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Do the different types and sizes of antigen make use of different CDRs or CDR residues? We have divided the antibody-antigen interfaces into three groups based on interface size (see Methods), but these also relate to antigen type as follows: small = haptens; medium = peptides, carbohydrates, nucleic acids; large = proteins, cyclosporin A (a cyclic peptide), and we generally refer to antigen classes by this size definition. The line graphs in Figures 2.1 & 2.2 show the differing contributions made by the three sizes of antigen.
As expected, we observe a preference for large antigens (thin solid lines in Figures 2.1 & 2.2) to contact residues at the extremities of the combining site, for example most of CDR-L2 and residues H30 to H32 in CDR-H1. Larger antigens also interact more with apical loop residues (for example residues L92 to L94 in CDR-L3). Conversely, at a number of central, non-apical CDR positions (L91, L96, H50) contacts are common with all antigen types. However, of the 9 antigens contacted by residue H35, 6 are haptens (see previous section for a discussion of the solvent accessibility of this residue).