Secondary structure

Alpha helix

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).

Highlight the helix

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 helix is
  • residues are needed for a full turn
  • Each residue means a rotation of degrees with respect to the former one

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.)


Please observe the sidechains and try to identify which amino acids form this peptide.

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.