Alpha-Helix Geometry Part. 2
Properties of the alpha-helix.
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The structure repeats itself every 5.4 Angstroms along the helix axis, ie
we say that the alpha-helix has a pitch of 5.4 Angstroms. Alpha-helices have
3.6 amino acid residues per turn, ie a helix 36 amino acids long would form
10 turns. The separation of residues along the helix axis is 5.4/3.6 or 1.5
Angstroms, ie the alpha-helix has a rise per residue of 1.5 Angstroms.
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Every mainchain C=O and N-H group is hydrogen-bonded to a peptide bond 4
residues away (ie O(i) to N(i+4)). This gives a very regular, stable arrangement.
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The peptide planes are roughly parallel with the helix axis and the dipoles
within the helix are aligned, ie all C=O groups point in the same direction
and all N-H groups point the other way. Side chains point outward from helix
axis and are generally oriented towards its amino-terminal end.
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All the amino acids have negative phi and psi angles, typical values being
-60 degrees and -50 degrees, respectively.
Distortions of alpha-helices.
The majority of alpha-helices in globular proteins are curved or distorted
somewhat compared with the standard Pauling-Corey model. These distortions
arise from several factors including:
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The packing of buried helices against other secondary structure elements
in the core of the protein.
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Proline residues induce distortions of around 20 degrees in the direction
of the helix axis. This is because proline cannot form a regular alpha-helix
due to steric hindrance arising from its cyclic side chain which also blocks
the main chain N atom and chemically prevents it forming a hydrogen bond.
Janet Thornton has shown that proline causes two H-bonds in the helix to
be broken since the NH group of the following residue is also prevented from
forming a good hydrogen bond. Helices containing proline are usually long
perhaps because shorter helices would be destabilised by the presence of
a proline residue too much. Proline occurs more commonly in extended regions
of polypeptide.
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Solvent. Exposed helices are often bent away from the solvent region. This
is because the exposed C=O groups tend to point towards solvent to maximise
their H-bonding capacity, ie tend to form H-bonds to solvent as well as N-H
groups. This gives rise to a bend in the helix axis.
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3(10)-Helices. Strictly, these form a distinct class of helix but they are
always short and frequently occur at the termini of regular alpha-helices.
The name 3(10) arises because there are three residues per turn and ten atoms
enclosed in a ring formed by each hydrogen bond (note the hydrogen atom is
included in this count). There are main chain hydrogen bonds between residues
separated by three residues along the chain (ie O(i) to N(i+3)). In this
nomenclature the Pauling-Corey alpha-helix is a 3.6(13)-helix. The dipoles
of the 3(10)-helix are not so well aligned as in the alpha-helix, ie it is
a less stable structure and side chain packing is less favourable.
Here's a coordinate file for a single turn of 3-10 helix,
which you may examine with RasMol (click
here
for a chemical MIME- stamped copy of file from Birkbeck).
j.cooper 2/1/95
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Last updated 4th Nov'96