Elixir IBT

DNATCO v3.1

Assignment of DNA and RNA conformers

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.

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*).
  • 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.
  • Contact the authors for off-line analysis of non-standard or large structures (multiple NMR MODELs or MD simulation trajectory).
Annotation CANA NtC Numbers of Steps in 1 2 3 4 5 6 7 8 9
DNA RNA GS, #    
# % # % δ ε ζ α1 β1 γ1 δ1 χ χ1 μ NN C'C'
the most frequent, "canonical" A form AAA AA00 1 802 3.1 21 173 37.1 291 82 206 288 293 173 55 82 199 200 18 4.8 5.5
A-DNA with B like χ/χ1 AAA AA02 570 1.0 80 0.1 170 88 202 274 293 161 54 88 245 246 18 4.7 5.2
A like, similar to AA00, high α1 AAA AA03 25 0.0 791 1.4 64 80 223 264 337 155 27 80 192 202 16 4.9 5.7
A like, similar to AA00, low α1 AAA AA04 123 0.2 1 761 3.1 65 80 202 299 259 175 85 80 199 193 19 4.7 5.4
A form variant AAA AA08 146 0.3 8 492 14.9 436 82 233 275 306 153 55 80 189 197 23 4.6 5.4
A form variant AAA AA09 20 0.0 220 0.4 27 87 232 272 302 154 52 85 217 233 24 4.7 5.4
A like, α1/ɣ1 crank (150/180) AAw AA01 276 0.5 1 886 3.3 159 81 197 291 149 192 182 85 204 188 14 4.7 5.3
A like, α1/ɣ1 crank (130/180) AAw AA05 1 0.0 270 0.5 32 83 221 285 134 237 187 84 210 184 65 4.5 4.8
A like, α1/ɣ1 crank (130/180) AAw AA06 14 0.0 473 0.8 32 80 214 256 135 229 180 82 196 180 16 4.6 5.2
A like, α1/ɣ1 crank (210/140) AAw AA10 12 0.0 456 0.8 151 79 203 313 210 154 143 80 199 183 13 4.8 5.4
A like, α1/ɣ1 crank (90/190) AAw AA11 5 0.0 211 0.4 34 81 261 226 91 257 192 83 189 179 11 4.6 5.0
A form with distant bases, low ζ AAu AA07 0 0.0 75 0.1 35 82 241 218 296 142 55 81 201 199 345 6.7 6.7
A like backbone, bases can be intercalated AAu AA12 6 0.0 588 1.0 78 82 198 261 298 176 50 81 201 197 354 6.2 6.4
A form with distant bases, low ζ AAu AA13 0 0.0 101 0.2 31 83 190 241 307 174 50 83 200 192 343 7.3 6.9
A-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A-B pattern A-B AB01 1 394 2.4 42 0.1 67 86 186 281 301 179 54 142 223 256 18 4.7 5.3
A-B: δ ~O4'-endo, extremely low ε, χ/χ1 are B like A-B AB02 104 0.2 0 0.0 22 94 59 56 208 188 66 131 239 250 23 4.4 4.8
A-B: similar to AB01 with high α1 and low ζ, β1, ɣ1 A-B AB03 577 1.0 0 0.0 28 103 195 255 321 162 40 136 228 256 23 4.6 5.1
A-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A/B pattern, C'C' high A-B AB04 220 0.4 164 0.3 28 87 215 297 280 209 55 139 194 233 8 5.6 6.6
A-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A/B pattern A-B AB05 540 0.9 975 1.7 50 83 214 287 303 176 58 145 196 239 17 4.8 5.7
BI-A complex conformer with δ1 from C3' to C4'-exo, χ/χ1 are B like B-A BA01 733 1.3 4 0.0 36 136 189 255 300 161 53 88 254 225 29 4.2 4.7
BI-A complex conformer with δ1 from C3' to C4'-exo, χ/χ1 are B like B-A BA05 1 952 3.4 0 0.0 70 131 184 269 296 169 52 104 251 235 24 4.1 4.6
BI-A: extremely low β1~60, α1/ɣ1 crank (260/170), χ1 A like B-A BA09 139 0.2 4 0.0 25 134 200 287 256 68 172 90 265 186 23 3.8 4.0
B-A: low β1 B-A BA08 606 1.1 20 0.0 39 139 208 213 301 141 49 89 263 215 33 4.4 4.9
B-A complex cluster: α1~90, ɣ1~180, χ1 A like B-A BA10 115 0.2 10 0.0 37 136 200 236 95 219 205 90 254 200 28 4.0 4.4
B-A complex cluster: α1~90, ɣ1~180, χ1 A like B-A BA13 168 0.3 40 0.1 44 141 222 199 81 230 196 88 265 198 31 4.2 4.6
BII-A: χ1 A like B-A BA16 37 0.1 39 0.1 220 150 251 183 61 230 199 83 262 196 31 4.5 4.8
BII-A: δ1~O4'-endo, β1~130 B-A BA17 122 0.2 2 0.0 30 149 253 177 295 131 44 98 271 233 38 4.5 4.9
the most frequent DNA conformer, "canonical" B form, also called BI BBB BB00 19 265 33.4 8 0.0 1 872 138 183 258 304 180 44 138 253 258 26 4.4 4.9
less populated variant of BI form BBB BB01 3 526 6.1 0 0.0 134 131 181 266 301 176 49 120 248 244 26 4.3 4.9
less populated variant of BI form, very low ε, α1, β1 BBw BB17 149 0.3 1 0.0 22 129 145 275 230 241 79 136 245 270 24 4.6 5.2
BI with α1/ɣ1 crank (30/300) BBw BB02 2 233 3.9 0 0.0 108 141 194 246 31 195 297 150 252 253 22 4.5 5.1
BI with α1/ɣ1 crank (160/170) BBw BB03 286 0.5 0 0.0 24 145 175 274 163 166 175 146 241 233 27 4.5 5.2
B form with α1/ɣ1 crank (120/190) and low both ε and ζ BBw BB11 208 0.4 0 0.0 23 145 199 200 123 227 187 144 256 223 29 4.6 5.1
B like, first χ A like BBw BB16 586 1.0 1 0.0 51 138 221 282 284 173 48 140 204 270 33 4.9 5.5
BI-BII conformer B12 BB04 3 543 6.1 3 0.0 235 140 201 214 315 153 46 140 263 253 29 4.6 5.1
BI-BII with α1/ɣ1 crank (70/220), χ1 A like B12 BB05 91 0.2 0 0.0 16 142 220 197 76 233 213 129 266 208 29 4.2 4.7
BII form, typical by ε/ζ switch compared to BI BB2 BB07 2 711 4.7 14 0.0 324 144 247 169 297 141 46 141 271 260 46 5.0 5.2
BII form variant with α1/ɣ1 switch (70/210) BB2 BB08 77 0.1 5 0.0 17 147 249 181 66 225 209 148 270 235 30 4.7 5.1
B form with extremely low values of α1, β1, ɣ1, and low ε and ζ miB BB10 777 1.3 0 0.0 50 138 196 192 22 106 19 129 257 258 26 4.4 4.9
BI like with α1/ɣ1 crank (260/170), low β1 70, χ1 A like miB BB12 445 0.8 0 0.0 90 140 196 280 257 76 171 140 269 205 24 3.9 4.2
BI like with α1/ɣ1 crank (220/160), low β1 70, χ1 A like miB BB13 214 0.4 0 0.0 30 143 187 293 219 98 161 146 253 219 25 4.4 4.9
B like with extremely low ε, high β miB BB14 148 0.3 0 0.0 33 110 104 305 220 255 83 133 259 265 29 4.3 4.9
BI with high α1 (340) and ɣ1 near 0 miB BB15 462 0.8 2 0.0 37 144 189 257 345 189 350 148 250 262 22 4.4 5.0
B like pucker, χ1 A like, unusual combination of ε, ζ, α1, ɣ1, χ1 miB BB20 23 0.0 0 0.0 12 143 294 110 150 199 54 152 261 185 277 5.5 5.2
A-B backbone, parallel distant bases can be intercalated ICL IC01 15 0.0 218 0.4 49 83 220 290 297 223 54 145 203 283 11 7.2 7.5
A-B backbone, parallel distant bases can be intercalated ICL IC02 4 0.0 58 0.1 66 82 220 281 297 226 54 145 204 233 3 7.6 7.8
A-B backbone, parallel distant bases can be intercalated, α1/ɣ1 crank (70/300), χ1 B like ICL IC03 1 0.0 29 0.1 70 81 231 251 71 179 299 146 201 265 349 7.6 7.7
A-B backbone, parallel distant bases can be intercalated, α1/ɣ1 crank (190/180), χ1 B like ICL IC04 10 0.0 28 0.0 25 85 206 287 194 181 183 149 212 244 25 7.0 7.2
BII backbone, parallel distant bases can be intercalated ICL IC05 28 0.0 5 0.0 22 141 255 174 289 178 50 147 273 275 46 7.3 7.1
B like, parallel distant bases can be intercalated, first χ A like ICL IC06 53 0.1 9 0.0 33 137 236 280 288 174 47 142 207 269 40 6.2 6.2
A-like intercalated ICL IC07 0 0.0 23 0.0 16 84 209 291 176 127 177 83 218 204 333 7.5 7.4
A pucker and χ torsions, unusual combination of backbone torsions, bases distant, parallel, low rise OPN OP01 0 0.0 80 0.1 35 83 221 122 279 145 45 82 205 194 195 8.3 7.4
A pucker and χ torsions, unusual combination of backbone torsions, bases distant, angled OPN OP02 0 0.0 37 0.1 12 83 226 156 292 159 43 86 207 176 259 9.0 8.3
A pucker and χ torsions, unusual combination of backbone torsions, base sangled, can be intercalated OPN OP03 0 0.0 219 0.4 61 78 226 300 175 138 51 84 199 195 202 7.5 7.5
A pucker and χ torsions, unusual combination of backbone torsions, base sangled, can be intercalated OPN OP04 0 0.0 286 0.5 63 80 221 285 166 171 52 85 206 194 206 7.2 7.1
A pucker and χ torsions, unusual combination of backbone torsions, bases distant, perpendicular OPN OP05 0 0.0 26 0.0 12 78 204 50 69 126 45 84 201 187 264 9.1 8.9
A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, low rise OPN OP06 0 0.0 31 0.1 32 81 214 151 297 169 47 78 204 207 245 10.1 8.9
A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, low rise OPN OP07 0 0.0 60 0.1 81 80 240 202 288 152 48 79 202 189 321 7.7 7.5
A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases parallel, low rise OPN OP08 0 0.0 105 0.2 33 80 203 278 252 83 167 84 201 177 318 7.2 5.9
A-B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP09 0 0.0 55 0.1 19 82 199 271 198 149 53 147 206 249 167 7.8 6.7
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, parallel OPN OP10 2 0.0 70 0.1 24 147 218 152 289 175 40 87 248 186 36 7.8 7.3
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, perpendicular OPN OP11 4 0.0 246 0.4 37 147 267 301 297 187 57 84 235 197 110 8.9 7.8
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP12 6 0.0 216 0.4 37 141 257 285 275 184 43 83 237 191 73 7.5 7.3
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, perpendicular OPN OP13 0 0.0 44 0.1 30 146 268 248 62 153 47 86 239 186 189 10.5 8.9
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP14 0 0.0 51 0.1 27 148 270 227 58 196 61 88 259 176 229 9.6 8.2
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases can pair with each other OPN OP15 8 0.0 144 0.3 42 150 196 149 292 147 41 84 265 186 18 6.9 6.6
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, perpendicular OPN OP16 0 0.0 26 0.0 28 149 270 154 308 175 49 79 229 197 102 8.8 7.3
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP17 0 0.0 19 0.0 12 145 267 294 291 138 177 84 234 195 191 10.1 7.9
B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP18 1 0.0 39 0.1 23 148 289 107 66 201 56 148 222 241 231 8.5 6.5
B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant OPN OP19 18 0.0 2 0.0 15 145 225 64 74 186 188 126 250 255 20 8.0 7.3
B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant in 4-way junction OPN OP20 33 0.1 58 0.1 22 140 271 283 298 190 56 148 260 217 67 8.6 7.8
B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant in 5'-end dsDNA OPN OP21 24 0.0 60 0.1 18 146 241 79 71 178 60 147 227 236 257 10.2 8.3
B pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant angled OPN OP22 39 0.1 50 0.1 36 147 245 126 286 162 49 142 233 231 44 6.9 6.4
B-like open, parallel bases OPN OP23 0 0.0 54 0.1 21 147 260 168 272 80 175 149 221 259 60 7.0 5.5
B-like open, low χ1, perpendicular bases OPN OP24 1 0.0 90 0.2 53 148 284 96 82 248 190 85 242 185 91 5.2 4.0
B-A open, perpendicular bases OPN OP25 0 0.0 27 0.0 21 145 261 178 95 209 63 86 283 192 260 8.1 7.2
B-A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases can pair with each other OPN OP26 0 0.0 50 0.1 16 145 265 161 211 166 50 81 240 191 16 7.0 6.9
B-A pucker, A-like χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP27 0 0.0 19 0.0 12 157 260 71 93 162 170 82 211 195 4 8.1 7.5
A-B pucker, A-like χ torsions, unusual combination of ε, ζ, α1, β1, bases distant, angled OPN OP28 0 0.0 33 0.1 10 82 226 166 292 159 43 145 196 233 235 8.6 7.9
A pucker and χ torsions, unusual combination of backbone torsions, bases distant OPN OP29 0 0.0 39 0.1 19 82 243 254 72 186 59 86 207 185 144 9.6 8.6
A pucker and χ torsions, unusual combination of backbone torsions, bases distant, parallel OPN OP30 0 0.0 13 0.0 10 82 244 196 76 171 49 89 197 181 81 10.5 9.7
A pucker and χ torsions, unusual combination of ε, ζ, α1, β1, bases distant angled OPN OP31 0 0.0 34 0.1 23 83 214 64 67 104 185 82 210 186 56 9.6 9.3
B-A pucker, unusual combination of ε, ζ, α1, β1, bases perpendicular, first syn OPN OPS1 3 0.0 63 0.1 23 146 263 289 283 184 53 82 63 192 94 8.2 7.5
B pucker, unusual combination of ε, ζ, α1, β1, bases angled, second syn OPN OP1S 26 0.0 0 0.0 12 144 207 60 82 203 191 147 242 68 65 7.6 7.0
A like with first base in syn orientation SYN AAS1 1 0.0 117 0.2 52 79 221 301 291 171 59 81 15 196 45 4.4 5.3
A-B, χ1 syn SYN AB1S 15 0.0 0 0.0 15 90 214 280 295 176 56 139 239 68 1 5.4 6.1
A-B, χ1 syn SYN AB2S 4 0.0 63 0.1 36 84 220 287 307 171 53 140 203 69 11 4.8 5.7
BI like, unusual β1 and ɣ1, χ1 syn SYN BB1S 28 0.0 0 0.0 24 139 199 281 306 258 308 151 237 66 357 6.5 6.6
BI like, α1 50, ɣ1 290, χ1 syn SYN BB2S 53 0.1 1 0.0 20 134 194 223 46 180 290 146 251 66 358 6.0 6.2
BI like, χ syn SYN BBS1 300 0.5 0 0.0 38 146 187 274 296 172 52 135 64 260 45 3.9 4.5
Z like conformer (ZZS2), both bases anti ZZZ ZZ01 4 0.0 301 0.5 237 81 210 49 166 150 49 147 208 226 306 4.6 6.0
similar toZZ1S with α1/ɣ1 switch (230/60), both bases anti ZZZ ZZ02 0 0.0 16 0.0 9 144 269 78 229 175 55 86 232 277 61 6.2 6.2
Z form, Y-R step ZZZ ZZ1S 139 0.2 16 0.0 24 147 263 76 66 186 178 96 207 61 359 6.4 6.3
Z form, Y-R step, d1 C2'-endo ZZZ ZZ2S 67 0.1 6 0.0 43 141 263 71 78 180 185 147 208 77 356 6.4 6.2
ZI form, R-Y step ZZZ ZZS1 99 0.2 0 0.0 40 97 243 293 210 231 56 144 63 206 332 5.7 6.8
ZII form, R-Y step ZZZ ZZS2 22 0.0 0 0.0 15 95 187 64 169 162 44 143 56 213 329 5.7 6.7
Unassigned conformations NAN NANT 12 175 21.1 15 864 27.8 0
Annotation CANA NtC 57 634 100.0 57 011 100.0 7 132 δ ε ζ α1 β1 γ1 δ1 χ χ1 μ NN C'C'
# % # % GS, #    
DNA RNA 1 2 3 4 5 6 7 8 9
Return up to random steps ( include large structures )

© Jiří Černý & Bohdan Schneider

News and changes:

  • v3.1:
    • User uploaded PDB and mmCIF formatted files are now supported.
    • Interactive scatter plot showing structural similarity of selected step.
    • Added an optional coloring of each NtC (represented as spheres centered at O3' and C5' atoms of a step).
  • 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 RCSB PDB and PDB-REDO uses PDBx (mmCIF) format internally.
      • This simplifies support for large structures, multiple MODELs, alternate positions, and insertion codes.
    • 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).

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

How to cite:

Download NtC data:

Definition of the conformers as torsion averages (csv) and their esd values (csv) or. as their Cartesian coordinates of the conformers

Download the papers:

description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
example of application:
Schneider et al., Genes, 8(10), 278, (2017).