The Alpha-Helix Structure

An alpha-helix is formed from a connected stretch of amino acids. Its main characteristics are:

• The R groups of the amino acids all extend to the outside.
• The helix makes a complete turn every 3.6 amino acids.
• It rises 1.5 A per residue.
• An alpha-helix is a right-handed helix. It twists in a clockwise direction.
• The carbonyl (-C=O) group of each peptide bond extends parallel to the axis of the helix and points directly at the -N-H group of the peptide bond 4 amino acids below it in the helix.
• Hydrogen bonds occur between the -C=O of residues and the -N-H of residues n+4.

Certain amino acids are preferred in an alpha helix, such as Ala, Glu, Leu, and Met. Pro, Gly, Tyr, and Ser have a small tendency to do the same. Proline cannot actually fit into a helix, and introduces a kink into the structure.

The side-chains point out of the helix. The overall hydrophobicity of a helix is determined by the side chains. If the side chains are hydrophobic, the helix is usually buried somewhere within the proteins core, away from the solvent. If the side chains are polar or charged (hydrophilic), the helix is probably exposed to the solvent. Some helices have a dual character (one side hydrophobic, the other side hydrophilic), and may be found at the protein's surface.