Table 1.
Protein sequence and structure-based characteristics calculated for 10 selected positions in the RNA-dependent RNA polymerase gene of DENV-2 from a full-length infectious clone [FLIC] used to test our predictions.
| RESIDUE-POSITION | SSE | ACC | EPI | ECON | SCON (FLIC) | SCON (REFSEQ) |
|---|---|---|---|---|---|---|
| C-91 | H | 0 | 0 | 4.9 | 5.6 (C) | 5.6 (C) |
| C-179 | E | 0 | 0 | 8.9 | 8.9 (C) | 8.9 (C) |
| G-226 | C | 1 | 1 | 8.9 | 8.9 (G) | 8.9 (G) |
| K-279 | H | 0 | 0 | −0.9 | 2.2 (K) | 2.2 (K) |
| C-400 | H | 0 | 0 | 4.9 | −3.0 (C) | 4.6 (T) |
| R-437 | H | 0 | 0 | 2.9 | 4.5 (R) | 2.1 (K) |
| F-483 | H | 0 | 0 | 5.9 | 7.7 (F) | 7.7 (F) |
| K-552 | H | 0 | 1 | 1.9 | 3.5 (K) | −1.2 (M) |
| W-700 | E | 1 | 1 | 6.9 | 8.9 (W) | 8.9 (W) |
| H-711 | E | 0 | 0 | 5.9 | 7.7 (H) | 7.7 (H) |
Abbreviations: SSE, secondary structure element assignments; ACC, solvent accessibility scores; EPI, predictions that indicate that a given position is a part of the epitope; eCON, estimated amino acid conservation using Shannon’s entropy and frequencies calculated by the SeqalSV and StralSV algorithms; sCON, sequence similarity conservation using Sum-of-Pairs algorithm; H, helix; C, coil; E, strand.