Document Detail

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.
MedLine Citation:
PMID:  1304904     Owner:  NLM     Status:  MEDLINE    
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.
J Overington; D Donnelly; M S Johnson; A Sali; T L Blundell
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Protein science : a publication of the Protein Society     Volume:  1     ISSN:  0961-8368     ISO Abbreviation:  Protein Sci.     Publication Date:  1992 Feb 
Date Detail:
Created Date:  1993-07-09     Completed Date:  1993-07-09     Revised Date:  2010-09-07    
Medline Journal Info:
Nlm Unique ID:  9211750     Medline TA:  Protein Sci     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  216-26     Citation Subset:  IM    
Department of Crystallography, Birkbeck College, University of London, UK.
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MeSH Terms
Amino Acid Sequence
Amino Acids / chemistry*,  genetics
Conserved Sequence
Databases, Factual
Mathematical Computing
Molecular Sequence Data
Pattern Recognition, Automated
Protein Folding*
Protein Structure, Tertiary*
Proteins / chemistry*,  genetics
Reference Values
Sequence Alignment / methods*
Sequence Homology, Amino Acid
Reg. No./Substance:
0/Amino Acids; 0/Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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