Intrahelical side chain-side chain contacts: the consequences of restricted rotameric states and implications for helix engineering and design.

Intrahelical side chain-side chain (sc-sc) interactions are assumed to play a crucial role in the formation and stability of alpha-helices, yet it was found that only 37.2% of all helical residues are involved in such close contacts, assuming a specific minimum contact distance. The majority (58.0%) of these were detected between residues with amino acid sequence spacing i, i + 4. The low frequency of intrahelical sc-sc contacts with sequence separations i, i + 1 and i, i + 3, each observed with only about one-third of the i, i + 4 counts, can be directly and generally attributed to the absence of the g- conformation in helices for the dihedral angle chi 1. However, if it was assumed that each side chain may maximally make only one sc-sc contact, as most commonly observed, the percentage of contacting pairs increased relative to the maximum possible pairs for a given sequence spacing by a factor of approximately 4, e.g. from 20.9 to 81.7% for i, i + 4 contacts. Stereochemical reasons are also given for the observation that i, i + 3 contacts are composed largely of ion or polar pairs, while hydrophobic residues dominate the i, i + 4 contacts. No significantly increased density of intrahelical sc-sc contacts with increasing helix length was found. Although there were generally fewer intrahelical contacts between buried helical residues when more contacts were made to the tertiary protein environment, the number of intrahelical contacts did not increase with increasing solvent exposure of the helices. Implications for helix design and the packing of helices are discussed.