Table of CDR Definitions
The Kabat definition is based on sequence variability and is the most commonly used
The Chothia definition is based on the location of the structural loop regions
The contact definition has been recently introduced by us and is based on an analysis of the available complex crystal structures. This definition is likely to be the most useful for people wishing to perform mutagenesis to modify the afinity of an antibody since these are residues which take part in interactions with antigen. Lists of CDR residues making contact in each antibody with summary data for each CDR
| Loop | Kabat | AbM | Chothia1 | Contact2 | IMGT |
|---|---|---|---|---|---|
| L1 | L24--L34 | L24--L34 | L24--L34 | L30--L36 | L27--L32 |
| L2 | L50--L56 | L50--L56 | L50--L56 | L46--L55 | L50--L51 |
| L3 | L89--L97 | L89--L97 | L89--L97 | L89--L96 | L89--L97 |
| H1 | H31--H35B (Kabat Numbering)3 |
H26--H35B | H26--H32..34 | H30--H35B | H26--H35B |
| H1 | H31--H35 (Chothia Numbering) |
H26--H35 | H26--H32 | H30--H35 | H26--H33 |
| H2 | H50--H65 | H50--H58 | H52--H56 | H47--H58 | H51--H56 |
| H3 | H95--H102 | H95--H102 | H95--H102 | H93--H101 | H93--H102 |
Note (1) some of these definitions (particularly for Chothia loops) vary depending on the individual publication examined.
Note (2) any of the numbering schemes can be used for these CDR defintions, except the contact definition uses the Chothia or Martin (Enhanced Chothia) definition.
Note (3) the end of the Chothia CDR-H1 loop when numbered using the Kabat numbering convention varies between H32 and H34 depending on the length of the loop. (This is because the Kabat numbering scheme places the insertions at H35A and H35B.). If neither H35A nor H35B is present, the loop ends at H32; If only H35A is present, the loop ends at H33; If both H35A and H35B are present, the loop ends at H34.
Reference
http://www.bioinf.org.uk/abs/info.html