Differences in the amino acid distributions of 310‐helices and α‐helices

• Published in: Protein science 1992-10, Vol.1 (10), p.1333-1342
• Main Authors: Karpen, Mary E., De Haseth, Pieter L., Neet, Kenneth E.
• Format: Article
• Language: English
• Subjects: 310‐helices; amino acid determinants; α‐helix
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.5560011013

Local determinants of 310‐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 310‐helices and multiple‐turn conformations, had strong amino acid sequence patterns not evident among α‐helices. Aspartate occurred over twice as frequently in the N‐cap position of 310‐helices as in the N‐cap position of α‐helices. Unlike α‐helices, 310‐helices had few C‐termini ending in a left‐handed α conformation; most 310 C‐caps adopted an extended conformation. Differences in the distribution of hydrophobic residues among 310‐ and α‐helices were also apparent, producing amphipathic 310‐helices. Local interactions that stabilize 310‐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 α‐helices have been postulated to proceed through reverse‐turn and 310‐helix intermediates, sequence differences between 310‐ and α‐helices can also lend insight into factors influencing α‐helix initiation and propagation.