IMGT Scientific chart

Rules for the gap and additional positions in C-DOMAIN and C-LIKE-DOMAIN

Introduction
A strand (positions 1.8 to 1.1,1-15)
AB turn additional positions (positions 15.1-15.3)
B strand (positions 16-26)
BC loop (positions 27-36)
C strand (positions 39-45)
CD transversal strand (positions 45.1-45.7)
D strand (positions 77-84)
DE turn additional positions (positions 84.1-84.7, 85.7-85.1)
E strand (positions 85-96)
EF turn additional positions (96.1-96.2)
F strand (positions 97-104)
FG loop (positions 105-117)
G strand (positions 118-128)

Gaps and additional positions in the C-DOMAIN and C-LIKE-DOMAIN are described by comparison to the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN.
The rules for gaps and additional positions apply to C-DOMAIN and C-LIKE-DOMAIN multiple alignments and IMGT Colliers de Perles.
Domains shown in the tables are those described in Protein displays. Gaps and additional positions have been confirmed for proteins with known 3D structures (PDB codes in Protein displays). Strand, turn and loop lengths are shown, in number of amino acids, between parentheses, in the table headers.

A strand (positions 1.8 to 1.1, 1-15)

Up to 8 additional positions may be found at the N-terminal end of the A strand. They are numbered 1.1 to 1.9, starting from position next to 1 towards the N-terminal end.
The maximal length of the A strand is 24 amino acids.
A strand gaps at the AB turn are described in Table 1.

Table 1. Length of the A and B strands and gaps at the AB turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps are equally distributed on strands A and B with, for an odd number, one more gap on strand A.

Number of gaps at the AB turn	Examples			A strand 1.8-1.1, 1-15			B strand 16-26
Number of gaps at the AB turn	Species	Gene	Domain	Number of additional positions at the N-terminus	Gap positions	A strand length (16-24)	Gap positions	B strand length (8-11)
0	Homo sapiens	IGHG1	CH1, CH3	4		19		11
0	Homo sapiens	IGHG1	CH2	6		21		11
2	Mus musculus	CD1D	C-LIKE [D3]	1	15	15	16	10
3	Homo sapiens	HLA-B	C-LIKE [D3]	1	14 15	14	16	10
4	Homo sapiens	TRAC	C-ALPHA	5	12 13 14 15	16	16	10
7	Homo sapiens	TRDC	C-DELTA	6	10 12 13 14 15	16	16 17 18	8

AB turn additional positions (positions 15.1-15.3)

C-DOMAIN and C-LIKE-DOMAIN may have additional amino acids (potentially 3) at the AB turn. The number of additional positions at the AB turn defines the AB length (Table 2).

Table 2. Length of the AB turn

Number of additional positions	Examples			AB additional positions	AB length (0-3)
Number of additional positions	Species	Gene	Domain	AB additional positions	AB length (0-3)
0	Homo sapiens	IGHG1	CH1, CH3		0
1	Homo sapiens	TRBC2	C-BETA2	15.1	1
2	Homo sapiens	IGHG1	CH2	15.1 15.2	2
3	Homo sapiens	CD4	C-LIKE [D2]	15.1 15.2 15.3	3

B strand (positions 16-26)

The maximal length of the B strand is 11 amino acids.
B strand gaps at the AB turn are described in Table 1

BC loop (positions 27-38)

The maximum length of the BC loop is 10 amino acids. If the number of amino acids is odd, there is one more amino acid position on the left (Table 3). There are no positions 32 and 33 in C-DOMAIN and C-LIKE-DOMAIN.

Table 3. Length of the BC loop

Number of gaps	Examples			BC gap positions (1)	BC length (6-10)
Number of gaps	Species	Gene	Domain	BC gap positions (1)	BC length (6-10)
0	Homo sapiens	IGHG1	CH2		10
0	Homo sapiens	IGHE	CH3		10
1	Mus musculus	IGHE	CH3	34	9
2	Homo sapiens	IGHG1	CH1, CH3	31 34	8
3	Homo sapiens	TRAC	C-ALPHA	31 34 35	7
4	Mus musculus	IGHD	CH1	30 31 34 35	6

C strand (positions 39-45)

The maximal length of the C strand is 7 amino acids.

CD transversal strand (positions 45.1-45.7)

The CD transversal strand is characteristic of the C-DOMAIN and C-LIKE-DOMAIN. In contrast, there are no C' and C" strands (that is no positions 46 to 76). The maximum length of the CD strand in the usual Collier de Perles is 7 amino acids, however CD strands of 9 amino acids are found in Teleostei IGIC (Table 4). Amino acid positions 45.1 to 45.7 are added from left to right in sequence alignments.

Table 4. Length of the CD transversal strand

Number of amino acid positions	Examples			CD additional positions	CD length (0-7)
Number of amino acid positions	Species	Gene	Domain	CD additional positions	CD length (0-7)
0	Homo sapiens	TRAC	C-ALPHA		0
1	Homo sapiens	CD4	C-LIKE [D4]	45.1	1
1	Homo sapiens	TRDC	C-DELTA	45.1	1
2	Homo sapiens	FCGR1A	C-LIKE [D1]	45.1 to 45.2	2
3	Homo sapiens	FCGR1A	C-LIKE [D2]	45.1 to 45.3	3
3	Homo sapiens	IGHG1	CH1	45.1 to 45.3	3
4	Homo sapiens	IGHG1	CH2, CH3	45.1 to 45.4	4
5	Homo sapiens	TRBC2	C-BETA2	45.1 to 45.5	5
	Homo sapiens	TRGC1	C-GAMMA1
	Homo sapiens	HLA-B	C-LIKE [D3]
6	Homo sapiens	IGHA1	CH3	45.1 to 45.6	6
7	Sus scrofa	IGHE	CH3	45.1 to 45.7	7

D strand (positions 77-84)

The maximal length of the D strand is 8 amino acids.
D strand gaps at the DE turn are described in Table 5.

Table 5. Gaps at the DE turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps at the DE turn are equally distributed on strands D an E with, for an odd number, one more gap on strand D.

Number of gaps at the DE turn	Examples			D strand 77-84		E strand 85-96
Number of gaps at the DE turn	Species	Gene	Domain	Gap positions	D strand length (5-8)	Gap positions	E strand length (10-12)
0	Homo sapiens	IGHG1	CH1, CH2, CH3		8		12
4	Homo sapiens	FCGR1A	C-LIKE [D2]	83 84	6	85 86	10
5	Homo sapiens	FCGR1A	C-LIKE [D1]	82 83 84	5	85 86	10

DE turn additional positions (positions 84.1-84.7, 85.7-85.1)

Most of the C-DOMAIN and C-LIKE-DOMAIN have additional amino acids (potentially 14) at the DE turn which extend the D and E antiparallel beta strands (Table 6). The number of additional positions at the DE turn defines the DE turn length.

Table 6. Length of the DE turn

Number of additional positions	Examples			DE additional positions (2)	DE length (6-14)
Number of additional positions	Species	Gene	Domain	DE additional positions (2)	DE length (6-14)
6	Mus musculus	IGHE	CH1	84.1 to 84.3, 85.1 to 85.3	6
4	Homo sapiens	TRDC	C-DELTA	84.1 to 84.4, 85.1 to 85.4	8
8	Homo sapiens	TRGC1	C-GAMMA1	84.1 to 84.4, 85.1 to 85.4	8
8	Homo sapiens	IGHG1	CH1, CH2, CH3	84.1 to 84.4, 85.1 to 85.4	8
9	Mus musculus	TRBC2	C-BETA2	84.1 to 84.5, 85.1 to 85.4	9
10	Canis lupus familiaris	IGHA	CH3	84.1 to 84.5, 85.1 to 85.5	10
11	Homo sapiens	IGHA1	CH3	84.1 to 84.6, 85.1 to 85.5	11
12	Homo sapiens	IGHM	CH2	84.1 to 84.6, 85.1 to 85.6	12
13	Homo sapiens	TRBC2	C-BETA2	84.1 to 84.7, 85.1 to 85.6	13
14	Homo sapiens	TRAC	C-ALPHA	84.1 to 84.7, 85.1 to 85.7	14

E strand (positions 85-96)

The maximal length of the E strand is 12 amino acids.
E strand gaps at the DE turn (gap positions 85,86 shown in italics, for Homo sapiens FCGR2A) and at the EF loop are described in Table 5 and Table 7, respectively.

Table 7. Gaps at the EF turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps are based on sequence alignments.

Number of gaps at the EF turn	Examples			E strand 85-96		F strand 97-104
Number of gaps at the EF turn	Species	Gene	Domain	Gap positions	E strand length (8-12)	Gap positions	F strand length (4-8)
0	Homo sapiens	IGHG1	CH2, CH3		12		8
1	Homo sapiens	FCGR2A	C-LIKE [D1]	85 86 96	9		8
1	Homo sapiens	IGHG1	CH1	96	11		8
2	Bos taurus	IGHG1	CH1	96	11	97	7
2	Homo sapiens	TRGC1	C-GAMMA1	96	11	97	7
3	Homo sapiens	HLA-B	C-LIKE [D3]	95 96	10	97	7
3	Rattus norvegicus	IGHG2B	CH1	91 92 (3)	10	97	7
4	Homo sapiens	TRDC	C-DELTA	95 96	10	97 98	6
4	Oryctolagus cuniculus	IGHG	CH1	95 96	10	97 98	6
8	Homo sapiens	TRAC	C-ALPHA	93 94 95 96	8	97 98 99 100	4

EF turn additional positions (96.1-96.2)

C-DOMAIN and C-LIKE-DOMAIN may have additional amino acids (potentially 2) at the EF turn. The number of additional positions defines the EF length.

Table 8. Length of the EF turn

Number of additional positions	Examples			EF additional positions	EF length (0-2)
Number of additional positions	Species	Gene	Domain	EF additional positions	EF length (0-2)
0	Homo sapiens	IGHG1	CH1, CH2, CH3		0
1	Homo sapiens	TRBC2	C-BETA2	96.1	1
2	Homo sapiens	IGHM	CH1	96.1 96.2	2

F strand (positions 97-104)

The maximal length of the F strand is 8 amino acids.
F strand gaps at the EF turn are described in Table 7.

FG loop (positions 105-117)

Except for the TRBC sequences (Table 10), the maximal length of the FG loop is 13 amino acids (Table 9). For an odd number of gaps, there is one more gap on the left (starting with position 111). TRBC sequences have an insertion of 12 positions between 111 and 112. The length of the FG loop in TRBC is 25 amino acids (Table 10).

Table 9. Length of the FG loop (except TRBC)

Number of gaps	Examples			FG gap positions	FG length (7-13)
Number of gaps	Species	Gene	Domain	FG gap positions	FG length (7-13)
0	Homo sapiens	IGHE	CH1		13
1	Mus musculus	TRAC	C-ALPHA	111	12
1	Homo sapiens	IGHG1	CH3	111	12
2	Homo sapiens	IGHG1	CH1 CH2	111 112	11
3	Homo sapiens	FCGR2A	C-LIKE [D2]	110 111 112	10
4	Ovis aries	IGHA	CH2	110 111 112 113	9
6	Homo sapiens	FCGR2A	C-LIKE [D1]	109 110 111 112 113 114	7

Table 10. Length of the FG loop of TRBC

Number of additional positions	Examples			FG additional positions (4)	FG length (25)
Number of additional positions	Species	Gene	Domain	FG additional positions (4)	FG length (25)
12	Homo sapiens	TRBC2	C-BETA2	111.1 to 111.6, 112.1 to 112.6	25
12	Mus musculus	TRBC2	C-BETA2	111.1 to 111.6, 112.1 to 112.6	25

G strand (positions 118-128)

The maximal length of the G strand is 11 amino acids. Positions are filled in, starting from position 118 and depending on the G strand length.

(1)	Gap positions start with 34, then 31, 35, 30.
(2)	The numbering of the additional positions starts positions next to 84 and 85, respectively, towards the top of the DE turn (gap positions 85, 86 shown in italics, for Homo sapiens FCGR2A). If the number of additional amino acids is odd, there is one more position on the left.
(3)	Gaps were assigned by sequence alignment with the CH1 of IGHG2A and IGHG2C CH1.
(4)	The numbering of the additional positions starts positions next to 111 and 112, respectively, towards the top of the FG loop.