Structural classification of CDR-H3 in antibodies.

Large varieties in the lengths and the amino acid sequences of the third complementarity determining region of the antibody heavy chain (CDR-H3) have made it difficult to establish a relationship between the sequences and the tertiary structures, in contrast to the other CDRs, which are classified by their canonical structures. A total of 55 CDR-H3 segments from well determined crystal structures were analyzed, and we have derived several remarkable rules, which could partly govern the CDR-H3 conformation dependence on the sequence. Since the rules are physically reasonable, they are expected to be applicable to structural modeling and design of antibodies.