49}4.315 -2.749 -6.434
{ca ile B 54}P 7.446 0.818 -7.118
{cb ile B 54}5.901 0.728 -7.306
{cg1 ile B 54}5.479 1.423 -8.634
{cd1 ile B 54}3.97 1.196 -8.981
{cb ile B 54}P 5.901 0.728 -7.306
{cg2 ile B 54}5.154 1.285 -6.081
{ca asn B 55}P 8.444 -1.745 -4.422
{cb asn B 55}7.383 -2.721 -3.938
{cg asn B 55}6.219 -2.185 -3.191
{od1 asn B 55}6.29 -1.148 -2.525
{cg asn B 55}P 6.219 -2.185 -3.191
{nd2 asn B 55}5.067 -2.838 -3.226
@group {interactions}
@subgroup dominant {Hbonds}
@vectorlist {Hb} color=purple
{ne2 gln B 44}P U -1.618 -4.774 -12.403
{n7 a 2 4}U -1.758 -3.554 -12.592
{oe1 gln B 44}P U -3.822 -4.754 -11.269
{n6 a 2 4}U -4.366 -3.568 -11.412
{ne2 gln B 44}P U -0.847 -5.91 -12.513
{oe1 gln B 33}U 0.233 -6.466 -12.881
{ne2 gln B 33}P U 2.85 -6.345 -14.823
{o1p a 2 4}U 3.332 -4.561 -15.495
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P U 1.563 -4.209 -16.264
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P U 1.563 -4.309 -16.164
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P U 1.881 0.773 -1.111
U 1.881 0.973 -1.111
P U 1.881 0.873 -1.011
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P U -0.084 -3.793 -2.841
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@kinemage 4
@caption 
Non-specific contacts with phosphate backbone
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{pro B 6}12.365 5.669 -3.602
{leu B 7}14.211 2.824 -5.345
{thr B 8}17.924 2.763 -6.075
{gln B 9}19.233 2.989 -9.637
{glu B 10}20.342 -0.66 -9.437
{gln B 11}17.076 -1.773 -7.745
{leu B 12}15.168 -0.11 -10.583
{glu B 13}17.307 -1.924 -13.164
{asp B 14}16.785 -5.374 -11.603
{ala B 15}13.045 -4.618 -11.797
{arg B 16}13.284 -3.67 -15.495
{arg B 17}15.316 -6.851 -16.071
{leu B 18}12.563 -8.789 -14.184
{lys B 19}9.659 -7.477 -16.299
{ala B 20}11.752 -8.033 -19.433
{ile B 21}12.101 -11.696 -18.436
{tyr B 22}8.398 -11.999 -17.564
{glu B 23}7.623 -10.432 -20.937
{lys B 24}9.656 -12.919 -22.983
{lys B 25}8.435 -15.998 -21.051
{lys B 26}4.812 -15.008 -20.43
{asn B 27}3.295 -16.878 -23.371
{glu B 28}5.68 -19.86 -23.268
{leu B 29}4.916 -20.369 -19.541
{gly B 30}1.43 -18.925 -20.065
{leu B 31}0.964 -16.562 -17.142
{ca ser B 32}-0.463 -13.297 -15.94
{c ser B 32}-0.004 -12.892 -14.532
{o ser B 32}0.282 -13.82 -13.734
{c ser B 32}P -0.004 -12.892 -14.532
{n gln B 33}0.046 -11.607 -14.27
{ca gln B 33}0.382 -11.085 -12.942
{c gln B 33}-0.73 -11.607 -12.013
{o gln B 33}-0.508 -11.785 -10.816
{c gln B 33}P -0.73 -11.607 -12.013
{n glu B 34}-1.871 -11.834 -12.634
{ca glu B 34}-3.066 -12.404 -11.95
{c glu B 34}-2.584 -13.696 -11.318
{o glu B 34}-2.471 -13.751 -10.081
{c glu B 34}P -2.584 -13.696 -11.318
{n ser B 35}-2.17 -14.658 -12.121
{ca ser B 35}-1.681 -15.971 -11.665
{ca val B 36}1.97 -15.173 -10.879
{ca ala B 37}0.391 -13.407 -7.864
{ca asp B 38}-1.641 -16.355 -6.497
{ca lys B 39}1.514 -18.499 -6.662
{ca met B 40}3.155 -15.943 -4.337
{ca gly B 41}0.26 -15.153 -2.012
{ca met B 42}-0.3 -11.517 -3.055
{c met B 42}-1.271 -11.236 -4.217
{o met B 42}-1.73 -12.17 -4.867
{c met B 42}P -1.271 -11.236 -4.217
{n gly B 43}-1.585 -9.964 -4.365
{ca gly B 43}-2.536 -9.525 -5.397
{c gly B 43}-1.763 -9.099 -6.628
{o gly B 43}-0.517 -9.071 -6.605
{c gly B 43}P -1.763 -9.099 -6.628
{n gln B 44}-2.512 -8.755 -7.659
{ca gln B 44}-1.924 -8.288 -8.919
{c gln B 44}-1.172 -6.982 -8.719
{o gln B 44}-0.227 -6.755 -9.5
{c gln B 44}P -1.172 -6.982 -8.719
{n ser B 45}-1.562 -6.15 -7.785
{ca ser B 45}-0.917 -4.852 -7.534
{c ser B 45}0.45 -5.01 -6.873
{o ser B 45}1.418 -4.247 -7.163
{c ser B 45}P 0.45 -5.01 -6.873
{n gly B 46}0.51 -5.999 -6.007
{gly B 46}1.75 -6.315 -5.26
{val B 47}3.194 -8.198 -8.246
{gly B 48}2.547 -5.058 -10.298
{ala B 49}4.666 -2.955 -7.91
{leu B 50}7.514 -5.436 -8.229
{phe B 51}7.579 -5.532 -12.036
{asn B 52}7.386 -1.711 -12.258
{gly B 53}9.952 -0.337 -9.756
{ile B 54}7.446 0.818 -7.118
{asn B 55}8.444 -1.745 -4.422
{ala B 56}11.938 -3.312 -4.206
{leu B 57}12.531 -7.058 -4.434
{asn B 58}14.134 -8.975 -1.579
{ala B 59}15.829 -12.39 -1.533
{tyr B 60}12.626 -14.342 -0.809
{asn B 61}10.6 -12.727 -3.579
@vectorlist {side ch} color=gold
{ca lys B 3}P 5.989 6.453 3.869
{cb lys B 3}7.191 7.064 4.559
{cg lys B 3}6.924 8.26 5.482
{cd lys B 3}8.244 8.975 5.818
{ce lys B 3}8.133 10.061 6.878
{nz lys B 3}9.503 10.466 7.357
{ca lys B 5}P 11.182 5.078 -0.04
{cb lys B 5}12.203 4.446 0.9
{cg lys B 5}13.65 4.59 0.445
{cd lys B 5}14.545 3.663 1.265
{ce lys B 5}15.988 3.876 0.918
{nz lys B 5}16.186 3.883 -0.558
{ca lys B 19}P 9.659 -7.477 -16.299
{cb lys B 19}9.207 -6.054 -16.447
{cg lys B 19}7.767 -5.718 -16.834
{cd lys B 19}7.766 -4.329 -17.478
{ce lys B 19}6.723 -3.36 -17.085
{nz lys B 19}5.353 -3.608 -17.564
{ca tyr B 22}P 8.398 -11.999 -17.564
{cb tyr B 22}7.672 -11.291 -16.39
{cg tyr B 22}6.171 -11.27 -16.578
{cd1 tyr B 22}5.559 -10.239 -17.29
{ce1 tyr B 22}4.178 -10.184 -17.478
{cz tyr B 22}3.395 -11.215 -16.977
{oh tyr B 22}2.04 -11.222 -17.153
{cg tyr B 22}P 6.171 -11.27 -16.578
{cd2 tyr B 22}5.355 -12.273 -16.071
{ce2 tyr B 22}3.971 -12.26 -16.259
{cz tyr B 22}3.395 -11.215 -16.977
{ca lys B 26}P 4.812 -15.008 -20.43
{cb lys B 26}4.187 -13.627 -20.641
{cg lys B 26}2.655 -13.71 -20.578
{cd lys B 26}2.03 -12.321 -20.578
{ce lys B 26}2.689 -11.449 -21.638
{nz lys B 26}2.217 -10.047 -21.382
{ca gln B 33}P 0.382 -11.085 -12.942
{cb gln B 33}0.479 -9.566 -12.868
{cg gln B 33}1.424 -9.002 -13.911
{cd gln B 33}1.636 -7.518 -13.808
{oe1 gln B 33}0.913 -6.817 -13.113
{cd gln B 33}P 1.636 -7.518 -13.808
{ne2 gln B 33}2.654 -7.071 -14.549
{ca met B 42}P -0.3 -11.517 -3.055
{cb met B 42}0.96 -10.707 -3.083
{cg met B 42}1.73 -10.865 -4.342
{sd met B 42}3.248 -9.896 -4.143
{ce met B 42}4.035 -10.851 -2.827
{ca asn B 52}P 7.386 -1.711 -12.258
{cb asn B 52}5.933 -1.154 -12.309
{cg asn B 52}5.151 -1.732 -13.466
{od1 asn B 52}5.627 -1.842 -14.606
{cg asn B 52}P 5.151 -1.732 -13.466
{nd2 asn B 52}3.912 -2.089 -13.187
{ca asn B 58}P 14.134 -8.975 -1.579
{cb asn B 58}13.334 -8.721 -0.325
{cg asn B 58}12.109 -9.531 -0.131
{od1 asn B 58}12.051 -10.658 -0.65
{cg asn B 58}P 12.109 -9.531 -0.131
{nd2 asn B 58}11.102 -9.105 0.61
{ca asn B 61}P 10.6 -12.727 -3.579
{cb asn B 61}10.218 -11.236 -3.505
{cg asn B 61}8.922 -11.119 -2.724
{od1 asn B 61}8.304 -12.157 -2.428
{cg asn B 61}P 8.922 -11.119 -2.724
{nd2 asn B 61}8.521 -9.896 -2.45
@group {interactions}
@subgroup dominant {Hbonds}
@vectorlist {Hb} color=purple
{n gly B 43}P U -1.469 -9.39 -3.82
{o1p t 1 15}U -1.266 -8.394 -2.876
{nd2 asn B 61}P U 8.004 -9.696 -1.873
{o1p g 1 14}U 6.778 -9.223 -0.503
{nd2 asn B 58}P U 10.971 -8.34 0.804
{o1p g 1 13}U 10.688 -6.675 1.225
{nd2 asn B 58}P U 11.181 -8.682 1.284
{o2p g 1 13}U 11.34 -7.838 2.631
{nz lys B 19}P U 4.594 -3.436 -17.75
{o2p a 2 4}U 3.863 -3.271 -17.93
{nz lys B 26}P U 1.8 -9.885 -20.719
{o2p t 2 3}U 0.827 -9.508 -19.173
{o1p a 2 4}P U 3.626 -3.39 -15.111
{nd2 asn B 52}U 3.814 -2.534 -13.845
{o1p a 2 4}P U 4.096 -3.764 -16.328
{nz lys B 19}U 4.785 -3.679 -17.005
{oh tyr B 22}P U 1.579 -10.692 -17.536
{o2p t 2 3}U 0.871 -9.876 -18.127
{n gln B 33}P U -0.315 -11.109 -14.782
{o1p t 2 3}U -1.132 -9.981 -15.94
{ne2 gln B 33}P U 2.399 -6.427 -14.949
{o3* t 2 3}U 1.818 -4.953 -15.864
{ne2 gln B 33}P U 2.85 -6.345 -14.823
{o1p a 2 4}U 3.332 -4.561 -15.495
{o1p g 1 11}P U 11.534 7.653 6.083
{nz lys B 3}U 9.943 9.857 7.081
@subgroup {atom marks}
@vectorlist {prot N} color=blue
{n gln B 33}P U -.054 -11.607 -14.27
U 0.146 -11.607 -14.27
P U 0.046 -11.507 -14.27
U 0.046 -11.707 -14.27
P U 0.046 -11.607 -14.17
U 0.046 -11.607 -14.37
{n glu B 34}P U -1.771 -11.834 -12.634
U -1.971 -11.834 -12.634
P U -1.871 -11.734 -12.634
U -1.871 -11.934 -12.634
P U -1.871 -11.834 -12.534
U -1.871 -11.834 -12.734
{n gly B 43}P U -1.485 -9.964 -4.365
U -1.685 -9.964 -4.365
P U -1.585 -9.864 -4.365
U -1.585 -10.064 -4.365
P U -1.585 -9.964 -4.265
U -1.585 -9.964 -4.465
{n gln B 44}P U -2.412 -8.755 -7.659
U -2.612 -8.755 -7.659
P U -2.512 -8.655 -7.659
U -2.512 -8.855 -7.659
P U -2.512 -8.755 -7.559
U -2.512 -8.755 -7.759
{n ser B 45}P U -1.462 -6.15 -7.785
U -1.462 -6.15 -7.785
P U -1.562 -6.05 -7.785
U -1.562 -6.25 -7.785
P U -1.562 -6.15 -7.685
U -1.562 -6.15 -7.885
{n gly B 46}P U 0.41 -5.999 -6.007
U 0.61 -5.999 -6.007
P U 0.51 -5.899 -6.007
U 0.51 -6.099 -6.007
P U 0.51 -5.999 -5.907
U 0.51 -5.999 -6.107
{ce lys B 3}P 8.133 10.061 6.878
{nz lys B 3}9.503 10.466 7.357
{ce lys B 5}P 15.988 3.876 0.918
{nz lys B 5}16.186 3.883 -0.558
{ce lys B 19}P 6.723 -3.36 -17.085
{nz lys B 19}5.353 -3.608 -17.564
{ce lys B 26}P 2.689 -11.449 -21.638
{nz lys B 26}2.217 -10.047 -21.382
@vectorlist {phosphate O} color=hotpink
{p g 1 11}P 13.191 6.267 6.189
{o1p g 1 11}11.974 7.044 5.807
{o1p g 1 13}P 10.557 -5.91 1.419
{p g 1 13}10.567 -6.329 2.792
{o2p g 1 13}11.419 -7.415 3.305
{p g 1 14}P 4.914 -8.837 0.564
{o1p g 1 14}6.261 -9.023 0.074
{p t 1 15}P -1.398 -7.999 -0.906
{o1p t 1 15}-1.15 -7.82 -2.331
{o1p t 2 3}P -1.493 -9.483 -16.452
{p t 2 3}-0.737 -9.14 -17.626
{o2p t 2 3}0.41 -9.346 -18.51
{o1p a 2 4}P 3.528 -3.835 -15.769
{p a 2 4}2.483 -3.292 -16.863
{o2p a 2 4}3.104 -3.099 -18.116