RNA Backbone Conformers
This table contains links which will lead to display of a representative example of a conformer in an interactive KiNG display window. Below is essentially Table 1 - Characteristics of the 46 consensus clusters of RNA backbone suite conformation - from the RNA Ontology Consortium paper, "RNA backbone: Consensus all-angle conformers and modular string nomenclature" doi/10.1261/rna.657708. To view and interact with the structural model of the immediate region of the chosen example, click the "KiNG" button in the column labeled example. We periodically update the statistics and representatives on this table (see table history).
| δ,δ,γ | name | comment | example | suite | δ-1 | ε-1 | ζ-1 | α | β | γ | δ |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 33p | 1a | A-form | ur0020 11 | 3'emmtp3' | 81 | -148 | -71 | -65 | 174 | 54 | 81 |
| 1m | -β shoulder on 1a; some intercalate |
rr0082 1940 | 3'emm-135p3' | 84 | -142 | -68 | -68 | -138 | 58 | 86 | |
| 1L | +β shoulder on 1a; some intercalate |
rr0082 1460 | 86 | -115 | -92 | -56 | 138 | 62 | 79 | ||
| &a | εζ shoulder on 1a; weak Hb O2'(-1)-O4' |
pr0037 B163 | 82 | -169 | -95 | -64 | -178 | 51 | 82 | ||
| 7a | stack switch | ar0041 A6 | 3'e-140mtp3' | 83 | -143 | -138 | -57 | 161 | 49 | 82 | |
| 3a | bases far 7a,3a,9a all touch in ζ | urb016 A2 | 3'etmtp3' | 85 | -144 | 173 | -71 | 164 | 46 | 85 | |
| 9a | bases far; starts or ends loops |
rr0082_2582 | 83 | -150 | 121 | -71 | 157 | 49 | 81 | ||
| 1g | GNRA1-2; U-turn | rr0082 1864 | 3'emttp3' | 81 | -141 | -69 | 167 | 160 | 51 | 85 | |
| 7d | bases far; can span 2 helices | rr0082 0636 | 3'emptp3' | 84 | -121 | -103 | 70 | 170 | 53 | 85 | |
| 3d | bases far; starts or ends A-helix | rr0082 2118 | 3'e-140ptp3' | 85 | -116 | -156 | 66 | -179 | 55 | 86 | |
| 5d | P(-1) to P(+1) close; end or end+1 A-helix |
ur0020 A9 | 3'epptp3' | 80 | -158 | 63 | 68 | 143 | 50 | 83 | |
| 33t | 1e | S-motif strand2 "dent"; Hb O2'9-10-O4'; low β |
ur0035 A2665 | 3'em-110 80tp3' | 81 | -159 | -79 | -111 | 83 | 168 | 86 |
| 1c | GNRA 4-5; ttt "crankshaft" version of 1a | ur0020 A28 | 3'emttt3' | 80 | -163 | -69 | 153 | -166 | 179 | 84 | |
| 1f | +β shoulder on 1c; stack switch or ∼intercalate |
tr0001 A22 | 3'emt135t3' | 81 | -157 | -66 | 172 | 139 | 176 | 84 | |
| 5j | bases far; 1-bulge return | ar0027 B17 | 3'epp110t3' | 87 | -136 | 80 | 67 | 109 | 176 | 84 | |
| 32p | 1b | leads into 2' suites; k-turn O'; syn G Hb N2-OP2 |
pr0113 D208 | 3'emmtp2' | 84 | -145 | -71 | -60 | 177 | 58 | 145 |
| 1[ | best intercalation conformation | pr0019 B658 | 3'emm-135p2' | 83 | -140 | -71 | -63 | -138 | 54 | 144 | |
| 3b | bases far; ends A-helix | rr0082 0904 | 3'etmtp2' | 85 | -134 | 168 | -67 | 178 | 49 | 148 | |
| 1z | UNCG 1-2; bulges | rr0082 01771 | 3'emttp2' | 83 | -154 | -82 | -164 | 162 | 51 | 145 | |
| 5z | S-motif 1-2; Z32a dna; Hb OP2(-1)-O2' |
ur0026 A2654 | 3'epttp2' | 83 | -154 | 53 | 164 | 148 | 50 | 148 | |
| 7p | bases far | pr0033 B8 | 3'e-140ptp2' | 84 | -123 | -140 | 68 | -160 | 54 | 146 | |
| 32t | 1t | ttt version of 1b | pte003 B907 | 3'emttt2' | 81 | -161 | -71 | 180 | -165 | 178 | 147 |
| 5q | bases far | pte003 B973 | 3'epp110t2' | 82 | -155 | 69 | 63 | 115 | 176 | 146 | |
| 32m | 1o | Starts 1-bulge; wide in β | rr0082_01108 | 3'emmtm2' | 84 | -143 | -73 | -63 | -135 | -66 | 151 |
| 7r | k-turn 1-2 | rr0082 0262 | 3'e-140ptm2' | 85 | -127 | -112 | 63 | -178 | -64 | 150 | |
| 23p | 2a | leads out of 2' suites; 1-bulge return |
rr0082 01711 | 2'emmtp3' | 145 | -100 | -71 | -72 | -167 | 53 | 84 |
| 4a | bases far | rr0082 02485 | 2'etmtp3' | 146 | -100 | 170 | -62 | 170 | 51 | 84 | |
| 0a | cross-stacked A-helix | rr0082 0265 | 149 | -137 | 139 | -75 | 158 | 48 | 84 | ||
| #a | i-1 to i base pair; S-motif 3-4; low ε |
rr0082 01371 | 2'etmtp3' | 148 | -168 | 146 | -71 | 151 | 42 | 85 | |
| 4g | i-1 to i base pair; non S-motif | ur0012 A226 | 2'etttp3' | 148 | -103 | 165 | -155 | 165 | 49 | 83 | |
| 6g | sheared stack | pr0122 R151 | 2'epttp3' | 145 | -97 | 80 | -156 | -170 | 58 | 85 | |
| 8d | some with Hb O2'(-1)-OP2(+1) | rr0009 C1062 | 2'emptp3' | 149 | -89 | -119 | 62 | 176 | 54 | 87 | |
| 4d | tRNA 58-9; Hb O2'(-1)-OP2(+1) | tr0001_A59 | 2'etptp3' | 150 | -110 | -172 | 80 | -162 | 61 | 89 | |
| 6d | starts A-helix | rr0082 0116 | 2'epptp3' | 147 | -119 | 89 | 59 | 161 | 52 | 83 | |
| 23t | 2h | bases far | rr0082 02540 | 2'emmtt3' | 148 | -99 | -70 | -64 | 177 | 176 | 87 |
| 4n | ∼stack or sheared stack | rr0082 0767 | 149 | -85 | 100 | 81 | -112 | -178 | 83 | ||
| 0i | -β next to 6n; bases perpendicular | rr0082 0940 | 149 | -85 | 100 | 81 | -112 | -178 | 83 | ||
| 6n | UNCG 3-4; Z23 dna; syn curled to base triple |
rr0082 01773 | 2'epptt3' | 150 | -92 | 85 | 64 | -169 | 177 | 86 | |
| 6j | -β next to 6n; bases far | pte003 B975 | 142 | -116 | 66 | 72 | 122 | -178 | 84 | ||
| 22p | 2[ | UNCG 2-3; near B dna; k-turn 3-4 |
rr0082 0264 | 2'emm-135p2' | 146 | -101 | -69 | -68 | -150 | 54 | 148 |
| 4b | Cross-stacked A-helix end | rr0082 0247 | 2'etmtp2' | 145 | -115 | 163 | -66 | 172 | 46 | 146 | |
| 0b | varied | rr0082 0453 | 2'epmtp2' | 148 | -112 | 112 | -85 | 165 | 57 | 146 | |
| 4p | often starts 1-bulge, Hb O2'(-1)-N7(+1) |
rr0096 A873 | 2'etptp2' | 150 | -100 | -146 | 72 | -152 | 57 | 148 | |
| 6p | k-turn 2-3 | rr0082 01315 | 2'epptp2' | 146 | -102 | 90 | 68 | 173 | 56 | 148 | |
| 22t | 4s | S-motif 2-3; low β | ur0026 A2655 | 150 | -112 | 170 | -82 | 84 | 176 | 148 | |
| 22m | 2o | bases perpendicular, something between |
pr0033 5 | 2'emmtm2' | 147 | -104 | -64 | -73 | -165 | -66 | 150 |