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Table 4.
V-ALPHA and V-BETA CDR interactions with MHC-II. TR positions in bold indi-
cate hydrogen bonds. Three dimensional (3D) structures are from IMGT/3Dstructure-DB
(Kaas et al. 2004), http://imgt.cines.fr. Lengths of the CDR-IMGT are shown within brackets.
Amino acids are shown in the one-letter code. Sequences of the peptides are reported in
Table 1, sequences of the TR V-ALPHA and V-BETA domains in Fig. 3, and sequences of the
MHC-II G-ALPHA and G-BETA in Fig. 4. (A) V-ALPHA CDR-IMGT interactions. (B) V-
BETA CDR-IMGT interactions. (C) V-ALPHA and V-BETA FR-IMGT interactions.
(A) V-ALPHA CDR-IMGT interactions
V-ALPHA CDR1-IMGT
PDB
Position G-ALPHA
Peptide
G-BETA
1j8h [6.]
28
S
2
K
76
H
29
V
2
K
4
V
76
H
36
P
4
V
72A
T
76
H
38
Y
72A
T
1d9k [6.]
27
D
3
S
28
S
72A
T
76
H
29
T
3
S
4
H
5
R
72A
T
76
H
36
F
5
R
72A
T
37
D
5
R
8
I
66
R
69
A
72A
T
38
Y
66
R
V-ALPHA CDR2-IMGT
PDB
Position G-ALPHA
Peptide
G-BETA
1j8h [.7.]
57
T
65
E
58
S
69
A
72A
T
59
A
65
E
1d9k [.6.]
57
S
65
E
66
R
69
A
58
L
69
A
72
D
72A
T
59
V
65
E
66
R
68
R
69
A
63
S
65
E
V-ALPHA CDR3-IMGT
PDB
Position G-ALPHA
Peptide
G-BETA
1j8h [.13]
108
E
63
E
2
K
4
V
110
P
7
N
66
Q
111
F
N
9
L
62
D
63
L
66
Q
114
E
66
G
69
A
70
N
5
K
1d9k [.10]
107
T
66
R
108
G
5
R
8
I
66
R
109
S
69
Q
8
I
66
R
113
F
69
Q
73
T
8
I
9
E
10
W
11
E
63
Y
66
R
114
N
69
Q
66
R
115
K
65
Q
(continued)
