Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

Protein Sci. 1992 Feb;1(2):216-26. doi: 10.1002/pro.5560010203.


The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Amino Acids / genetics
  • Conserved Sequence
  • Databases, Factual
  • Mathematical Computing
  • Molecular Sequence Data
  • Pattern Recognition, Automated
  • Probability
  • Protein Folding*
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Proteins / genetics
  • Reference Values
  • Sequence Alignment / methods*
  • Sequence Homology, Amino Acid


  • Amino Acids
  • Proteins