Table 2.

Total numbers and frequencies of acceptor and donor atoms in long-range RNA–RNA H-bonds^a

	All H-bonds		BH-bondsb
Atom	Number	Frequency (%)	Number	Frequency (%)
N7A	407	32.0	85	6.7
N7G	93	5.3	69	3.9
N6A	1088	85.6	301	23.7
O6G	1333	75.9	65	3.7
N4C	1247	88.3	103	7.3
O4U	430	46.1	33	3.5
N1A	675	53.1	195	15.3
N1G	1509	85.9	180	10.3
N3C	1207	85.5	26	1.8
N3U	699	75.0	61	6.5
N2G	2018	114.9c	400	22.8
O2C	1313	93.0	98	6.9
O2U	390	41.8	34	3.6
N3A	280	22.0	144	11.3
N3G	171	9.7	34	1.9
O2′	704	13.1	359	6.7
O2′	1766	32.9	983d	18.3d
O4′	234	4.4	122	2.3
O3′	205	3.8	148	2.8
O5′	52	1.0	14	0.3
OP1	369	6.9	216	4.0
OP2	464	8.6	124	2.3

^aNon-intraresidue, non-sequential RNA–RNA H-bonds have been identified as described in the Methods section for the eight multi-domain RNA structures listed in Table 1. Table rows with the acceptor atoms are aligned left, and rows with donor groups are aligned right. The frequencies are calculated as percent of the total number of relevant residues, i.e., 1271 A, 1412 C, 1756 G, and 932 U residues for specific nucleobase acceptors and donors and 5372 nt for the acceptors and donors in the sugar-phosphate backbone.

^bFor the acceptor atoms, total numbers and frequencies of the H-bonds with the sugar–phosphate donors (i.e., 2′OH) are shown. For the donor groups, the data are shown for the H-bonds with acceptors on the sugar-phosphate backbone (i.e., O2′, O4′, O3′, O5′, OP1, and OP2).

^cFrequency is greater than 100% here, because each guanine amino group participates in more than one H-bond on average.

^dO2′–O2′ H-bonds.