... class II molecules. As a result, class I molecules can accommodate peptides that are 8 to 11 residues long whereas class II molecules optimally bind peptides with a length of 12 to 16 residues. One way in which the molecular interaction between peptide and MHC has been studied is by introducing mutations in an immunogenic peptide. With this technique, it is possible to identify certain residues that make contact with the MHC molecule and others that are essential for TCR recognition. Together with the evidence presented above, this has lead to the idea that MHC molecules only recognize certain anchor residues of the bound peptide. Typically, a MHC I molecule has been found to have six pockets (A-F) which bind certain AA residues of the peptide. Two or three of these pockets (in MHC I often B and F) are particularly important in binding the residues that serve as anchors. Similar ...

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