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Nucleic Acids Research, Vol 25, Issue 24 4940-4945, Copyright © 1997 by Oxford University Press

ARTICLES

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions

NM Luscombe, RA Laskowski and JM Thornton
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK.

Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar- phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.
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