To analyze the molecular basis of MHC class I allele-restricted peptide recognition, a set of eight Ld/Lq mutants was constructed and tested for peptide recognition by allele-restricted and peptide-specific CTL. The MHC molecules H-2Ld and H-2Lq differ at six amino acid positions (95, 97, 107, 116, 155, 157) located within the alpha 2 domain of the molecule. Both molecules present the lymphocytic choriomeningitis virus (LCMV) nucleoprotein-derived peptide RPQASGVYM and the murine cytomegalovirus (MCMV) pp89-derived peptide YPHFMPTNL to the respective virus-specific CD8+ CTL is a strictly allele-restricted fashion. All mutated MHC class I molecules did still bind the LCMV peptide and seven of eight mutants retained MCMV peptide binding. The exchange Arg-->Trp at position 97 of Lq in pocket C of the peptide binding groove prevented binding of the MCMV ligand and this loss was compensated by the additional exchange of Ile-->Leu in position 95 (pocket F). Within the Lq molecule, single mutations at either position 97 on the floor of the groove or position 155 of the wall sufficed for a gain of LCMV peptide recognition by Ld-restricted CTL. Altogether, six of eight mutants resulted in a gain of recognition by CTL specific for the other allele. Thus, six of the eight mutants lost MHC-restricted recognition and were accepted by both Ld- as well as Lq-restricted CTL when presenting the LCMV peptide. Only one case of simultaneous recognition of the MCMV peptide by both Ld- as well as Lq-restricted CTL was noted. In other mutations, a gain of recognition by Ld-restricted CTL was associated with a loss of recognition of Lq-restricted CTL. Analysis of extracted MCMV peptide from mutant molecules excluded quantitative differences in presented MCMV peptide as a reason for the lack of CTL recognition. Altogether, the results show that, rather than aminoacids at certain residue positions, individual peptides govern MHC allele specificity of CTL recognition.