Table 4.
Other non-bonding interactions around unpaired RNA bases
| Interactions with RNA atoms | Crystal packing interactions | Interactions with atoms of proteins, ligands, and ions | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Base | Nb* | Na** | d | Nb* | Na** | d | Nb* | Na** | d |
| Adenine | 7 | 92 | 5 | 25 | 325 | 12 | 87 | 1.868 | 55 |
| Guanine | 7 | 93 | 5 | 20 | 258 | 11 | 96 | 2.381 | 68 |
| Cytosine | 7 | 41 | - | 10 | 98 | 5 | 33 | 532 | 19 |
| Uracil | 5 | 30 | - | 30 | 351 | 13 | 75 | 1.071 | 34 |
Number of the unpaired RNA bases participating in the atom-atom interactions within 5 Å and number of atoms around these unpaired bases. For example, 25 from 197 unpaired adenine bases (see the numbers of the unpaired bases in Table 1) have crystal packing contacts within 5 Å and the number of surrounding atoms that participate in these interactions is 325. The empirical parameter d, used for cluster detection (see Method section), is also reported for each type of interaction.
* - number of unpaired bases.
** - number of atoms surrounding the base