Systematic analysis of CDR contacts and pairing constraints between T cell receptor <i>αβ</i> chains

Abstract Motivation The six complementarity determining regions (CDRs) of the T cell receptor (TCR) form multiple contacts with cognate peptide and major histocompatibility complex, thus determining antigen specificity. However, the contacts between the CDRs themselves are less understood. Results Our systematic study of all available TCR crystallographic structures identified consistent patterns of intra- and inter-chain CDR contacts in both free and antigen-bound TCRs. In addition, the protein sequences of TCRα and TCRβ from sets of TCRs which recognise a shared antigen shared mutual information and were not independent. As a result, sequence-based models can partially predict TCRα/TCRβ pairing de novo. The conserved patterns of CDR amino acid contacts, and the mutual sequence constraints between antigen-specific sets of TCR α and β chains represent an under-appreciated element of TCR structure, which may play an important role in T cell antigen recognition. Availability and Implementation The code and data necessary to reproduce the analyses are available at https://github.com/mm523/TCRab-pairing. Supplementary Information Supplementary data are available at Bioinformatics online.