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 ... 5 15 50 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). you can see a portion with 8 residues (slightly over two helix turns) seen from the axis. The alpha carbons in the first turn are coloured, and all of them have been joined with a fictitious line representing the peptide backbone.
The peptide bacbone of the helix forms its core, while the sidechains point outwards.
the 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): Show just the schematic rendering.