In this type of secondary structure, the peptide backbone curls over itself tracing a compact helicoid around the longitudinal axis of the molecule.
Here we can see the alpha helix formed by a pentadecapeptide (that is, a peptide with
amino acid residues).
Each residue is shifted 0.15 nm along the axis with respect to the former residue, and each whole turn of the helix means a rise of 0.54 nm (helix pitch).
peptide bacbone of the helix forms its core, while the sidechains point outwards.
peptide backbone is displayed as a fictitious line that joins the alpha carbons, and the sidechains as a ball-and-stick model.
The helix is stabilised by
between the nitrogens and the carbonyl groups in the peptide bonds.
These are intrachain bonds; specifically, the hydrogen bonds are set between the carbonyl oxygen in a residue (n) and the nitrogen in the residue located at position (n+4):
(The spheres correspond to alpha carbons.)
To end this section, we'll show the schematic rendering (or “cartoon”) of alpha helices, which is useful in large proteins: it's either a spiral ribbon or a cylinder; it may end in an arrowhead that indicates the chain direction (from the amino terminal to the carboxy terminal):