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Protein Engineering, Vol. 12, No. 12, 1055-1062, December 1999
© 1999 Oxford University Press

Analysis and prediction of inter-strand packing distances between ß-sheets of globular proteins

Hampapathalu A. Nagarajaram1, Boojala V.B. Reddy2 and Tom L. Blundell1,3

1 Department of Biochemistry, 80, Tennis Court Road, Old Addenbrooks Site, Cambridge CB2 1GA, UK and 2 Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India

Any two ß-strands belonging to two different ß-sheets in a protein structure are considered to pack interactively if each ß-strand has at least one residue that undergoes a loss of one tenth or more of its solvent contact surface area upon packing. A data set of protein 3-D structures (determined at 2.5 Å resolution or better), corresponding to 428 protein chains, contains 1986 non-identical pairs of ß-strands involved in interactive packing. The inter-axial distance between these is significantly correlated to the weighted sum of the volumes of the interacting residues at the packing interface. This correlation can be used to predict the changes in the inter-sheet distances in equivalent ß-sheets in homologous proteins and, therefore, is of value in comparative modelling of proteins.

Keywords: ß-strand packing/comparative modelling/helix packing/protein data analysis/structure prediction

3 To whom correspondence should be addressed.E-mail: tom{at}cryst.bioc.cam.ac.uk


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