Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures

The present work describes the computer program Hom-Bond, which allows to identify and compare intra-molecular interactions performed by side chain polar atoms as observed in a family of homologous protein structures with known and conserved 3-D conformation. For this purpose, the side chain to side chain and the side chain to main chain hydrogen bonds, the disulfide and the salt bridges are identified in each considered protein structure. Subsequently, the side chain interactions are displayed according to the multiple sequence alignment. The presented approach allows to easily identify bonds which are conserved in homologous proteins and to analyse rearrangements of the network of side chain interactions that characterize each protein structure.