Table 6. Summary table for the clustering of CDR-H1.
Level-2 clusters are shown exceptionally (marked with an asterisk) when no level-1 cluster is formed (minimum of 2 members required).
| Cluster | Population | Unique sequences |
Medoid PDB entry |
Medoid Ramachandran conformation |
Level-3 clusters |
Level-2 clusters |
Cluster diameter (Å) (furthest members) |
Best resolution in cluster (Å) (PDB) |
Species in cluster |
|---|---|---|---|---|---|---|---|---|---|
| CDR-H1 10-residues, total population: 6, total unique sequences: 2, clusters: 1, outliers/singletons: 0, Av.Silhouette: N/A | |||||||||
| H1-10-I | 6 | 2 (100%) | 1kxq_H | BPABPBABBB | 2 | 1 | 0.61 (3eba_A-1kxq_F) | 1.6 (1kxq_E) | CAMEL, HUMAN |
| CDR-H1 12-residues, total population: 2, total unique sequences: 2, clusters: 0, outliers/singletons: 2, Av.Silhouette: N/A | |||||||||
| H1-12-O-1* | 1 | 1 (50%) | 1ghf_H | BBBBPAAABPBB | 1 | 1 | N/A | 2.7 (1ghf_H) | MOUSE |
| H1-12-O-2* | 1 | 1 (50%) | 3IY2_B | PBBLBABBABBB | 1 | 1 | N/A | 18.0 (3IY2_B) | MOUSE |
| CDR-H1 13-residues, total population: 1845, total unique sequences: 450, clusters: 11, outliers/singletons: 164, Av.Silhouette: 0, 54 | |||||||||
| H1-13-I | 1555 | 390 (87%) | 2OSL_A | PPBLBPAADBPBB | 214 | 23 | 1.74 (2GK0_B-1rzi_J) | 1.2 (3D9A_H) | MOUSE, HUMAN, RAT, RABBIT, LLAMA, HAMSTER, CHIMPANZEE, CHIMERA OF MOUSE/HUMAN, SYNTHETIC HUMANIZED ANTIBODY |
| H1-13-II | 49 | 6 (1%) | 3F7Y_A | PBBGPBBAAPBBB | 19 | 6 | 1.77 (3QXW_D-3GKZ_A) | 1.72 (2IH3_A) | MOUSE, HUMAN, RAT, LLAMA, CHIMERA OF MOUSE/HUMAN |
| H1-13-III | 24 | 4 (1%) | 1bzq_K | BPBLPABBPABBB | 11 | 3 | 1.12 (2P42_D-1jtp_B) | 1.1 (2P45_B) | MOUSE, DROMEDARY, CAMEL |
| H1-13-IV | 8 | 2 (0.4%) | 3QXV_A | BBABPBAPPBPBB | 7 | 2 | 0.97 (3QXV_B-1YC7_A) | 1.6 (1YC7_A) | DROMEDARY, CAMEL |
| H1-13-V | 9 | 3 (1%) | 2X7L_J | PPBLPAPABBPBB | 4 | 2 | 1.11 (2W9E_H-1YC8_B) | 2.7 (1YC8_B) | CAMEL |
| H1-13-VI | 9 | 1 (0.2%) | 2WZP_E | BPABBABPLPBBB | 4 | 2 | 0.35 (2WZP_J-2BSE_E) | 2.6 (2WZP_D) | CAMELID |
| H1-13-VII | 2 | 1 (0.2%) | 1SHM_A | PPBGPAAPPBPBB | 2 | 1 | 0.19 (1SHM_A-1SHM_B) | 1.9 (1SHM_A) | HUMAN, MOUSE, LLAMA |
| H1-13-VIII | 8 | 5 (1%) | 3EZJ_B | BPBGPAAAPDBBB | 6 | 2 | 1.05 (1zvy_A-1SJX_A) | 1.5 (1zvh_A) | HUMAN, CAMEL, LLAMA |
| H1-13-IX | 3 | 1 (0.2%) | 3GBM_H | BBPGGAPBDBPBB | 3 | 1 | 0.17 (3GBN_H-3GBM_I) | 2.2 (3GBN_H) | HUMAN |
| H1-13-X | 3 | 1 (0.2%) | 2X89_A | BBBLPPLLBBPBB | 2 | 1 | 0.22 (2X89_C-2X89_B) | 2.16 (2X89_A) | HUMAN |
| H1-13-XI | 2 | 1 (0.2%) | 1ngx_B | PPALPPBABBPBB | 1 | 1 | 0.01 (1ngx_H-1ngx_B) | 1.8 (1ngx_B) | HUMAN, MOUSE |
| CDR-H1 14-residues, total population: 72, total unique sequences: 17, clusters: 1, outliers/singletons: 2, Av.Silhouette: 0, 64 | |||||||||
| H1-14-I | 70 | 16 (94%) | 1kcv_H | BBBLBPAAABGBBB | 47 | 11 | 1.37 (2f58_H-2ajz_H) | 1.3 (1ncw_H) | HUMAN, MOUSE |
| CDR-H1 15-residues, total population: 128, total unique sequences: 29, clusters: 3, outliers/singletons: 3, Av.Silhouette: 0, 62 | |||||||||
| H1-15-I | 117 | 25 (86%) | 2HWZ_H | BBBLBBAAPPLPBBB | 43 | 12 | 1.68 (3BQU_B-3B2V_H) | 1.5 (3IFL_H) | HUMAN, MOUSE |
| H1-15-II | 6 | 2 (7%) | 3BAE_H | BBBLBBAAAALPPBB | 4 | 2 | 0.86 (3BKC_H-3AAZ_A) | 1.59 (3BAE_H) | HUMAN, MOUSE |
| H1-15-III | 2 | 1 (3%) | 3FZU_H | BBBLPAPPAADBPBB | 2 | 1 | 0.28 (3FZU_C-3FZU_H) | 2.5 (3FZU_H) | HUMAN |
| CDR-H1 16-residues, total population: 3, total unique sequences: 2, clusters: 1, outliers/singletons: 1, Av.Silhouette: N/A | |||||||||
| H1-16-I | 2 | 1 (50%) | 3eak_B | PBBGLAABPAAAPPBB | 1 | 1 | 0.42 (3eak_A-3eak_B) | 1.95 (3eak_A) | CAMEL |
| CDR-H1 24-residues, total population: 1, total unique sequences: 1, clusters: 0, outliers/singletons: 1, Av.Silhouette: N/A | |||||||||
| H1-24-O-1* | 1 | 1 (100%) | 3K3Q_A | PPBLBALDLGAAG AADAADBGBBB |
1 | 1 | N/A | 2.6 (3K3Q_A) | LLAMA |
|
Total
(level-1 clusters only) |
1884 | 379 | 77 | ||||||