Abstract
Table 4.1 lists all 20 proteinogenic amino acids present in peptides which interact with MHC molecules. There are different criteria for grouping amino acids, such as the size of side chains, polarity, charge or hydrophobicity. Regarding the specific characteristics that are required in one distinct contact site, usually one of the different sets of amino acids is best at meeting the needs. Although grouped into separate sets in Table 4.1, some of the amino acids are able to fulfill completely different requirements and therefore act as jokers. As an example, T belongs to the set of hydrophilic amino acids. Because of the methyl group at the end of its side chain, it may interact via hydrophobic interactions with an MHC pocket which is shaped in such a way that methyl groups fit optimally into it. In this case, T interacts similarly to aliphatic amino acids, which also have a methyl group at the end of their side chains. Another joker is Y, which belongs to the set of large aromatic/hydrophobic amino acids. Its hydroxyl group at the end of the side chain enables Y to interact by hydrogen bonding and therefore act like hydrophilic residues.
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Rammensee, HG., Bachmann, J., Stevanović, S. (1997). The Function. In: MHC Ligands and Peptide Motifs. Molecular Biology Intelligence Unit. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-22162-4_4
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