T cell differentiation in the thymus is driven by positive selection through the interaction of ␣ T cell receptors (TCRs) with selfpeptides bound to self-major histocompatibility complex molecules, yet the influence of the peptide sequence on this process remains unknown. To address this issue, we have compared CD4 ؉ T cell differentiation between two sets of mouse lines in which MHC class II I-A b molecules are occupied with either E␣ chainderived peptide ( pE␣) or its variant, p60K, with one amino acid substitution from leucine to lysine at P5 residue of TCR contacts. Here, we show that despite the comparable expression of I-A bpeptide complex in the thymus, this substitution from leucine to lysine affects efficiency of positive selection, resulting in extremely small numbers of CD4 ؉ T cells to be selected to mature on I-A b -p60K complex. Furthermore, we show that, although I-A b -pE␣ complex selects diverse T cells, T cell repertoire shaped by I-A b -p60K complex is markedly constrained. Our findings thus suggest that positive selection is both specific and degenerate, depending on the amino acid residues at TCR contacts of the selecting self-peptides.A lthough the diversity of ␣ T cell receptors (TCRs) theoretically reaches 10 15 by random rearrangement of five gene segments (V␣, J␣, V, D, and J) and random nucleotide addition (1), mature T cells express highly selected TCRs in that they exhibit tolerance to self-antigenic peptides and restriction by self-MHC molecules. This mainly results from two reciprocal selection processes, positive and negative selection, acting during T cell development in the thymus. Positive selection is the process that induces the differentiation of CD4 ϩ CD8 ϩ immature thymocytes into CD4 Ϫ CD8 ϩ or CD4 ϩ CD8 Ϫ mature thymocytes only when their TCRs recognize self-MHC class I or class II molecules with sufficient, albeit weak, affinity and ensures that the specificity of mature T cell repertoire is directed against antigenic peptides bound to self-MHC molecules. On the other hand, negative selection plays a central role in tolerance induction by eliminating immature thymocytes bearing TCRs specific for self-peptides bound to self-MHC molecules.Since the discovery that positive selection is influenced by the substitutions at amino acid residues of MHC molecules positioned toward the peptide-binding groove (2-5), the role of self-peptides in positive selection has been the subject of considerable debate. This was first directly addressed for CD8 ϩ T cells using fetal thymic organ cultures derived from mutant mouse strains where a particular MHC class I-peptide complex is expressed by exogenously adding a given peptide to the culture (6-8). Subsequently, several groups developed in vivo experimental system focusing on the role of self-peptides in positive selection of CD4 ϩ T cells by creating mouse strains in which all or a large fraction of the MHC class II molecules are occupied with a single peptide (9-13). With the use of in vitro and in vivo experimental systems, it wa...