Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

BiopolymersVolume 22, Issue 12 p. 2577-2637 Article Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Wolfgang Kabsch, Wolfgang Kabsch Biophysics Department, Max Planck Institute of Medical Research, 6900 Heidelberg, Federal Republic of GermanySearch for more papers by this authorChristian Sander, Christian Sander Biophysics Department, Max Planck Institute of Medical Research, 6900 Heidelberg, Federal Republic of GermanySearch for more papers by this author Wolfgang Kabsch, Wolfgang Kabsch Biophysics Department, Max Planck Institute of Medical Research, 6900 Heidelberg, Federal Republic of GermanySearch for more papers by this authorChristian Sander, Christian Sander Biophysics Department, Max Planck Institute of Medical Research, 6900 Heidelberg, Federal Republic of GermanySearch for more papers by this author First published: December 1983 https://doi.org/10.1002/bip.360221211Citations: 10,752AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat 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 Cα positions and is positive for right-handed helices and negative for ideal twisted β-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. Citing Literature Volume22, Issue12December 1983Pages 2577-2637 RelatedInformation