Figure 5. Amino acid characteristics of coherent CDR3s.

(A, B) Separation of CDR3 clusters in the spaces bounded by principal components (Prin) 1, 2 and 3, which represent residue-by-residue scores for hydrophilicity, molecular weight and isoelectric pH for all CDR3s with V_H usage and length identical to the convergent (A) 13-mer and (B) 10-mer CDR3s. All CDR3s that cluster with the (A) 13-mer and (B) 10-mer CDR3s identified by mismatch cross-validation are highlighted; members from all other clusters are faded. The top right quadrants are magnified images of the boxed graph areas. (C) Sequences and residue-specific characteristics of V_H CDR1 regions and CDR2 regions associated with the highlighted 13-mer (top panel) and 10-mer (bottom panel) convergent CDR3 clusters. Amino acids in black, consensus residues; amino acids in red, germline-encoded residues different from consensus; *junctional residues with undeterminable germline sequence. Colored circles indicate deviations in molecular weight, isoelectric pH or hydrophilicity scores from germline encodings for CDR1 and CDR2, or from median scores computed across all CDR3s with lengths identical to the corresponding CDR3s. See also Figure S5 and Table S4.