A demonstration of the various alpha helix conformations in protein secondary structure. An alpha helix is a right-handed coil in which every backbone N-H group donates a hydrogen bond to the C=O group of the amino acid four residues earlier. In pi and 3-10 helices, the bonding occurs at the amino acid five and three residues earlier, respectively, resulting in either a wider helix (pi) or a tighter helix (3-10).

This helix consists of 20 amino acid peptides of poly-L-alanine, and were produced using the peptide builder in Chimera, with phi and psi angles set as follows: 

• Alpha helix-  phi=-57.0, psi=-47.0
• Pi helix-        phi=-57.0, psi=-70.0
• 3-10 helix-   phi=-49.0, psi=-26.0

This combined structure is 7 amino acids of alpha helix, followed by 7 amino acids of pi helix, followed by 6 amino acids of 3-10 helix.

Download the original PDB file here.