Preferred CDRH3 lengths for antibodies with defined specificities

The third complementarity determining regions of heavy chain Variable regions (CDRH3) confer the fine specificities of antibodies. The CDRH3 length distribution of all human or all mouse antibodies appears to be more or less random, with the human distribution having a wider spread. Since the Kabat database of aligned amino and nucleotide sequences of proteins of immunological interest has grown at least 4 times during the past 7 years, we attempt to study CDRH3 length distributions of human and mouse antibodies with defined specificities, where enough complete and distinct CDRH3 sequences are available. For mouse antibodies against small haptens or carbohydrates, a preferred length usually dominates for a given specificity. There are not enough human sequences of small hapten or carbohydrate antibodies for a similar study. Both human and mouse anti-protein antibodies have wider ranges of CDRH3 length distributions, probably due to the presence of different antigenic epitopes on the protein molecules, and thus many different antibodies. For anti-DNA antibodies, both humans and mice exhibit even wider length distributions, since DNA can be double stranded, single stranded, supercoiled, etc.