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. 2007 Jul;35(Web Server issue):W473-6.
doi: 10.1093/nar/gkm423. Epub 2007 Jun 21.

PIC: Protein Interactions Calculator

K G Tina  1 , R Bhadra, N Srinivasan
Affiliations

PIC: Protein Interactions Calculator

K G Tina et al. Nucleic Acids Res. 2007 Jul.

Abstract

Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

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Figures

Figure 1.
Figure 1.
Interactions between oppositely charged amino acid sidechains in the interaction interface of cyclic dependent protein kinase 2 (CDKs) and cyclin identified using PIC server. The folds of CDK2 and cyclin and the charged residues in the interface formed by the two proteins are represented in different colours. The ion pairs are highlighted by black dotted lines. This figure is produced using SETOR (35).
Figure 2.
Figure 2.
Structure of crambin with solvent exposed and interacting apolar sidechains, recognized using PIC. Interactions between apolar sidechains is shown by green dots. Disulphide bonds are shown in yellow. This figure is produced using SETOR (35).
See this image and copyright information in PMC

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