IMGT Scientific chart

IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN

Citing IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN:
Lefranc, M.-P., Immunology Today, 18, 509 (1997) PMID: 9386342
Lefranc, M.-P., The Immunologist, 7, 132-136 (1999)

Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003) PMID: 12477501

with permission from Elsevier

IMGT unique numbering for V-DOMAIN
IMGT unique numbering for V-LIKE-DOMAIN

Correspondence between the IMGT unique Lefranc numbering and the different Kabat numberings (vertical display of examples) 1997
Correspondence between the IMGT unique Lefranc numbering and the different numberings (horizontal display) 1998
Correspondence between numberings for CDR of different lengths (horizontal display) 2001
IMGT unique numbering (Lefranc) and structural correspondence for the different CDR-IMGT lengths with the diverse Kabat/Chothia numberings and CDR/loop delimitations (horizontal display per locus) 2008

'IMGT Protein display for V domain' header:

The V-DOMAIN corresponds to the V-J-REGION and V-D-J-REGION of the immunoglobulin (IG) and T cell receptor (TR) chains.
The V-LIKE-DOMAIN corresponds to a domain of similar structure as V-DOMAIN, found in chains other than IG or TR.

IMGT unique numbering for V-DOMAIN

The IMGT numbering for V-DOMAIN (IG and TR) is derived from the princeps of IMGT unique numbering for V-REGION [1]. Up to position 104, the IMGT unique numbering for V-DOMAIN follows that numbering.

The IMGT unique numbering has been defined to compare the variable domains whatever the antigen receptor, the chain type, or the species [1-3]. In the IMGT unique numbering, the conserved amino acids always have the same position, for instance cysteine 23 (1st-CYS), tryptophan 41 (CONSERVED-TRP), hydrophobic amino acid 89, cysteine 104 (2nd-CYS), phenylalanine or tryptophan 118 (J-PHE or J-TRP). The IMGT unique numbering provides a standardized delimitation of the framework regions (FR1-IMGT: positions 1 to 26, FR2-IMGT: 39 to 55, FR3-IMGT: 66 to 104 and FR4-IMGT: 118 to 128) and of the complementarity determining regions: CDR1-IMGT: 27 to 38, CDR2-IMGT: 56 to 65 and CDR3-IMGT: 105 to 117. As gaps represent unoccupied positions, the CDR-IMGT lengths (shown between brackets and separated by dots, e.g. [8.8.13]) become crucial information. The IMGT unique numbering is used in 2D graphical representations, designated as IMGT Colliers de Perles [4, 5], and in 3D structures in IMGT/3Dstructure-DB [6].

Gaps in the CDR1-IMGT and CDR2-IMGT (less than 12 and 10 amino acid long, respectively) are put at the top of the CDR-IMGT loops, as in IMGT/3Dstructure-DB (gaps shown as dashes, in the table below).

CDR1-IMGT lengths	CDR1-IMGT 27-38
CDR1-IMGT lengths	(5-12)
12	27	28	29	30	31	32	33	34	35	36	37	38
11	27	28	29	30	31	32	-	34	35	36	37	38
10	27	28	29	30	31	-	-	34	35	36	37	38
9	27	28	29	30	31	-	-	-	35	36	37	38
8	27	28	29	30	-	-	-	-	35	36	37	38
7	27	28	29	30	-	-	-	-	-	36	37	38
6	27	28	29	-	-	-	-	-	-	36	37	38
5	27	28	29	-	-	-	-	-	-	-	37	38

CDR2-IMGT lengths	CDR2-IMGT 56-65
CDR2-IMGT lengths	(0-10)
10	56	57	58	59	60	61	62	63	64	65
9	56	57	58	59	60	-	62	63	64	65
8	56	57	58	59	-	-	62	63	64	65
7	56	57	58	59	-	-	-	63	64	65
6	56	57	58	-	-	-	-	63	64	65
5	56	57	58	-	-	-	-	-	64	65
4	56	57	-	-	-	-	-	-	64	65
3	56	57	-	-	-	-	-	-	-	65
2	56	-	-	-	-	-	-	-	-	65
1	56	-	-	-	-	-	-	-	-	-
0	-	-	-	-	-	-	-	-	-	-

The basic length of a rearranged CDR3-IMGT is 13 amino acids (positions 105 to 117), which corresponds to a JUNCTION of 15 amino acids (2nd-CYS 104 to J-TRP or J-PHE 118).

This length and corresponding numbering were chosen since they are convenient to use. Indeed, 80% of the IG and TR rearranged sequences in IMGT/LIGM-DB have a CDR3-IMGT length less than or equal to 13 amino acids.

If the CDR3-IMGT length is less than 13 amino acids, gaps are created from the top of the loop, in the following order 111, 112, 110, 113, 109, 114, etc.

CDR3-IMGT lengths	Gaps for CDR3-IMGT lengths < 13 amino acids
13	105	106	107	108	109	110	111	112	113	114	115	116	117
12	105	106	107	108	109	110	-	112	113	114	115	116	117
11	105	106	107	108	109	110	-	-	113	114	115	116	117
10	105	106	107	108	109	-	-	-	113	114	115	116	117
9	105	106	107	108	109	-	-	-	-	114	115	116	117
8	105	106	107	108	-	-	-	-	-	114	115	116	117
7	105	106	107	108	-	-	-	-	-	-	115	116	117
6	105	106	107	-	-	-	-	-	-	-	115	116	117
5	105	106	107	-	-	-	-	-	-	-	-	116	117
---

If the CDR3-IMGT length is more than 13 amino acids, additional positions are created between positions 111 and 112 at the top of the CDR3-IMGT loop in the following order 112.1,111.1, 112.2, 111.2, 112.3, 111.3, etc.
Additional positions are given below for CDR3-IMGT lengths 14-31, 32-51, 52-71 and 72-91.

CDR3-IMGT lengths	1. Additional positions between 111.1 and 112.1 for CDR3-IMGT lengths 14-31
31	111	111.1	111.2	111.3	111.4	111.5	111.6	111.7	111.8	111.9	112.9	112.8	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
30	111	111.1	111.2	111.3	111.4	111.5	111.6	111.7	111.8	-	112.9	112.8	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
29	111	111.1	111.2	111.3	111.4	111.5	111.6	111.7	111.8	-	-	112.8	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
28	111	111.1	111.2	111.3	111.4	111.5	111.6	111.7	-	-	-	112.8	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
27	111	111.1	111.2	111.3	111.4	111.5	111.6	111.7	-	-	-	-	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
26	111	111.1	111.2	111.3	111.4	111.5	111.6	-	-	-	-	-	112.7	112.6	112.5	112.4	112.3	112.2	112.1	112
25	111	111.1	111.2	111.3	111.4	111.5	111.6	-	-	-	-	-	-	112.6	112.5	112.4	112.3	112.2	112.1	112
24	111	111.1	111.2	111.3	111.4	111.5	-	-	-	-	-	-	-	112.6	112.5	112.4	112.3	112.2	112.1	112
23	111	111.1	111.2	111.3	111.4	111.5	-	-	-	-	-	-	-	-	112.5	112.4	112.3	112.2	112.1	112
22	111	111.1	111.2	111.3	111.4	-	-	-	-	-	-	-	-	-	112.5	112.4	112.3	112.2	112.1	112
21	111	111.1	111.2	111.3	111.4	-	-	-	-	-	-	-	-	-	-	112.4	112.3	112.2	112.1	112
20	111	111.1	111.2	111.3	-	-	-	-	-	-	-	-	-	-	-	112.4	112.3	112.2	112.1	112
19	111	111.1	111.2	111.3	-	-	-	-	-	-	-	-	-	-	-	-	112.3	112.2	112.1	112
18	111	111.1	111.2	-	-	-	-	-	-	-	-	-	-	-	-	-	112.3	112.2	112.1	112
17	111	111.1	111.2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.2	112.1	112
16	111	111.1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.2	112.1	112
15	111	111.1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.1	112
14	111	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.1	112
Code number		1	2	3	4	5	6	7	8	9	9	8	7	6	5	4	3	2	1

CDR3-IMGT lengths	2. Additional positions between 111.10 and 112.10 for CDR3-IMGT lengths 32-51
51	111.10	111.11	111.12	111.13	111.14	111.15	111.16	111.17	111.18	111.19	112.19	112.18	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
50	111.10	111.11	111.12	111.13	111.14	111.15	111.16	111.17	111.18	-	112.19	112.18	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
49	111.10	111.11	111.12	111.13	111.14	111.15	111.16	111.17	111.18	-	-	112.18	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
48	111.10	111.11	111.12	111.13	111.14	111.15	111.16	111.17	-	-	-	112.18	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
47	111.10	111.11	111.12	111.13	111.14	111.15	111.16	111.17	-	-	-	-	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
46	111.10	111.11	111.12	111.13	111.14	111.15	111.16	-	-	-	-	-	112.17	112.16	112.15	112.14	112.13	112.12	112.11	112.10
45	111.10	111.11	111.12	111.13	111.14	111.15	111.16	-	-	-	-	-	-	112.16	112.15	112.14	112.13	112.12	112.11	112.10
44	111.10	111.11	111.12	111.13	111.14	111.15	-	-	-	-	-	-	-	112.16	112.15	112.14	112.13	112.12	112.11	112.10
43	111.10	111.11	111.12	111.13	111.14	111.15	-	-	-	-	-	-	-	-	112.15	112.14	112.13	112.12	112.11	112.10
42	111.10	111.11	111.12	111.13	111.14	-	-	-	-	-	-	-	-	-	112.15	112.14	112.13	112.12	112.11	112.10
41	111.10	111.11	111.12	111.13	111.14	-	-	-	-	-	-	-	-	-	-	112.14	112.13	112.12	112.11	112.10
40	111.10	111.11	111.12	111.13	-	-	-	-	-	-	-	-	-	-	-	112.14	112.13	112.12	112.11	112.10
39	111.10	111.11	111.12	111.13	-	-	-	-	-	-	-	-	-	-	-	-	112.13	112.12	112.11	112.10
38	111.10	111.11	111.12	-	-	-	-	-	-	-	-	-	-	-	-	-	112.13	112.12	112.11	112.10
37	111.10	111.11	111.12	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.12	112.11	112.10
36	111.10	111.11	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.12	112.11	112.10
35	111.10	111.11	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.11	112.10
34	111.10	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.11	112.10
33	111.10	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.10
32	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.10
Code number	0	1	2	3	4	5	6	7	8	9	9	8	7	6	5	4	3	2	1	0

CDR3-IMGT lengths	3. Additional positions between 111.20 and 112.20 for CDR3-IMGT lengths 52-71
71	111.20	111.21	111.22	111.23	111.24	111.25	111.26	111.27	111.28	111.29	112.29	112.28	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
70	111.20	111.21	111.22	111.23	111.24	111.25	111.26	111.27	111.28	-	112.29	112.28	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
69	111.20	111.21	111.22	111.23	111.24	111.25	111.26	111.27	111.28	-	-	112.28	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
68	111.20	111.21	111.22	111.23	111.24	111.25	111.26	111.27	-	-	-	112.28	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
67	111.20	111.21	111.22	111.23	111.24	111.25	111.26	111.27	-	-	-	-	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
66	111.20	111.21	111.22	111.23	111.24	111.25	111.26	-	-	-	-	-	112.27	112.26	112.25	112.24	112.23	112.22	112.21	112.20
65	111.20	111.21	111.22	111.23	111.24	111.25	111.26	-	-	-	-	-	-	112.26	112.25	112.24	112.23	112.22	112.21	112.20
64	111.20	111.21	111.22	111.23	111.24	111.25	-	-	-	-	-	-	-	112.26	112.25	112.24	112.23	112.22	112.21	112.20
63	111.20	111.21	111.22	111.23	111.24	111.25	-	-	-	-	-	-	-	-	112.25	112.24	112.23	112.22	112.21	112.20
62	111.20	111.21	111.22	111.23	111.24	-	-	-	-	-	-	-	-	-	112.25	112.24	112.23	112.22	112.21	112.20
61	111.20	111.21	111.22	111.23	111.24	-	-	-	-	-	-	-	-	-	-	112.24	112.23	112.22	112.21	112.20
60	111.20	111.21	111.22	111.23	-	-	-	-	-	-	-	-	-	-	-	112.24	112.23	112.22	112.21	112.20
59	111.20	111.21	111.22	111.23	-	-	-	-	-	-	-	-	-	-	-	-	112.23	112.22	112.21	112.20
58	111.20	111.21	111.22	-	-	-	-	-	-	-	-	-	-	-	-	-	112.23	112.22	112.21	112.20
57	111.20	111.21	111.22	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.22	112.21	112.20
56	111.20	111.21	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.22	112.21	112.20
55	111.20	111.21	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.21	112.20
54	111.20	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.21	112.20
53	111.20	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.20
52	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.20
Code number	0	1	2	3	4	5	6	7	8	9	9	8	7	6	5	4	3	2	1	0

CDR3-IMGT lengths	4. Additional positions between 111.30 and 112.30 for CDR3-IMGT lengths 72-91
91	111.30	111.31	111.32	111.33	111.34	111.35	111.36	111.37	111.38	111.39	112.39	112.38	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
90	111.30	111.31	111.32	111.33	111.34	111.35	111.36	111.37	111.38	-	112.39	112.38	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
89	111.30	111.31	111.32	111.33	111.34	111.35	111.36	111.37	111.38	-	-	112.38	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
88	111.30	111.31	111.32	111.33	111.34	111.35	111.36	111.37	-	-	-	112.38	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
87	111.30	111.31	111.32	111.33	111.34	111.35	111.36	111.37	-	-	-	-	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
86	111.30	111.31	111.32	111.33	111.34	111.35	111.36	-	-	-	-	-	112.37	112.36	112.35	112.34	112.33	112.32	112.31	112.30
85	111.30	111.31	111.32	111.33	111.34	111.35	111.36	-	-	-	-	-	-	112.36	112.35	112.34	112.33	112.32	112.31	112.30
84	111.30	111.31	111.32	111.33	111.34	111.35	-	-	-	-	-	-	-	112.36	112.35	112.34	112.33	112.32	112.31	112.30
83	111.30	111.31	111.32	111.33	111.34	111.35	-	-	-	-	-	-	-	-	112.35	112.34	112.33	112.32	112.31	112.30
82	111.30	111.31	111.32	111.33	111.34	-	-	-	-	-	-	-	-	-	112.35	112.34	112.33	112.32	112.31	112.30
81	111.30	111.31	111.32	111.33	111.34	-	-	-	-	-	-	-	-	-	-	112.34	112.33	112.32	112.31	112.30
80	111.30	111.31	111.32	111.33	-	-	-	-	-	-	-	-	-	-	-	112.34	112.33	112.32	112.31	112.30
79	111.30	111.31	111.32	111.33	-	-	-	-	-	-	-	-	-	-	-	-	112.33	112.32	112.31	112.30
78	111.30	111.31	111.32	-	-	-	-	-	-	-	-	-	-	-	-	-	112.33	112.32	112.31	112.30
77	111.30	111.31	111.32	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.32	112.31	112.30
76	111.30	111.31	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.32	112.31	112.30
75	111.30	111.31	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.31	112.30
74	111.30	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.31	112.30
73	111.30	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.30
72	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	112.30
Code number	0	1	2	3	4	5	6	7	8	9	9	8	7	6	5	4	3	2	1	0

Code number is the code used when the full position cannot be displayed:

CDR3-IMGT length 14-31

111.1-111.9
123456789

112.9-112.1
987654321

CDR3-IMGT length 32-51

111.1-111.9
123456789

111.10-111.19
0123456789

112.19-112.10
9876543210

112.9-112.1
987654321

CDR3-IMGT length 52-71

111.1-111.9
123456789

111.10-111.19
0123456789

111.20-111.29
0123456789

112.29-112.20
9876543210

112.19-112.10
9876543210

112.9-112.1
987654321

CDR3-IMGT length 72-91

111.1-111.9
123456789

111.10-111.19
0123456789

111.20-111.29
0123456789

111.30-111.39
0123456789

112.39-112.30
9876543210

112.29-112.20
9876543210

112.19-112.10
9876543210

112.9-112.1
987654321

The IMGT unique numbering for V-DOMAIN is used in IMGT Colliers de Perles [2], IMGT Protein displays, and 3D representations of the V-J-REGION and V-D-J-REGION of the immunoglobulin and T cell receptor chains. The same rules are used for both the numbering of the CDR3-IMGT of V-DOMAIN and the numbering of the FG loop of C-DOMAIN. Indeed, we showed that the hydrogen bonds between 2nd-CYS 104 and position 119 in the C-DOMAIN correspond structurally to the hydrogen bonds between 2nd-CYS 104 and the Glycine which follows the J-TRP or J-PHE in the J-REGION (and therefore numbered as Glycine 119) [1]. The IMGT unique numbering for V-DOMAIN and the IMGT unique numbering for C-DOMAIN allow therefore, for the first time, to compare the length and the structure of the CDR3-IMGT of V-DOMAIN with the FG loop of C-DOMAIN.

IMGT unique numbering for V-LIKE-DOMAIN

The IMGT unique numbering for V-LIKE-DOMAIN (proteins other than IG or TR) follows exactly the same rules as those of the IMGT unique numbering for V-DOMAIN [1].

Positions 118 and 119 are identified by amino acid sequence alignment. Analysis of the 3D structure may be useful to identify position 119 which usually has hydrogen bonds to 2nd-CYS 104.

[1]	Lefranc M.-P., "Unique database numbering system for immunogenetic analysis" Immunology Today, 18, 509 (1997). PMID: 9386342
[2]	Lefranc M.-P., "The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains" The Immunologist, 7, 132-136 (1999).
[3]	Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc, G., "IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains" Dev. Comp. Immunol., 27, 55-77 (2003). PMID: 12477501
[4]	Ruiz, M. and Lefranc, M.-P. "IMGT gene identification and Colliers de Perles of human immunoglobulin with known 3D structures" Immunogenetics, 53, 857-883 (2002). PMID: 11862387
[5]	Kaas, Q. and Lefranc, M.-P. "IMGT Colliers de Perles: standardized sequence-structure representations of the IgSF and MhcSF superfamily domains" Current Bioinformatics, 2, 21-30 (2007).
[6]	Kaas, Q., Ruiz, M. and Lefranc, M.-P. "IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data" Nucl. Acids. Res., 32, D208-D210 (2004). PMID: 14681396