Table 4. Bioinformatic analysis of isolated NS1 ED strand-strand dimer characteristics.
Strain | Dimer | Symmetry relationship | Interface accessible surface area (Å2)* | Interface accessible surface area (%)* | Planarity (Å)* | Local density** | Gap Volume (Å3)* | Gap Volume Index (Å)* |
PR8 | 2GX9_ABSS | asymmetric | 603 | 7.7 | 2.51 | 32.3 | 5812 | 4.82 |
3O9U_AF | asymmetric | 345 | 5.2 | 2.66 | 22.9 | 4357 | 6.31 | |
3O9U_BD | asymmetric | 442 | 6.6 | 2.47 | 25.5 | 4165 | 4.71 | |
3O9U_CH | asymmetric | 482 | 7.3 | 2.21 | 30.4 | 5461 | 5.67 | |
3O9U_EG | asymmetric | 514 | 7.7 | 2.48 | 31.6 | 5883 | 5.73 | |
Mean | 477 | 6.9 | 2.47 | 28.5 | 5135 | 5.45 | ||
Standard deviation | 95 | 1.1 | 0.16 | 4.1 | 817 | 0.67 |
ED strand-strand dimers identified as PDB ID_chains (e.g. dimer 3O9U_AF is formed by chains A and F of structure 3O9U). The strand-strand dimer formed by chains A and B of PR8 structure 2GX9 is identified by a superscript SS to distinguish it from the helix-helix dimer also made by those chains (see Table 3). All values calculated using either ProtorP (*) or ProFace (**).