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Protein Science, Vol 1, Issue 10 1333-1342, Copyright © 1992 by Cold Spring Harbor Laboratory Press

ARTICLE

Differences in the amino acid distributions of 3(10)-helices and {alpha}-helices

M. E. KARPEN, P. L. DE-HASETH and K. E. NEET
Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106

Local determinants of 3(10)-helix stabilization have been ascertained from the analysis of the crystal structure data base. We have clustered all 5-length substructures from 51 nonhomologous proteins into classes based on the conformational similarity of their backbone dihedral angles. Several clusters, derived from 3(10)-helices and multiple-turn conformations, had strong amino acid sequence patterns not evident among {alpha}-helices. Aspartate occurred over twice as frequently in the N-cap position of 3(10)-helices as in the N-cap position of {alpha}-helices. Unlike {alpha}-helices, 3(10)-helices had few C-termini ending in a left-handed {alpha} conformation; most 3(10) C-caps adopted an extended conformation. Differences in the distribution of hydrophobic residues among 3(10)-and {alpha}-helices were also apparent, producing amphipathic 3(10)-helices. Local interactions that stabilize 3(10)-helices can be inferred both from the strong amino acid preferences found for these short helices, as well as from the existence of substructures in which tertiary interactions replace consensus local interactions. Because the folding and unfolding of {alpha}-helices have been postulated to proceed through reverse-turn and 3(10)-helix intermediates, sequence differences between 3(10)- and {alpha}-helices can also lend insight into factors influencing {alpha}-helix initiation and propagation.
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