UCMB CP 160/16 , ave. F. Roosevelt, Universite Libre de Bruxelles, Belgium
We present a repertoire of recurrent spatial arrangements of three consecutive secondary structure elements along the sequence, irrespective of the length and conformation of the intervening loops. We consider the two possible sequential arrangements of one alpha-helix and two consecutive hydrogen-bonded beta-strands, which can be parallel or antiparallel. The fragments displaying these arrangements are obtained from a representative structure set of 141 polypeptide chains. Using a variant of our automatic structure alignment algorithm SoFiSt, the fragments are classified into structural families according to the root mean square deviation of the backbone in the secondary structure elements, after optimal structure superposition. This procedure yields eleven families with at least three members and a number of intermediate fragments that are structurally similar to members of different families. The existence of intermediates indicates that there is a structural continuity between the various spatial arrangements. We characterize the structure of the families by their chain topology, the relative arrangement of secondary structures and the contacts between the side chains. We also examine if certain sequence characteristics are conserved within each family. The intrinsic stability of the motifs is evaluated using database-derived potentials and is compared to available experimental data.