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Stick model showing the polypeptide backbone and hydrogen bonds, i.e. green lines between the two heavy atoms of the peptide hydrogen bond, C=O···H–N.
Each residue in the helix is involved in two hydrogen bonds (except for the residues at the ends). These hydrogen bonds are nearly parallel to the axis. However, the hydrogen bond geometry is not perfect, as the peptide N-H is not directed precisely toward the lone-pair electrons of the oxygen atom.
In a moment we'll examine an α-helix from a high resolution structure with all the hydrogen atoms. However, H atoms are not visible at the low resolution of many protein X-ray structures. Thus, you should be familiar with different ways of depicting α-helices in JSmol.
Alternative ways to display an α-helix:
backbone model vs. trace model. Although the trace model doesn't show the exact position of the α-carbons, it is perhaps the most widely used representation of an α-helix.
The a-helix is an elegant structure. The repetitive pattern results in a conformation that compacts the chain, thereby expelling water while favoring hydrogen bonds and exquisite van der Waals contacts. Although peptide groups have a strong tendency to enter water, the helix per se can be an even better "solvent".
along the axis of an α-helix. This helix contains ten residues; it comes from a protein kinase (human lymphocyte kinase p56) structure at high resolution (1.0 Å). All side chains have been omitted for clarity. Notice the small hole running lengthwise through the helix. The four N-H groups at this end of the helix lack hydrogen-bonding partners within the helix.
from the C-terminus. The four carbonyl groups at this end also lack hydrogen-bonding partners.
Thus, a 10-residue α-helix has only 6 hydrogen bonds, despite having 10 backbone N-H (donors) and 10 backbone C=O (acceptors). The N- and C-terminal ends of an isolated helix contain four N-H donors and four C=O acceptors each. In proteins, α-helices are stabilized by helix capping interactions that occur at both ends of the helix.
of helix backbone at half the original magnification. The β carbons (magenta) of the side chains point outward from the helix. The hydrogen bond lengths are given in angstroms.
spacefilling (including the side chains). Would you agree that the exterior surface of this helix is not a smooth surface? Is any α-helix likely to have a smooth surface?
Secondary structure is not just hydrogen bonds. The stability of the α-helix depends on other favorable interactions in addition to the hydrogen bonds. The regular spacing of side chains creates a highly textured surface, allowing complementary helix surfaces to fit together like "knobs-into-holes".
Since α-helices often run through the protein molecule from one side to the other, some of the orphan peptide groups at the ends of the α-helix can form hydrogen bonds to the solvent. Otherwise the orphan N-H and C=O groups will form hydrogen bonds with functional groups of certain side chains at or near the ends of the helix.
Observe the space-filling model. Instead of orphan amide N-H bonds, there are only when all the side chains of this helix are shown. Describe the helix capping in this helical segment.