Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets.

ABSTRACT: To help elucidate the role of secondary structure packing preferences in protein folding, here we present an analysis of the packing geometry observed between alpha-helices and between alpha-helices and beta-sheets in 1316 diverse, nonredundant protein structures. Finite-length vectors were fit to the alpha-carbon atoms in each of the helices and strands, and the packing angle between the vectors, Omega, was determined at the closest point of approach within each helix-helix or helix-sheet pair. Helix-sheet interactions were found in 391 of the proteins, and the distributions of Omega values were calculated for all the helix-sheet and helix-helix interactions. The packing angle preferences for helix-helix interactions are similar to those previously observed. However, analysis of helix-str

SUBMITTER: Hespenheide BM 

PROVIDER: S-EPMC2323881 | biostudies-literature | 2003 May

REPOSITORIES: biostudies-literature