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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features (1983)
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@MISC{Kabsch83dictionaryof,
author = {Wolfgang Kabsch and Christian Sander},
title = {Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features},
year = {1983}
}
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Abstract
For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn ” and “bridge. ” Repeating turns are “helices, ” repeating bridges are “ladders, ” connected ladders are “sheets. ” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality ” is the torsional handedness of four consecutive Ca positions and is positive for right-handed helices and negative for ideal twisted @-sheets. Curved pieces are defined as “bends. ” Solvent “exposure ” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10,925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.
Keyphrases
secondary structure solvent exposure successful analysis end result local chain chirality geometric structure computer-readable form overall view meaningful definition water molecule protein structure s bond amino acid sequence differential geometry elementary hydrogen-bonding pattern turn concept torsion cooperative secondary structure torsional handedness x-ray coordinate protein structure prediction work primary structure different globular protein pattern-recognition process consecutive ca position right-handed helix strip table linear form geometrical feature possible contact strip graph
