Amino Acid Preferences for Specific Locations at the Ends of α Helices

TLDR

The interface residue that is half inside and half outside the helix is termed the N‑cap or C‑cap, depending on its position. The authors defined helix end positions using α‑carbon coordinates and analyzed 215 helices from 45 globular proteins to tabulate amino‑acid preferences at 16 positions relative to the helix termini. The analysis confirmed asymmetrical charge distributions at the first and last turns and revealed sharp new preferences, including a 3.5:1 Asn preference at the N‑cap, a 2.6:1 Pro preference at N‑cap + 1, Gly dominating the C‑cap (34 % of helices), and hydrophobic residues peaking at N‑cap + 4 and C‑cap − 4.

Abstract

A definition based on α-carbon positions and a sample of 215 α helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which is half in and half out of the helix, is called the N-cap or C-cap, whichever is appropriate. The results confirm earlier observations, such as asymmetrical charge distributions in the first and last helical turn, but several new, sharp preferences are found as well. The most striking of these are a 3.5:1 preference for Asn at the N-cap position, and a preference of 2.6:1 for Pro at N-cap + 1. The C-cap position is overwhelmingly dominated by Gly, which ends 34 percent of the helices. Hydrophobic residues peak at positions N-cap + 4 and C-cap - 4.