Assignment of DNA and RNA conformers (DNATCO v3.0)

Tutorial

Test run (PDB ID 1bna)

The server assigns 84 DNA/RNA conformers based on values of their 12 backbone torsion parameters.

  • Table defining the conformers is below; definition of the conformers, their esd values and Cartesian coordinates of their representative samples can be downloaded.
  • Conformers are identified by four-letter symbols. "A", "B", "Z" letters imply stacked bases with first/second nucleotide in A, B, or Z like conformation. "IC" corresponds to steps with InterCalated bases. "OP" corresponds to steps with OPened bases. "S" at 3rd or 4th position means that the 1st or 2nd base is in syn orientation.
  • Conformationally extreme conformers are not assigned to any of the above; these steps formally represent the 85th conformer.
  • How to cite:

Please, read before you upload coordinates of your DNA:

  • DNA steps are identified based on atom names as defined by the PDB format, version 3.1 or above (sugar atoms as O4' not O4*).
  • Contact the authors for off-line analysis of non-standard or large structures (multiple NMR MODELs or MD simulation trajectory).
  • Steps with non-standard or missing atoms that define torsions δ ... δ+1, χ, and χ+1 are not considered in the assignment process.
  • Conformers are assigned for modified residues that contain standard names for atoms defining the step torsions between δ and δ+1 and χ and χ+1.


or


or

News and changes:

  • v3.0:
    • Introducing a universal set of conformer classes for analysis of DNA as well as RNA structures.
    • Additional parameters (NN, CC, NCCN) were defined for better description of intercalated or open steps.
    • Analysis of structures deposited in the wwPDB and PDB-REDO databases uses PDBx (mmCIF) format internally.
      • This simplifies support for large structures, multiple MODELs, alternate positions, and insertion codes. (reliable visualization still under development)
    • Files uploaded by users still expected in PDB format.
  • v2.3:
    • Interactive 3D Complement pages for publications from 2017 (I3D) and 2018 (I3D) can be found at Proteopedia.
    • the improved assignment protocol involves known δ/pseudorotation angle correlation for detection of outliers
    • a reference (representative NtC structure) is superposed upon the selected step and cartesian RMSD for atoms defining the nine torsions is reported
    • protein/hetero/water groups from the original PDB can be displayed (P/H/W buttons)
    • introduced a tetrahedron centered at the phosphate:
      • its size represents the confal value
      • its user adjustable color allows simple recognition of A/BI/BII/miB/Z/NS/SYN character of a step
    • new buttons (D) reset to default colors; (Q) toggle quality, and (T) transparent tetrahedrons
  • v2.2:
    • confal (conformer validation score) was introduced. The confal is a Gaussian weighted value ranging from 1 to 100 (lowest to perfect fit to the reference) or 0 for outliers.
    • the "most similar" conformation is now reported for non-assigned (NANT) steps.
    • a list of accepted residues is included for reference.
  • v2: the version described in Černý et al., Nucleic Acids Research, 44, W284 (2016).
  • v1: the initial implementation based on Svozil et al., Nucleic Acids Research, 36, 3690 (2008).
Annotation CANA NtC 1 2 3 4 5 6 7 8 9 Numbers of Steps in
  DNA RNA golden set, #
δ ε ζ α1 β1 γ1 δ1 χ χ1 NN CC NCCN # % # %
the most frequent, "canonical" A-DNA (identical to A-RNA) AAA AA00 82 206 288 293 173 55 82 199 201 4.8 5.4 18 1 819 3.2 21 218 37.7 293
A-DNA with a1/g1 crank (150/180) AAA AA01 82 197 291 149 192 182 85 204 188 4.7 5.3 14 299 0.5 1 952 3.5 167
A-DNA with BI-like c/c1 AAA AA02 88 202 274 293 161 54 88 245 246 4.7 5.2 18 557 1.0 78 0.1 170
A-DNA similar to AA00, high a1 AAA AA03 80 224 263 337 155 27 80 192 202 4.9 5.6 16 33 0.1 797 1.4 66
A-DNA similar to AA00, low a1 AAA AA04 80 202 299 259 175 86 80 200 193 4.7 5.4 19 147 0.3 1 827 3.2 66
A-form variant, retro AAA AA05 83 221 285 134 237 187 84 210 184 4.5 4.8 65 1 0.0 285 0.5 32
A-form variant AAA AA06 80 214 256 135 229 181 82 196 180 4.6 5.2 16 21 0.0 523 0.9 34
A-form variant AAA AA07 82 241 218 296 140 55 80 201 198 6.7 6.7 345 0 0.0 92 0.2 39
A-form variant AAA AA08 82 234 275 306 152 56 80 189 197 4.6 5.4 23 152 0.3 8 572 15.2 447
A-form variant AAA AA09 89 231 273 300 155 52 85 214 232 4.7 5.4 25 59 0.1 262 0.5 36
A-DNA with a1/g1 crank (210/140) AAA AA10 79 203 313 210 154 143 80 199 183 4.8 5.4 13 13 0.0 490 0.9 161
A-DNA with a1/g1 crank (90/190) AAA AA11 81 261 225 91 257 192 83 190 180 4.6 5.1 10 6 0.0 240 0.4 35
A-like backbone but the bases can be partially intercalated AAA AA12 82 198 261 299 176 49 81 201 198 6.2 6.4 355 0 0.0 0 0.0 90
A-form variant with high z AAA AA13 83 190 241 307 174 51 82 197 190 7.3 6.9 343 0 0 0.0 37
A-to-B: d C3'-endo, d1 C2'-endo, c/c1 have A/B pattern A-B AB01 86 186 281 301 179 54 142 223 256 4.7 5.3 18 1 356 2.4 44 0.1 67
A-to-B: d~O4'-endo, extremely low e, c/c1 are B-like A-B AB02 93 59 56 208 189 65 131 237 251 4.4 4.9 23 133 0.2 1 0.0 28
A-to-B: similar to AB01 with high a1 and low z, b1, g1 A-B AB03 104 194 254 322 163 38 137 228 256 4.6 5.1 24 897 1.6 6 0.0 48
A-to-B A-B AB04 86 214 296 280 210 56 139 194 234 5.6 6.6 7 270 0.5 194 0.3 32
A-to-B A-B AB05 83 214 287 303 176 58 145 196 239 4.8 5.7 17 544 0.9 1 017 1.8 50
BI-to-A complex conformer with d1 from C3' to C4'-exo, c/c1 are B-like B1A BA01 136 189 255 300 161 53 88 254 225 4.2 4.7 29 721 1.3 4 0.0 36
BI-to-A complex conformer with d1 from C3' to O4'-endo, c/c1 are B-like B1A BA05 131 184 269 296 169 52 104 250 235 4.1 4.6 24 2 042 3.5 0 0.0 72
B-to-A: b1~120, c1 A-like B1A BA08 139 209 213 300 142 49 89 262 215 4.5 4.9 33 715 1.2 29 0.1 55
BI-to-A: b1~60, a1/g1 crank (250/170), c1 A-like B1A BA09 135 200 287 256 69 172 90 264 186 3.8 4.0 23 144 0.2 6 0.0 26
B-to-A complex cluster: a1~100, g1~180, c1 A-like B1A BA10 135 199 236 98 219 204 90 254 200 4.0 4.4 28 162 0.3 18 0.0 50
BII-to-A complex cluster: a1~60, g1~180, c1 A-like B2A BA13 141 222 199 81 230 196 88 265 198 4.2 4.6 31 175 0.3 41 0.1 44
BII-to-A: c1 A-like B2A BA16 150 251 183 61 230 199 83 262 196 4.5 4.8 31 38 0.1 39 0.1 220
BII-to-A: d1~O4'-endo, b1~120 B2A BA17 149 253 176 295 131 45 98 269 232 4.6 4.9 40 141 0.2 4 0.0 32
the most frequent DNA conformer, "canonical" B form, also called BI BBB BB00 138 183 258 303 180 44 138 253 258 4.4 5.0 26 19 289 33.5 8 0.0 1 925
less populated variant of BI form 2B1 BB01 130 181 266 301 176 49 120 247 244 4.3 4.9 26 3 562 6.2 0 0.0 136
less populated variant of BI form 2B1 BB17 130 147 275 229 241 80 136 243 269 4.6 5.2 24 203 0.4 1 0.0 25
BI with a1/g1 crank (30/300) 3B1 BB02 141 194 246 31 195 297 150 252 253 4.5 5.1 22 2 396 4.2 0 0.0 111
BI with a1/g1 crank (170/170) 3B1 BB03 144 176 275 163 164 174 147 240 233 4.5 5.2 26 345 0.6 1 0.0 28
BI-to-BII conformer B12 BB04 140 201 214 315 153 46 140 263 253 4.6 5.1 29 3 601 6.2 3 0.0 237
BI-to-BII with a1/g1 crank (70/230), c1 A-like B12 BB05 143 218 199 74 232 216 129 269 211 4.2 4.7 29 115 0.2 0 0.0 19
BII form, typical by e/z switch compared to BI BB2 BB07 144 247 169 297 141 46 141 271 260 5.0 5.2 46 2 780 4.8 18 0.0 325
BII form, variant, a1/g1 crank (60/210) BB2 BB08 146 248 184 67 225 208 147 268 235 4.7 5.1 30 145 0.3 8 0.0 28
B form with extremely low values of a1, b1, g1 miB BB10 138 196 192 22 106 19 130 257 258 4.4 4.9 26 936 1.6 0 0.0 52
B form with a1/g1 crank (120/180) miB BB11 145 200 199 123 227 187 144 256 222 4.7 5.2 29 248 0.4 1 0.0 24
BI with a1/g1 crank (250/170), low b1 70, c1 A-like miB BB12 140 196 280 257 76 171 140 268 205 3.9 4.2 24 462 0.8 0 0.0 92
BI with a1/g1 crank (210/160), low b1 100, c1 A-like miB BB13 143 187 293 219 99 161 146 253 218 4.4 4.9 25 250 0.4 0 0.0 31
B-form with extremely low e miB BB14 111 105 304 219 256 83 131 260 265 4.3 4.9 28 164 0.3 0 0.0 38
BI with high a1 and g1 near 0 miB BB15 144 188 256 345 189 350 150 252 264 4.4 5.0 23 551 1.0 3 0.0 45
B-like conformers but first c A-like, occurs where backbone accommodates deformation (metal ion near, strand crossing in Holliday junctions, ends of duplexes) miB BB16 138 224 283 285 170 48 140 203 271 5.0 5.5 33 647 1.1 1 0.0 67
B-like conformers with open and unparallel bases miB BB18 140 238 281 288 173 47 142 205 269 6.2 6.2 38 72 0.1 18 0.0 43
part. unstacked T-T in quadruplexes, unusual combination of e, z, a1, g1, c1 miB BB20 143 294 110 150 199 54 152 261 185 5.5 5.2 277 23 0.0 0 0.0 12
A-like with first base in syn orientation SYN AAS1 79 221 302 291 171 59 81 15 196 4.3 5.3 45 2 0.0 128 0.2 54
A-to-B-like but c1 syn, mostly in duplexes SYN AB1S 90 214 280 295 176 56 139 239 68 5.4 6.1 1 15 0.0 0 0.0 15
A-to-B-like but c2 syn, mostly in duplexes SYN AB2S 84 221 286 307 170 53 140 203 69 4.8 5.7 11 4 0.0 67 0.1 37
BI-like but c syn, may be in duplex but many G-G in quadruplexes SYN BBS1 147 187 275 296 172 52 135 64 260 3.9 4.5 45 305 0.5 0 0.0 39
G-G in quadruplexes, unusual b1, g1, c1 syn SYN BB1S 139 199 281 306 258 308 151 237 66 6.5 6.6 357 29 0.1 0 0.0 24
BI-like but c1 syn, mostly G-G in quadruplexes, a1 g+, g1 g- SYN BB2S 134 194 223 46 180 290 146 251 66 6.0 6.2 358 53 0.1 1 0.0 20
A-to-B like backbone but the bases can be intercalated ICL IC02 83 220 290 297 223 54 145 203 283 7.3 7.5 11 16 0.0 230 0.4 50
A-to-B like backbone but the bases can be intercalated ICL IC03 82 222 282 297 227 53 145 204 234 7.7 7.9 5 3 0.0 72 0.1 72
A-to-B like backbone but the bases can be intercalated ICL IC05 81 231 251 71 178 300 146 201 265 7.6 7.7 349 3 0.0 41 0.1 74
A-to-B like backbone but the bases can be intercalated ICL IC06 85 208 287 193 182 184 148 211 244 7.0 7.2 25 11 0.0 38 0.1 33
BII-like intercalated ICL IC07 141 256 172 290 178 49 147 275 275 7.3 7.1 45 28 0.0 7 0.0 24
unusual combination of backbone torsions, bases distant, parallel OPN OP01 83 224 122 276 146 46 82 202 193 8.3 7.4 196 0 0.0 93 0.2 41
unusual combination of backbone torsions, bases distant, parallel OPN OP02 83 226 156 292 159 43 86 207 176 9.0 8.3 259 0 0.0 39 0.1 12
unusual combination of backbone torsions, bases distant, perpendicular OPN OP03 78 226 301 175 138 51 84 199 194 7.5 7.4 202 0 0.0 221 0.4 64
unusual combination of backbone torsions, bases distant, parallel OPN OP04 80 221 285 166 170 52 85 205 194 7.3 7.2 205 0 0.0 306 0.5 68
unusual combination of backbone torsions, bases distant, open OPN OP05 78 204 51 69 127 45 84 201 187 9.1 8.9 264 0 0.0 40 0.1 14
unusual combination of backbone torsions, bases very distant OPN OP06 81 214 152 296 169 48 78 204 207 10.1 8.9 246 0 0.0 38 0.1 35
unusual combination of backbone torsions, bases very distant OPN OP07 81 240 202 288 152 48 79 202 189 7.7 7.5 321 0 0.0 62 0.1 85
unusual combination of backbone torsions, bases distant, skewed OPN OP08 82 199 271 199 149 52 147 205 249 7.8 6.7 168 0 0.0 65 0.1 20
unusual combination of backbone torsions, bases parallel OPN OP09 147 218 152 289 175 40 87 248 186 7.8 7.3 36 3 0.0 84 0.1 24
unusual combination of backbone torsions, bases distant, parallel OPN OP10 146 263 299 298 190 57 84 235 198 8.9 7.8 111 13 0.0 296 0.5 53
unusual combination of backbone torsions, bases distant, parallel OPN OP11 141 258 286 274 185 43 83 237 191 7.6 7.3 73 10 0.0 255 0.5 43
unusual combination of backbone torsions, bases distant, parallel OPN OP12 146 268 248 62 153 47 86 239 186 10.5 8.9 189 0 0.0 53 0.1 30
unusual combination of backbone torsions, bases distant OPN OP13 148 270 227 58 196 61 88 259 176 9.6 8.2 229 0 0.0 57 0.1 27
unusual combination of backbone torsions, bases parallel and hydrogen bonded OPN OP14 150 199 151 292 147 41 83 264 187 6.8 6.5 21 11 0.0 168 0.3 52
unusual combination of backbone torsions, bases distant OPN OP15 149 271 152 307 176 50 80 229 197 8.7 7.3 103 0 0.0 33 0.1 31
unusual combination of backbone torsions, bases distant OPN OP16 149 289 107 67 200 57 148 222 240 8.5 6.5 232 1 0.0 40 0.1 24
unusual combination of backbone torsions, bases distant OPN OP17 145 267 294 291 138 177 84 234 195 10.1 7.9 191 0 0.0 24 0.0 12
unusual combination of backbone torsions, bases distant OPN OP18 146 263 289 283 185 53 82 63 192 8.2 7.5 93 5 0.0 77 0.1 25
start of loop in quadruplex or hairpin, G-X, untypical z, a1, g1 OPN OP19 145 225 64 74 186 188 126 250 255 8.0 7.3 20 18 0.0 2 0.0 15
unstacked, in 4-way junction, e, z high values OPN OP20 141 271 283 299 192 55 147 259 217 8.7 7.9 67 52 0.1 95 0.2 28
5'-end of dsDNA, base open (unstacked), z, a1 ~60 OPN OP21 146 241 80 70 178 61 147 227 237 10.2 8.3 257 26 0.0 68 0.1 19
part. unstacked T-G/G-T in quadruplexes, c1 syn, unusual z, a1, g1 OPN OP22 144 207 60 82 203 191 147 242 68 7.6 7.0 65 26 0.0 0 0.0 12
unstacked OPN OP24 80 203 278 252 83 167 84 201 177 7.2 5.9 318 0 0.0 106 0.2 33
Z-like conformer (ZZS2), both bases in the anti orientation ZZZ ZZ01 81 210 49 166 150 49 147 208 226 4.6 6.0 306 4 0.0 303 0.5 238
Z form, Y-R step ZZZ ZZ1S 147 263 76 66 186 178 96 207 61 6.4 6.3 359 139 0.2 16 0.0 24
Z form, Y-R step, d1 C2'-endo ZZZ ZZ2S 141 263 71 78 180 185 147 208 77 6.4 6.2 356 67 0.1 6 0.0 43
ZI form, R-Y step ZZZ ZZS1 97 243 293 210 230 55 144 63 206 5.7 6.8 332 100 0.2 0 0.0 41
ZII form, R-Y step ZZZ ZZS2 95 187 64 169 162 44 143 56 213 5.7 6.7 329 22 0.0 0 0.0 15
Unassigned conformations NAN NANT x x x x x x x x x x x x 10 427 18.1 15 341 27.3 0
Annotation CANA NtC δ ε ζ α1 β1 γ1 δ1 χ χ1 NN CC NCCN 57 627 100.0 56 273 100.0 7 241
  # % # % golden set
1 2 3 4 5 6 7 8 9 DNA RNA

The previous versions of the server are available v1 here and v2 here.

© Jiří Černý & Bohdan Schneider