Displaying inter-main chain hydrogen bond patterns in proteins.

K Belhadj-Mostefa; R Poet; E J Milner-White

doi:10.1016/0263-7855(91)80010-w

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Displaying inter-main chain hydrogen bond patterns in proteins.

K Belhadj-Mostefa·R Poet·E J Milner-White

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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.)

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K Belhadj-Mostefa, R Poet, E J Milner-White. 1991. Displaying inter-main chain hydrogen bond patterns in proteins.. https://doi.org/10.1016/0263-7855(91)80010-w

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