Puzzle pieces defined: locating common packing units in tertiary protein contacts

Abstract

Puzzle pieces are defined as small packing units which make up the unique tertiary interactions in proteins. Anti-parallel and perpendicular helix-helix contacts were broken down into basic puzzle-piece pairs in order to study the traits of such contacts: their limited geometry, preferred residue involvement, residue conformation and other common constraints. These traits can then be used for continued comparison of other protein structures, improving models of and designing proteins de novo and, in time, predicting 3D structure from primary sequence. Results from a small (100 proteins) database of anti-parallel helix-helix contacts and from preliminary work on a large database (600 proteins) of perpendicular helix-helix contacts are presented.