Alpha helix

An alpha helix is a type of secondary structure, i.e. a description of how the main chain of a protein is arranged in space. It is a repetitive regular secondary structure (just like the beta strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.

In an alpha helix, the main chain arranges in a with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by (shown as dashed lines) from the carbonyl group of one amino acid to the amino group of a second amino acid. Because the amino acids connected by each hydrogen bond are four apart in the primary sequence, these main chain hydrogen bonds are called "n to n+4". There are . If you to a Spacefilling representation, you can see how tightly packed the main chain is (no space in the middle). [The previous scenes were inspired by a beautiful set of figures in Stryer's biochemistry textbook.]

Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles . If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation with examples of Ramachandran plots, see Ramachandran Plot or Birkbeck's PPS95 course.

Which amino acids are found in alpha helices?

Some amino acids are commonly found in alpha helices and others are rare. Knowing the so-called helix propensities, it is possible to predict where helices occur in a protein sequence. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices.

Proline is considered a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Here is an example of a at the position of a . Prolines are often found near the beginning or end of an alpha helix, as in this example of (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds. Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see Helices in Proteins). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).

The beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting sequence and structural patterns involving main chain or side chain hydrogen bonding.