Table 1.
Details of the Size 30 Library
| Cluster center |
Sequence content |
Most common sequences |
Res1 |
Res2 |
||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Label | ⟨RMSD⟩ | Size of cluster | Description | Seq | RR | RY | YR | YY | 1st | 2nd | 3rd | 4th | PDB ID | # | Ch | # | Ch | |||||
| 1 | 0.39 | 1363 | Stack | C | C | 0.0 | 0.0 | 0.0 | 6.6 | CC | 8.0 | CU | 7.6 | UC | 5.3 | UU | 4.6 | 1jj2 | 2268 | 0 | 2269 | 0 |
| 2 | 0.42 | 1351 | Stack | G | C | 0.0 | 3.8 | 0.0 | 0.0 | GU | 5.0 | AC | 4.0 | GC | 3.8 | AU | 2.4 | 1n78 | 540 | C | 541 | C |
| 3 | 0.52 | 1465 | Stack | G | G | 3.1 | 0.0 | 0.0 | 0.0 | GG | 5.0 | AA | 2.4 | AG | 2.3 | GA | 2.2 | 1qcu | 6 | A | 7 | A |
| 4 | 0.53 | 1416 | Stack | C | G | 0.0 | 0.0 | 3.7 | 0.0 | CA | 4.4 | UG | 4.2 | CG | 3.6 | UA | 2.6 | 1jj2 | 2130 | 0 | 2131 | 0 |
| 5 | 0.56 | 1314 | Watson-Crick base-pair | C | G | 0.1 | 0.0 | 3.5 | 0.2 | CG | 5.8 | UA | 4.0 | UG | 1.7 | CA | 0.5 | 1jj2 | 2335 | 0 | 2349 | 0 |
| 6 | 0.57 | 1354 | Watson-Crick base-pair | G | C | 0.1 | 3.6 | 0.0 | 0.2 | GC | 5.7 | AU | 4.3 | GU | 1.9 | UU | 0.5 | 1rxb | 5 | A | 12 | B |
| 7 | 0.63 | 658 | Diagonal interaction | C | A | 0.0 | 0.0 | 3.3 | 0.7 | CG | 4.4 | CA | 3.5 | UG | 3.1 | UA | 1.2 | 1m5o | 20 | A | 3 | B |
| 8 | 0.65 | 505 | Variant of stack | A | A | 3.1 | 0.0 | 0.1 | 0.0 | AG | 5.7 | AA | 3.9 | GG | 2.0 | GA | 1.3 | 1lng | 219 | B | 220 | B |
| 9 | 0.75 | 202 | Variant of stack | A | C | 0.2 | 3.4 | 0.0 | 0.4 | AC | 8.9 | AU | 4.5 | GU | 1.7 | GC | 1.0 | 1fjg | 1188 | A | 1189 | A |
| 10 | 0.84 | 762 | Diagonal interaction | A | G | 3.1 | 0.0 | 0.0 | 0.0 | GG | 4.6 | GA | 2.7 | AG | 2.5 | AA | 1.9 | 1duq | 110 | A | 120 | B |
| 11 | 0.89 | 1073 | Diagonal interaction | G | U | 0.0 | 2.5 | 0.0 | 2.2 | GU | 3.2 | GC | 3.0 | CC | 2.5 | CU | 2.4 | 1hr2 | 234 | A | 241 | A |
| 12 | 0.98 | 712 | Diagonal interaction | G | G | 2.5 | 0.4 | 0.4 | 0.0 | GG | 3.1 | GA | 2.3 | AG | 2.2 | AA | 2.0 | 1hq1 | 131 | B | 176 | B |
| 13 | 1.37 | 171 | Variant of stack | U | U | 0.0 | 0.8 | 0.2 | 4.7 | UU | 8.5 | UC | 5.5 | CC | 3.3 | CU | 3.1 | 1csl | 77 | B | 78 | B |
| 14 | 1.50 | 382 | Diagonal interaction | U | A | 0.4 | 0.1 | 2.4 | 1.2 | CA | 4.0 | UG | 3.1 | UA | 2.5 | UC | 1.9 | 1jj2 | 1310 | 0 | 1345 | 0 |
| 15 | 1.65 | 309 | Reverse Hoogsteen pair | U | A | 1.1 | 0.2 | 2.0 | 0.5 | UA | 5.9 | CA | 2.2 | AA | 2.1 | AG | 1.4 | 1gid | 224 | A | 248 | A |
| 16 | 1.69 | 314 | Connected nucleotides | U | U | 0.6 | 1.0 | 0.9 | 2.2 | UC | 4.0 | UU | 3.0 | AC | 2.0 | UG | 1.3 | 1ehz | 7 | A | 8 | A |
| 17 | 1.71 | 489 | Sheared pair | G | A | 2.2 | 0.6 | 0.5 | 0.2 | GA | 4.8 | AA | 2.1 | UA | 1.5 | AU | 1.0 | 1gid | 150 | A | 153 | A |
| 18 | 1.74 | 192 | Variant of diagonal | G | C | 1.3 | 1.5 | 0.2 | 0.9 | AC | 4.3 | UC | 2.2 | AA | 2.2 | GA | 1.7 | 1fjg | 46 | A | 366 | A |
| 19 | 1.76 | 434 | Sheared pair | A | G | 2.3 | 0.5 | 0.5 | 0.1 | AG | 4.8 | AA | 2.6 | GA | 1.5 | AU | 1.4 | 1jbr | 12 | C | 19 | F |
| 20 | 1.76 | 504 | Similar to A-platform | G | A | 1.8 | 1.0 | 0.5 | 0.2 | GA | 2.8 | AA | 2.4 | AG | 1.9 | GU | 1.5 | 1fjg | 115 | A | 116 | A |
| 21 | 1.79 | 443 | Variant of stack | C | A | 1.2 | 0.3 | 1.5 | 0.8 | GA | 2.6 | UA | 2.2 | UG | 2.2 | CA | 2.1 | 1kd5 | 4 | A | 5 | A |
| 22 | 1.84 | 178 | Variant of diagonal | U | C | 0.4 | 1.2 | 1.0 | 1.8 | AU | 2.9 | UC | 2.2 | CC | 2.0 | CU | 1.6 | 1yfg | 8 | A | 13 | A |
| 23 | 1.84 | 541 | Tertiary interaction | G | G | 1.1 | 1.2 | 1.0 | 0.4 | AC | 3.3 | CA | 3.1 | AU | 1.5 | GA | 1.5 | 1jj2 | 1071 | 0 | 1292 | 0 |
| 24 | 1.85 | 313 | Connected nucleotides | C | C | 0.8 | 1.0 | 1.0 | 1.3 | UU | 2.8 | UC | 1.8 | AU | 1.6 | UA | 1.6 | 1jj2 | 1651 | 0 | 1652 | 0 |
| 25 | 1.85 | 314 | Tertiary interaction | U | G | 0.9 | 0.6 | 1.3 | 1.4 | UG | 2.1 | CU | 2.0 | UC | 1.6 | CA | 1.4 | 1jj2 | 1807 | 0 | 2884 | 0 |
| 26 | 1.90 | 280 | Tertiary interaction | A | A | 1.7 | 0.9 | 0.6 | 0.4 | AA | 2.5 | AG | 1.8 | AU | 1.7 | GA | 1.5 | 1jj2 | 151 | 0 | 441 | 0 |
| 27 | 1.91 | 270 | Tertiary interaction | G | A | 1.6 | 0.6 | 0.8 | 0.8 | GA | 3.2 | AA | 1.7 | CA | 1.6 | UG | 1.1 | 1fjg | 292 | A | 608 | A |
| 28 | 1.92 | 274 | Connected nucleotides | U | G | 0.9 | 0.5 | 1.8 | 0.6 | UG | 2.5 | UA | 1.8 | AA | 1.8 | CA | 1.8 | 1fjg | 884 | A | 885 | A |
| 29 | 1.97 | 208 | Connected nucleotides | C | U | 0.7 | 1.1 | 0.8 | 1.9 | UU | 2.8 | CU | 2.4 | UC | 1.9 | AA | 1.3 | 1euy | 934 | B | 935 | B |
| 30 | 2.35 | 167 | Tertiary interaction | G | C | 0.9 | 1.4 | 0.5 | 1.2 | GU | 2.2 | GG | 1.7 | UC | 1.6 | CC | 1.4 | 1g1x | 666 | D | 732 | E |
The entries in the Table are sorted by increasing ⟨RMSD⟩ of the members fit to their cluster center. For each cluster we include the number of members, a description of the cluster center and the sequence of the cluster center (column entitled Seq). We also look at the sequence content in terms of RR, RY, YR and YYpairs, where R is purine and Y is pyrimidine. The sequence content is given in terms of frequency of occurrence normalized such that 1.0 is what would occur by chance. Bold face numbers are significantly larger than expected by chance. The four most commonly occurring sequences for each cluster are also given. Finally the PDB ID and sequence information for each doublet is listed.
Signifies the number in the chain, and Ch signifies the chain ID.