title: Displaying inter-main chain hydrogen bond patterns in proteins.
abstract: Two computer graphics techniques for displaying hydrogen bonds between the main chains of different proteins are described, and illustrated for two thiol proteases. (The X-ray crystallography was performed by Kamphuis et al. in 1984, and by Baker and Dodson in 1980.) One is a three-dimensional model that can be manipulated in space; the hydrogen bonds are represented with the smoothed alpha-carbon plot of the polypeptide chain. In the other type of display, hydrogen bonds are viewed in relation to the one-dimensional sequence. Both types of picture facilitate visualization of hydrogen bond patterns, such that loop motifs, as well as alpha-helices and beta-sheets, can be examined easily. We suggest that such displays are useful as a general means of displaying whole proteins and whole domains because they reveal more information than do conventional simplified pictures of proteins, which focus exclusively on alpha-helices and beta-sheets. These techniques can be implemented on a UNIX-based computer graphics workstation. (UNIX is a trademark of Bell Telephone laboratories.)
authors.affiliation: Department of Computing Science, University of Glasgow, UK.
authors.forename: K
authors.initials: K
authors.lastname: Belhadj-Mostefa
authors.forename: R
authors.initials: R
authors.lastname: Poet
authors.forename: E J
authors.initials: EJ
authors.lastname: Milner-White
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D003546:Cysteine Endopeptidases / Q000737:chemistry; D006860:Hydrogen Bonding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins; D003546:Cysteine Endopeptidases; C018745:actinidain