Nucleic Acids Research, 2007, Vol. 35, Web Server issue W475 proteins. The aromatic–aromatic, aromatic–sulphur and cation–p interactions are recognized between appropriate sidechains using the criteria proposed by Burley and Petsko (17), Reid et al. (18) and Satyapriya and Vishveshwara (19), respectively. Disulphide bonds are recognized using the distance criteria employed originally in the MODIP program (31). Hydrogen bonds are recognized using HBOND routine developed by Overington et al. (32) and described in Mizuguchi et al. (33). The hydrogen bonds are categorized as main chain– main chain, main chain– sidechain and sidechain–side- chain. Only standard hydrogen bonds are recognized in PIC as NCI server (30) is available for identiﬁcation of interactions such as C–H . . . O. Interactions between hydrophobic sidechains are identiﬁed using a distance cut-oﬀ of 5 A˚ between apolar groups in the apolar sidechains. Though various interactions are recognized using the standard criteria, user has an option of changing the distance cut-oﬀ in recognizing any of the types of interactions. CONCLUSIONS Analysing the interactions that stabilize tertiary and quaternary structures and protein–protein complexes is a common situation in structural biology. For example, a structure just solved using X-ray analysis or nuclear magnetic resonance may be subjected to such an analysis. In protein engineering and design experiments, a good understanding of the structural roles of various residues is essential before taking decisions on residues to mutate by site-directed mutagenesis and the replacing residue. Use of combinations of features available in PIC such as various kinds of interactions and solvent exposure or buried nature or depths of residues is also expected to aid recognition of common and uncommon structural fea- tures in a given protein structure. 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