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Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures

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Abstract

Many different factors contribute to secondary structure propensities, including φ,ψ preferences, side-chain interactions, steric effects and hydrophobic tertiary contacts. To deconvolute these competing factors, we have adopted a novel approach which quantifies the intrinsic φ,ψ propensities for residues in coil regions (that is, residues not in α-helix and not in β-strand). Comparisons of intrinsic φ,ψ propensities with their equivalent secondary structure propensities show that while correlations for helix are relatively weak, those for strand are much stronger. This paper describes our new φ,ψ propensities and provides an explanation for the variations observed.

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Authors and Affiliations

  1. Biomolecular Structure and Modelling Unit, Department of Biochemistry, University College London, Gower Street, London, WC1E 6BT, UK

    Mark B. Swindells, Malcolm W. MacArthur & Janet M. Thornton

  2. Department of Molecular Design, Yamanouchi Pharmaceutical Co. Ltd., 21 Miyukigaoka, Tsukuba, 305, Japan

    Mark B. Swindells

Authors
  1. Mark B. Swindells
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  2. Malcolm W. MacArthur
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  3. Janet M. Thornton
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Swindells, M., MacArthur, M. & Thornton, J. Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures. Nat Struct Mol Biol 2, 596–603 (1995). https://doi.org/10.1038/nsb0795-596

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