Intrinsic Phi, Psi Propensities of Amino Acids, Derived from the Coil Regions of Known Structures

Many different factors contribute to secondary structure propensities, including phi, psi 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 phi, psi propensities for residues in coil regions (that is, residues not in alpha-helix and not in beta-strand). Comparisons of intrinsic phi, psi 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 phi, psi propensities and provides an explanation for the variations observed.