Using the information in the TCR amino acid position specific scoring matrices, we estimate the number of ligands recognized by a given T cell clone by assuming that recognizable peptides contain only those amino acids giving a detectable ELISPOT response in the Lee et al. [10] study. Non-recognized peptides are the ones containing at least one prohibited amino acid for which no response was detected. The number of recognizable peptides was computed by the following procedure. The degeneracy of a TCR on a single position was measured as the diversity of amino acids present at that position defined in terms of the Simpson index (see Materials and Methods). This diversity measure yields a value between 1 and 20. Here, 20 means that all amino acids are used with equal frequency at a position, and 1 means that only a single amino acid is found. The higher the diversity the more degenerate the TCR is at this position. In the binding motif of T4 clone (Fig. 1A ) the first position diversity is very high, 13.26, as [14] which is a measure of how conserved a position is. Rigid positions have few but tall letters, while very degenerate positions have many but very short letters. For example, position 1 was mutated 19 times of which 18 variants preserved TCR binding, only the S1R variant compromised TCR binding while the MHC binding was preserved (see [38] ). The frequency of amino acids occurring in this TCR motif can also be used to estimate the number of distinct ligands this T cell clone can recognize (see text for details). (B) Sequence motif of HLA-A2 binding peptides (277 HLA-A2 restricted peptides were extracted from the SYFPEITHI database [15] ). (C) The average Shannon information at each position, for the CTL clones: G10 and T4, and PBMC. doi:10.1371/journal.pone.0001831.g001 expected, because this position is highly degenerate. In the conserved position five, the Simpson diversity drops to 1.29. The product of the tolerated amino acid diversity at each position can provide an estimate of the number of ligands a T cell clone can recognize. For T4, we estimate a total of 5.6?10 5 ligands in this way and this value is in good agreement with previous estimates [8] . For the G10 clone, we estimate 3.2?10 6 ligands, suggesting that this clone is more degenerate. Similarly, one can estimate the number of ligands that can bind to a MHC molecule. For example, the HLA-A*0201 molecule (see Fig. 1B for the binding motif) can bind 4.8?10 9 distinct peptides [15] . Thus, measured in this way the CTL binding event is three orders of magnitudes more specific than that of the MHC.