Fig. 4.

Average amino acid frequencies in antibodies. (a) Average amino acid frequencies in the paratope. The frequencies were obtained by calculating the frequency of each amino acid relative to the total number of uPRs in the individual PDB files. The average frequency was then found for each of the three groups of Ab-Ag complexes. (b) Average frequencies of uPRs in the binding interface grouped according to the type of amino acids. The frequencies were calculated similar to pane (a) and then grouped as non-polar (ALA, VAL, PRO, LEU, ILE, TRP, PHE), polar (SER, THR, TYR, ASN, GLN), positively charged (LYS, HIS, ARG), negatively charged (GLU, ASP) or special (GLY, CYS, MET). (c) Average amino acid frequencies in VH (left) and VL (right). The frequencies were calculated from amino acid usage in the given domain relative to total number of uPRs in that domain i.e., the frequencies sum to 100% for each domain. All frequencies were calculated on the uPRs to avoid any bias towards multi-contact residues. Error bars represent 95% confidence intervals.