Journal of Protein Chemistry

, Volume 4, Issue 1, pp 23–55 | Cite as

Statistical analysis of the physical properties of the 20 naturally occurring amino acids

  • Akinori Kidera
  • Yasuo Konishi
  • Masahito Oka
  • Tatsuo Ooi
  • Harold A. Scheraga
Article

Abstract

In order to describe the conformational and other physical properties of the 20 naturally occurring amino acid residues with a minimum number of parameters, several multivariate statistical analyses were applied to 188 of their physical properties and ten orthogonal properties (factors) were obtained for the 20 amino acids without losing the information contained in the original physical properties. The analysis consisted of three main steps. First, 72 of the physical properties were eliminated from further consideration because they did not pass statistical tests that they follow a normal distribution. Second, the remaining 116 physical properties of the amino acids were classified by a cluster analysis to eliminate duplications of highly correlated physical properties. This led to nine clusters, each of which was characterized by an average characteristic property, namely bulk, two hydrophobicity indices for free amino acids, one hydrophobicity index for amino acid residues in a protein, two types of β-structure preference, α-helix preference, and two types of bend-structure preference. The physical properties within a given cluster were highly correlated with each other, but the correlation between clusters was low. Third, a factor analysis was applied to the nine average classified properties and 16 additional physical properties to obtain a small number of orthogonal properties (ten factors). Four of these factors arise from the nine characteristic properties, and the remaining six factors were obtained from the 16 physical properties not included in the nine characteristic properties. Finally, most of the 188 physical properties could be expressed as a sum of these ten orthogonal factors, with appropriate weighting factors. Since these factors contain information relating almost all properties of all 20 amino acids, it is possible to estimate the numerical values of a property for one or two amino acids for which experimental data for this property are not available. For example, the estimated values for the Zimm-Bragg parameters at 20°C are 0.66 and 0.92 for proline and cysteine, respectively, computed from the first four factors.

Key words

amino acid physical properties characteristic properties bulk hydrophobicity β-structure preference α-helix preference bend-structure preference statistical analysis cluster analysis factor analysis 

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Copyright information

© Plenum Publishing Corporation 1985

Authors and Affiliations

  • Akinori Kidera
    • 1
  • Yasuo Konishi
    • 1
  • Masahito Oka
    • 1
  • Tatsuo Ooi
    • 2
  • Harold A. Scheraga
    • 1
  1. 1.Baker Laboratory of ChemistryCornell UniversityIthaca
  2. 2.Institute for Chemical ResearchKyoto UniversityUjiJapan

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