Most of the polymorphic residues in class I MHC molecules are concentrated in the alpha 1- and alpha 2-domains with their side chains pointing towards the antigen peptide site. Previous crystal structure analysis revealed six pockets inside the peptide-binding groove and the "extra" electron density in some of the pockets indicated that the pockets are involved in direct peptide binding. In order to investigate the functional role of individual positions from each pocket in antigen presentation, 37 HLA-A2 variants with single amino acid substitution in the peptide-binding groove were generated and used to analyse the specificity of influenza A virus matrix peptide-specific, HLA-A2-restricted CTL. The ability to present peptide by each variant was studied in detail by peptide titration, cold target inhibition, time course and limiting dilution analysis. The direct effect on peptide binding by these substitutions was determined by cell surface class I MHC molecule reconstitution analysis. The results demonstrated that each of the six peptide binding pockets plays a role in T cell recognition. Substitutions introduced into pocket F had less effect on CTL recognition than substitutions introduced in other pockets. With the exception of Tyr substitution for Phe9, single amino acid substitutions in the peptide-binding groove had only minor effects on peptide binding. Therefore, the impact of the substitutions in altering the epitopes recognized by CTL seems to be mediated through an alteration in the conformation of the bound peptide.