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ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structures at different distance threshold



Ahmad Firoz1*, Adeel Malik1, Obaid Afzal2, Vivekanand Jha1, 3*



1Biomedical Informatics Center, PGIMER, Chandigarh, India; 2Faculty of Pharmacy, Jamia Hamdard, New Delhi, India; 3Department of Nephrology, PGIMER, Chandigarh, India


E-mail*; * Corresponding author


Article Type






received  May8, 2010; accepted  June8, 2010; published online July6, 2010




To investigate the functional sites on a protein and the prediction of binding sites (residues) in proteins, it is often required to identify the binding site residues at different distance threshold from protein three dimensional (3D) structures. For the study of a particular protein chain and its interaction with the ligand in complex form, researchers have to parse the output of different available tools or databases for finding binding-site residues. Here we have developed a tool for calculating amino acid contact distances in proteins at different distance threshold from the 3D-structure of the protein. For an input of protein 3D-structure, ContPro can quickly find all binding-site residues in the protein by calculating distances and also allows researchers to select the different distance threshold, protein chain and ligand of interest. Additionally, it can also parse the protein model (in case of multi model protein coordinate file) and the sequence of selected protein chain in Fasta format from the input 3D-structure. The developed tool will be useful for the identification and analysis of binding sites of proteins from 3D-structure at different distance thresholds.




It can be accessed at:





Firoz et al. Bioinformation 5(2) 55-57 (2010)


Edited by


P. Kangueane








Biomedical Informatics




This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.