Antibody-Antigen Interactions

To determine which residues are involved in antibody-antigen contacts, the antibody-antigen complex structures in the PDB were sorted according to the type of antigen into Hapten-binders (small molecules), Oligomer-binders (peptides and polysaccharidess) and protein binders. The PDB files were dissected into separate files containing VL, VH, Antigen, FV (VL+VH) and the antigen complex (FV+Antigen). For each of the files, the residue solvent accessible surface was calculated using the program NACCESS. Using the macros provided on this site, the residues contributing to the antigen binding interface were identified by comparing the solvent accessible surface of each residue in the FV-Antigen complex to that of the FV alone. In the same way, the residues contributing to the VL/VH dimer interface, to the VL/CL interface, to the VH/CH interface and to the CL/CH dimer interface were identified.