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contact sites and the previously defined pockets is more approximative. For
MHC-I with a peptide of 8-amino acids, C3, C4, C6, and C9 correspond roughly
to the B, D, C, and E pockets, and for MHC-I with a peptide of 9-amino acids C3,
C4, and C9 correspond to the B, D, and E pockets.
Table 2.
IMGT reference pMHC contact sites. (A) MHC-I. Results for 104 pMHC-I 3D struc-
tures (30 with 8-amino acid peptides and 74 with 9-amino acid peptides). (B) MHC-II. Results
from 44 pMHC-II 3D structures with 9 amino acids in the groove.
(A) MHC-I
8-amino acid peptides
G-ALPHA1
G-ALPHA2
C1
1
59 62 63 66
73 77 81
C3
2
7 24 45
9
C4
3
9 24 63 66 67 70
C5
4
C6
5
7 9 22 70 74
7 9 24 26
C9
6
59 61A 63 66
C10 7
77 73 76
C11 8
77 80 81 84
5 26 33 34 55 59
9-amino acid peptides
G-ALPHA1
G-ALPHA2
C1
1
5 59 62 63 66
73 77 81
C3
2
7 9 22 24 34 45 63 66 67 70
C4
3
7 9 24 66 67 70
C5
4
65 66
66
C6
5
70 73 74
7 26 66 67
C8
6
66 69 70 73 74
7 24 62 66
C9
7
7 24 59 61A 63 66
C10 8
72 73 76 80
58
C11 9
77 80 81 84
5 26 33 34 55 59
(B) MHC-II
G-ALPHA
G-BETA
C1
1
26 33 34 47 60 61 62
77 80 81 82 84 85
C2
2
72A 73 76
C3
3
7 24 62 63 66 67 69
C4
4
7
9 11 22 24 66 67 70 73 74
C5
5
66
C6
6
9 69 70 73 74
7 26
C9
7
24 26 45 59 63 66
C10
8
73 76
C11
9
77 80 81 84
5 33 55
