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Analysis of interactive packing of secondary structural elements in α/β units in proteins

Published online by Cambridge University Press:  01 March 1999

BOOJALA V.B. REDDY
Affiliation:
Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
HAMPAPATHALU A. NAGARAJARAM
Affiliation:
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooks Site, Cambridge CB2 1GA, United Kingdom
TOM L. BLUNDELL
Affiliation:
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooks Site, Cambridge CB2 1GA, United Kingdom
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Abstract

An α-helix and a β-strand are said to be interactively packed if at least one residue in each of the secondary structural elements loses 10% of its solvent accessible contact area on association with the other secondary structural element. An analysis of all such 5,975 nonidentical α/β units in protein structures, defined at ≤2.5 Å resolution, shows that the interaxial distance between the α-helix and the β-strand is linearly correlated with the residue-dependent function, log[(V/nda)/n-int], where V is the volume of amino acid residues in the packing interface, nda is the normalized difference in solvent accessible contact area of the residues in packed and unpacked secondary structural elements, and n-int is the number of residues in the packing interface. The β-sheet unit (βu), defined as a pair of adjacent parallel or antiparallel hydrogen-bonded β-strands, packing with an α-helix shows a better correlation between the interaxial distance and log(V/nda) for the residues in the packing interface. This packing relationship is shown to be useful in the prediction of interaxial distances in α/β units using the interacting residue information of equivalent α/β units of homologous proteins. It is, therefore, of value in comparative modeling of protein structures.

Type
Research Article
Copyright
© 1999 The Protein Society

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