Table 1.
Average branch length distance and number of clusters (#n) per peptide in the hierarchical clustering tree for the PDB set considering different versions of TCRpcDist to calculate the distance: considering only CDR3β TCRpcDistCDR3β, or all CDRs, TCRpcDist6CDRs, and all CDRs+ nSESA based on experimental 3D structure (PDB) and all CDRs+ nSESA based on 3D structural models, TCRpcDist‐3D. Each peptide contributes with the same weight (1/16) to the final pMHC‐distance, to prevent this measure to be biased by the most frequent pMHCs. The number of TCRs per peptide is also presented, in column1.
| n. TCRS | peptide | TCRpcDist‐CDR3β | TCRpcDIist‐6CDRs | TCRpcDist‐3D (PDB structures) | TCRpcDist‐3D (3D models) | ||||
|---|---|---|---|---|---|---|---|---|---|
| pMHC‐distance | n. clusters | pMHC‐distance | n. clusters | pMHC‐distance | n. clusters | pMHC‐distance | n. clusters | ||
| 2 | APRGPHGGAASGL | 0.90 | #2 | 0.52 | #2 | 0.49 | #2 | 0.66 | #2 |
| 2 | ASNENMETM | 0.68 | #2 | 0.11 | #1 | 0.14 | #1 | 0.16 | #1 |
| 8 | ELAGIGILTV | 0.67 | #5 | 0.60 | #3 | 0.42 | #2 | 0.47 | #3 |
| 3 | FLRGRAYGL | 0.83 | #3 | 0.74 | #3 | 0.71 | #2 | 0.73 | #3 |
| 7 | GILGFVFTL | 0.66 | #5 | 0.64 | #3 | 0.48 | #3 | 0.55 | #3 |
| 3 | HPVGEADYFEY | 0.00 | #1 | 0.00 | #1 | 0.00 | #1 | 0.00 | #1 |
| 2 | ILAKFLHWL | 0.00 | #1 | 0.16 | #1 | 0.06 | #2 | 0.12 | #2 |
| 2 | IPLTEEAEL | 0.12 | #1 | 0.69 | #2 | 0.85 | #2 | 0.92 | #2 |
| 2 | KLVALGINAV | 0.76 | #2 | 0.17 | #1 | 0.18 | #1 | 0.19 | #1 |
| 3 | LLFGXPVYV | 0.45 | #3 | 0.57 | #2 | 0.33 | #2 | 0.26 | #2 |
| 3 | LPEPLPQGQLTAY | 0.72 | #3 | 0.47 | #2 | 0.58 | #2 | 0.55 | #2 |
| 3 | NLVPMVATV | 0.77 | #3 | 0.54 | #2 | 0.64 | #2 | 0.64 | #3 |
| 4 | QLSPFPFDL | 0.00 | #1 | 0.22 | #1 | 0.20 | #1 | 0.12 | #1 |
| 4 | RXPLTFGWCF | 0.85 | #4 | 0.64 | #4 | 0.65 | #4 | 0.76 | #4 |
| 4 | SLLMWITQX | 0.00 | #1 | 0.10 | #1 | 0.03 | #1 | 0.09 | #1 |
| 2 | VMAPRTLIL | 0.96 | #2 | 0.91 | #2 | 0.53 | #2 | 0.70 | #2 |
| – | Average | 0.52 | – | 0.44 | – | 0.39 | – | 0.43 | – |
| – | STDEV | 0.37 | – | 0.28 | – | 0.27 | – | 0.29 | – |