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DeLisi 1997). Peptide/MHC binding prediction and epitope prediction remain a
big challenge. In order to compare data from different MHC sequences and 3D
structures, the IMGT unique numbering for G-DOMAIN has been set up
(Lefranc et al. 2005b) (Figs. 4 and 5). This has allowed to graphically represent,
in the IMGT Colliers de Perles for G-DOMAIN (Fig. 5), the MHC amino acid
positions that have contacts with the peptide side chains. Eleven IMGT pMHC
contact sites were defined (C1 to C11, in Figs. 6-8) which can be used to com-
pare pMHC interactions (Kaas and Lefranc 2005). Examples of contact sites for
an MHC-I binding an 8-mer peptide (1jtr), for an MHC-I binding a 9-mer pep-
tide (1ao7), and for an MHC-II binding the nine amino acids of a peptide (1j8h)
are shown in Figs. 6, 7, and 8, respectively.
In contrast to previous attempts to define pockets (Zhang, Anderson, and De-
Lisi 1998), structural data for defining the IMGT pMHC contact sites take into
account the length of the peptides and are considered independently of the MHC
class and sequence polymorphisms. The interactions between the peptide amino
acid side chains and MHC amino acids were computed using an interaction scor-
ing scheme based on true mean energy ratio (Kaas and Lefranc 2005). All direct
contacts (defined with a cutoff equal to the sum of the atom van der Waals radii
and of the diameter of a water molecule) and water-mediated hydrogen bonds
were taken into account for the definition of the IMGT pMHC contact sites
(Kaas and Lefranc 2005). The analysis was carried out for the pMHC available
in IMGT/3Dstructure-DB (Kaas et al. 2004), http://imgt.cines.fr. One hundred
fourteen 3D structures with peptides of 8, 9, and 10 amino acids bound to MHC-I
and forty-four 3D structures of pMHC-II were identified. The contact analysis
was performed for the peptide amino acid side chains of the 9 amino acids lo-
cated in the groove. Results for MHC-I with 8-amino acid peptides (30 pMHC-I
3D structures), MHC-I with 9-amino acid peptides (74 pMHC-I 3D structures),
and MHC-II for the 9 amino acids located in the groove (44 pMHC-II 3D struc-
tures) are reported in Table 2 (the results for the 10 pMHC-I with 10-amino acid
peptides are not shown). These “IMGT reference pMHC contact sites” are also
available as IMGT Colliers de Perles. They will be updated as the number of 3D
structures increases. IMGT Colliers de Perles for IMGT pMHC contact sites are
provided for each individual pMHC and TR/pMHC entry in IMGT/3Dstructure-
DB. They allow easy identification of the amino acid contacts between the MHC
and the peptide amino acid side chains and comparison of them with the “IMGT
reference pMHC contact sites”.
C1 to C11 refer to the 11 IMGT pMHC contact sites (Kaas and Lefranc
2005). 1 to 9 refer to the numbering of the peptide amino acids in the groove.
The peptide binding mode to MHC-I is characterized by the N and C peptide
ends docked deeply with C1 and C11 contact sites that correspond to the two
conserved pockets A and F, and by the peptide length that mechanically con-
strains the peptide conformation in the groove. There are no C2, C7, and C8
contact sites for MHC-I with 8-amino acid peptides and no C2 and C7 contact
sites for MHC-I with 9-amino acid peptides. In contrast, for MHC-II, C2 is pre-
sent but there are no C7 and C8. Whereas C1 and C11 correspond to the
conserved pockets A and F, respectively, the correspondence between the other
