H3-rules: identification of CDR-H3 structures in antibodies.

For the third complementarity determining region of the antibody heavy chain (CDR-H3), we propose the 'H3-rules', which should identify the tertiary structure from the amino acid sequence of the CDR-H3 segment. A total of 100 CDR-H3 segments from well-determined crystal structures were analyzed. Distinctive relationships between the structures and the sequences were revealed from 55 segments, and the rules were examined for the other 45 segments and were verified. In some antibodies, basic residues at specific positions were revealed to be notable signals, with their ability to form salt bridges and to assume conformations inconsistent with the rules.