In molecular description of proteins in PDB, they can represented by different Polymers consisting variable number of chains as Insulin (PDB ID: 1XDA) forming dimers of dimer. While analyzing 3D environment of an amino acid in a particular chain to mimic physiological behavior, what is significance of other chains? The chains form dimers/multimers, Is it then necessary to eliminate other chain entries form downloaded PDB files to study single amino acid environments?
Insulin Polymer 1 consists Chains A, C, E, G. To study immediate environment of single amino acid in Chain A, my PERL program also displays amino acids form other chains as well. As the chains are dimers of dimers, would it be feasible to take into account other chains? Do these chains exist at normal physiological conditions too?