Alpha-Helix: Hydrogen Bonding
along the Polypeptide Backbone
The next series of exercises focus on the
hydrogen bonds (H-bonds), represented by green lines connecting atoms of
the α-helix
polypeptide
backbone.
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Toggle on/off
H-bonds
along
the
α-helix
backbone. |
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Toggle
on/off H-bonds
with sidechains off.
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| AA residues 60-67
of sperm whale oxyMb define of four hydrogen
bonds between backbone atoms (N-H...O=C)
of the polypeptide chain. Each green line
connects
the center of
a N atom to the
center of an O atom
thereby defining donor/acceptor pair (Hydrogen
atoms are not
visible in this image.) |
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Toggle on/off
labels for N
atoms at ends of the H-bonds. |
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N.HIS64,
N.GLY65, N.VAL66,
N.THR67 |
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Toggle on/off
labels for
O
atoms at ends of H-bonds |
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O.ASP60,O.LEU61,O.LYS62,O.LYS63 |
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Optimal H-bonds -- that is, H-bonds
with lowest free energy -- are created when
the interatomic distances and angles of the atoms forming the
H-bond meet certain criteria. For example, an optimal N-H...O
=C
H-bond is formed when the donor H atom is optimally aligned with
the unshared electron pair orbitals of the O
atom.
| Note that the green
lines representing the H-bonds in these images are not
co-linear with the lines defining the C=O
bonds. Rather each green line intersects the
corresponding O atom at slight angle
relative to the carbonyl bond. Optimally, this angle
corresponds to an unshared electron pair orbital of
oxygen. |
Optimal H-bonds also occur when the
interatomic distances are as short as possible. In the case of
the N-H...O=C H-bond, the optimal N-O atom center-to-center distance is
2.79 +/- 1.2 Å, the so-called
hydrogen-bond length.
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|
Toggle on or
off the hydrogen-bond
lengths. |
| Note that the N-H...O=C
hydrogen-bond lengths for the a-helix backbone
atoms vary slightly but are not too much greater than the
predicted optimal value. |
One additional property that can easily
be measured here for the a-helix is the vertical distance the helix rises for one
complete turn or its pitch (p). The number of residues
(n) per
complete turn of the α-helix equals 3.6. The pitch is approximately equal to
the distance between Cα and the carbonyl carbon (C=O) directly above it
along the backbone. These distances are found by toggling the
following button.
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|
Toggle on
or off the Cα-C(=O)
distance
measurements. |
| Note: These values
yield an average of 5.75 Å which is
somewhat larger than the 5.4 Å value
usually reported for the pitch of the a-helix.
The
discrepancy here arises because a line drawn between the
alpha carbon, Cα
and the carbonyl carbon, C(=O),
is not exactly parallel to the axis of the α-helix. |
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α-Helix Topic Outline