Antibody CDR annotation

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