Table 2. Stacking interactions as calculated by 3DNA-DSSR (41) among residues belonging to the duplex, the junction and the quadruplex of RE31.
| Nucleotide 1 | Nucleotide 2 | Structural motif | Base stacking (Å2)* |
|---|---|---|---|
| Thy2 | Gua3 | Duplex | 4.5 |
| Gua3 | Ade4 | Duplex | 3.7 |
| Ade4 | Cyt5 | Duplex | 3.4 |
| Cyt5 | Gua6 | Duplex | 1.4 |
| Gua6 | Thy7 | Junction | 7.0 |
| Thy7 | Thy17 | Junction | 7.4 |
| Thy17 | Gua16 | Junction | 8.0 |
| Gua16 | Gua14 | Junction | 3.2 |
| Gua14 | Gua13 | Quadruplex | 4.4 |
| Ade30 | Cyt29 | Duplex | 1.3 |
| Cyt29 | Thy28 | Duplex | 7.1 |
| Thy28 | Gua27 | Duplex | 7.0 |
| Gua27 | Cyt26 | Duplex | 1.3 |
| Cyt26 | Gua25 | Junction | 4.6 |
| Gua25 | Ade8 | Junction | 2.2 |
| Ade8 | Gua24 | Junction | 4.6 |
| Gua24 | Gua23 | Junction | 2.5 |
| Gua23 | Gua22 | Quadruplex | 4.3 |
*Base-stacking is quantified as the area of the overlapped polygon defined by the two bases of the interacting nucleotides, where the base atoms are projected onto the mean base plane.