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Protein Engineering, Vol. 12, No. 10, 825-832, October 1999
© 1999 Oxford University Press

Spare parts for helix–helix interaction

R. Preissner, A. Goede and C. Frömmel1

Institute of Biochemistry, Charité, Medical Faculty of the Humboldt University, Monbijoustr 2, 10117 Berlin, Germany

About 6000 contact regions (patches) of helix-to-helix packing from 300 well-resolved non-homologous protein structures were considered. The patches were defined by the spatial helical neighbors and were estimated in atomic detail using a variable distance criterion. The following questions are addressed. (1) Are the amino acid preferences and atomic composition of distinct types of helical patches indicative for the type of their neighbor? Distributions of size, atomic composition and packing density are compared for different types of helical interfaces. Thereby contact preferences are derived for parts of secondary structures adjoining each other or pointing towards the solvent. (2) Is it possible to cluster helical patches according to their structural similarity? For these purposes the patches were classified with an automatic sequence-independent superposition procedure which yields a distinctively reduced set of representative interfaces. On this basis, the methodology for finding exchangeable patches in different proteins is demonstrated.

Keywords: classification/helix packing/mimicry/similarity

1 To whom correspondence should be addressed


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