The T lineage repertoire is shaped by opposing processes of positive and negative selection. To probe the specificity of selection, N15 TCR-transgenic (tg) recombinase-activating gene (RAG)-2(- / -) H-2(b) mice recognizing the VSV8 octapeptide RGYVYQGL bound to K(b) were utilized in conjunction with VSV8 variants differing only at the central p4 position. The V4I mutant octamer, like VSV8, induces negative selection of immature double-positive thymocytes on the beta(2)-microglobulin (beta(2)M)(+ / +) background and is a strong agonist for mature N15 T cells. In contrast, V4L or V4norvaline octamers promote positive selection in N15tg RAG-2(-/-) beta(2)M(-/-) H-2(b) fetal thymic organ culture and are weak agonists for N15 T cells. Hence, the absence of a p4 side chain Cbeta-methyl group results in positive selection of the N15 TCR. Hydrophobicity of the p4 residues also modulates thymocyte fate: the positively selecting norvaline and leucine variants have one and two Cgamma-methyl groups, respectively, while the weakly selecting gamma-methylleucine p4 contains three Cgamma-methyl groups. Moreover, the most hydrophobic octamer containing p4 cyclohexylglycine substitution fails to select. Thus, for N15 and presumably other MHC class I-restricted TCR, there is a high degree of structural specificity to peptide-dependent thymic selection processes.