Side chains in transmembrane helices are shorter at helix-helix interfaces

Transmembrane helices from crystallographically determined structures were analyzed to determine the distribution of side chains inside and outside he lix-helix interfaces. Two structural characteristics were explored: (1) the number of atoms outside the interfaces that belong to the side chains with the C-alpha atoms inside the interfaces, as well as the opposite, inside/o utside number (conformation-dependent values) and (2) the side-chain length (depends only on the residue type and does not depend on the side chain co nformation). The results showed that the interface side chains tend to be b ent away from the interacting helix. The most important finding, however, i s that the side chains in the interface areas, on average, are shorter than in the noninterface areas. Proteins 2000;40:429-435, (C) 2000 Wiley-Liss, Inc.