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 helix-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/outside number (conformation-dependent values) and (2) the side-chain length (depends only on the residue type and does not depend on the side-chain conformation). The results showed that the interface side chains tend to be bent away from the interacting helix. The most important finding, however, is that the side chains in the interface areas, on average, are shorter than in the noninterface areas. Proteins 2000;40:429-435.