Table 2. Nucleotide hydrogen contacts observed in a trajectory.

Nucleotide	Hydrogen bond contacts
G527	C522 A535: 87%
C528	G521 A535: 74%
G529	G517 C519 A520: 39%	C519 A520: 37%
G530	no contatcs: 100%
U531	no contatcs: 83%
A532	no contatcs: 51%	U516 A520: 15%
A533	U516 A520 A535: 22%
U534	no contacts: 57%	C511: 20% U512: 16%
A535	G527 C528 A533: 48%	G527 C528: 18%
C536	G515 G521: 43%

Each row lists: the nucleotide type with its number, the nucleotides it hydrogen bonds with, the percentage of trajectory time these contacts were formed. The ‘no contacts’ denote the percentage of frames the nucleotide did not create any hydrogen bonds. Only the contacts present in more than 10% of the trajectory are listed so the contacts in a row do not have to sum up to 100%. For example, A535 for 48% of trajectory time contacts G527, C528 and A533, but 18% of time only G527 and C528 (Figure 7). This dynamic interaction is revealed in MD—in the crystal A535 pairs only with U516. For full output which includes also the number of hydrogen bonds see Supplementary Table S2.