MoBio Alpha Helix Chapter 2

An α helix has the following features:

  • every 3.6 residues make one turn,
  • the distance between two turns is 0.54 nm,
  • the C=O (or N-H) of one turn is hydrogen bonded to N-H (or C=O) of the neighboring turn.

Hydrogen bonds play a role in stabilizing the α helix conformation. However, the size and charges of sidechains are also important factors. Alanine has a greater propensity to form α helices than proline.

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Figure 2-C-4. α helix conformations. (a) The ideal right-handed α helix. C: green; O: red; N: blue; H: not shown; hydrogen bond: dashed line. (b) The right-handed α helix without showing atoms. (c) the left-handed α helix.

The right-handed or left-handed helix may be distinguished by stretching out your thumb and curling the other four fingers. Imaging that in the above figure the helix is spiraling upward. Stretch your right thumb upward, then the other four fingers of the right hand will be able to curl in the same direction as each turn in the spiral. The same result can be obtained if you imagine that the helix is spiraling downward and point your thumb downward. The left hand works for the left-handed α helix.

Amphipathic α helix

In an amphipathic α helix, one side of the helix contains mainly hydrophilic amino acids and the other side contains mainly hydrophobic amino acids. The amino acid sequence of amphipathic α helix alternates between hydrophilic and hydrophobic residues every 3 to 4 residues, since the α helix makes a turn for every 3.6 residues. An example is shown below.

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Figure 2-C-5. The amphipathic α helix structure of CAP18, which is a molecule capable of binding to the endotoxin of bacteria. (a) Amino acid sequence of the amphipathic part of CAP18. Hydrophobic residues are boxed with red lines. (b) The 3D structure determined by nuclear magnetic resonance. Hydrophobic residues are located on the lower side. PDB ID = 1LYP.