alexa IntGeom: A Server for the Calculation of the Interaction Geometry between Planar Groups in Proteins
ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
Open Access

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Research Article

IntGeom: A Server for the Calculation of the Interaction Geometry between Planar Groups in Proteins

Arumay Pal1, Rajasri Bhattacharyya1,2,3, Maitrayee Dasgupta1,2, Saptarshi Mandal1 and Pinak Chakrabarti1,2*

1Department of Biochemistry

2Biotechnology Department, Barkatullah University, Bhopal-462026, India

3Present address: Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India

*Corresponding Author:
Dr. Pinak Chakrabarti
Bioinformatics Centre,
Bose Institute, P-1/12 CIT Scheme VIIM
Calcutta 700 054, India
Tel: +91-33-2355-0256,
Fax: +91-33-2355-3886,
E-mail: [email protected]

Received Date: December 17, 2008; Accepted Date: January 15, 2009; Published Date: January 15, 2009

Citation: Arumay P, Rajasri B, Maitrayee D, Saptarshi M, Pinak C (2009) IntGeom: A Server for the Calculation of the Interaction Geometry between Planar Groups in Proteins. J Proteomics Bioinform 2:060-063. doi:10.4172/jpb.1000061

Copyright: © 2009 Arumay P, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.



IntGeom is a server for the calculation of the relative orientation between any two planar groups in protein side chains. IntGeom1 considers ten planar groups, while IntGeom2 is meant for studying the contact between a S-containing group and an aromatic residue. When the interaction is between two aromatic residues or involving an aromatic ring with Pro or Arg or an amide side chain, the occurrence of any C−H⋅⋅⋅π (N−H⋅⋅⋅π) interaction is also studied. All contacts between any two of the above types of residues juxtaposed on the protein structure can be displayed. The software is available at:


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