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 10 11 12
DNA RNA GS, #    
# % # % δ1 ε1 ζ1 α2 β2 γ2 δ2 χ1 χ2 μ NN C'C'
the most frequent, canonical A form AAA AA00 1 805 3.1 21 177 37.1 291 82 206 288 293 173 55 82 199 200 18 4.8 5.5
A-DNA with B like χ AAA AA02 595 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 α AAA AA03 32 0.1 806 1.4 64 80 223 264 337 155 27 80 192 202 16 4.9 5.7
A like, similar to AA00, low α AAA AA04 148 0.3 1 830 3.2 65 80 202 299 259 175 85 80 199 193 19 4.7 5.4
A form variant AAA AA08 150 0.3 8 527 15.0 436 82 233 275 306 153 55 80 189 197 23 4.6 5.4
A form variant AAA AA09 22 0.0 230 0.4 27 87 232 272 302 154 52 85 217 233 24 4.7 5.4
A like, α/ɣ switch (150/180) AAw AA01 284 0.5 1 859 3.3 159 81 197 291 149 192 182 85 204 188 14 4.7 5.3
A like, α/ɣ switch (130/180) AAw AA05 7 0.0 385 0.7 51 82 214 291 140 225 182 85 209 184 57 4.3 4.8
A like, α/ɣ switch (130/180) AAw AA06 18 0.0 513 0.9 32 80 214 256 135 229 180 82 196 180 16 4.6 5.2
A like, α/ɣ switch (210/140) AAw AA10 15 0.0 488 0.9 151 79 203 313 210 154 143 80 199 183 13 4.8 5.4
A like, α/ɣ switch (90/190) AAw AA11 6 0.0 240 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 1 0.0 95 0.2 41 83 243 216 296 144 53 82 203 203 345 6.8 6.8
A like backbone, bases can be intercalated AAu AA12 7 0.0 616 1.1 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 0.0 105 0.2 31 83 190 241 307 174 50 83 200 192 343 7.3 6.9
A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A-B pattern A-B AB01 1 438 2.5 43 0.1 67 86 186 281 301 179 54 142 223 256 18 4.7 5.3
A-B: δ1 O4'-endo, extremely low ε, χ1/χ2 are B like A-B AB02 120 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 α and low ζ, β, ɣ A-B AB03 627 1.1 0 0.0 28 103 195 255 321 162 40 136 228 256 23 4.6 5.1
A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A/B pattern, C'C' high A-B AB04 247 0.4 189 0.3 28 87 215 297 280 209 55 139 194 233 8 5.6 6.6
A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A/B pattern A-B AB05 549 1.0 1 024 1.8 50 83 214 287 303 176 58 145 196 239 17 4.8 5.7
BI-A complex conformer with δ2 from C3' to C4'-exo, χ1/χ2 are B like B-A BA01 735 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 δ2 from C3' to C4'-exo, χ1/χ2 are B like B-A BA05 2 001 3.5 0 0.0 70 131 184 269 296 169 52 104 251 235 24 4.1 4.6
BI-A: extremely low β~60, α/ɣ switch (260/170), χ2 A like B-A BA09 668 1.2 23 0.0 39 139 208 213 301 141 49 89 263 215 33 4.4 4.9
B-A: low β B-A BA08 143 0.2 6 0.0 25 134 200 287 256 68 172 90 265 186 23 3.8 4.0
B-A with α~90, ɣ~180, χ1 A like B-A BA10 129 0.2 13 0.0 37 136 200 236 95 219 205 90 254 200 28 4.0 4.4
B-A with α~90, ɣ~180, χ1 A like B-A BA13 158 0.3 31 0.1 38 142 220 200 81 231 196 88 265 197 31 4.2 4.6
BII-A: χ2 A like B-A BA16 66 0.1 54 0.1 59 146 246 190 61 229 199 85 266 199 29 4.4 4.8
BII-A: δ2~O4'-endo, β~130 B-A BA17 143 0.2 3 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 19 360 33.6 8 0.0 1 872 138 183 258 304 180 44 138 253 258 26 4.4 4.9
less populated variant of the BI form BBB BB01 3 558 6.2 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, α, β BBw BB17 191 0.3 1 0.0 22 129 145 275 230 241 79 136 245 270 24 4.6 5.2
BI with α/ɣ switch (30/300) BBw BB02 2 362 4.1 0 0.0 108 141 194 246 31 195 297 150 252 253 22 4.5 5.1
BI form with α/ɣ switch (160/170) BBw BB03 331 0.6 0 0.0 24 145 175 274 163 166 175 146 241 233 27 4.5 5.2
B form with α/ɣ switch (120/190) and low ε and ζ BBw BB11 250 0.4 1 0.0 23 145 199 200 123 227 187 144 256 223 29 4.6 5.1
B like conformer, χ2 A like BBw BB16 636 1.1 2 0.0 51 138 221 282 284 173 48 140 204 270 33 4.9 5.5
Conformer bridging BI and BII forms B12 BB04 3 584 6.2 3 0.0 235 140 201 214 315 153 46 140 263 253 29 4.6 5.1
Conformer bridging BI and BII forms with α/ɣ switch (70/220), χ2 A like B12 BB05 104 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 2 774 4.8 17 0.0 324 144 247 169 297 141 46 141 271 260 46 5.0 5.2
BII form variant with α/ɣ switch (70/210) BB2 BB08 92 0.2 6 0.0 17 147 249 181 66 225 209 148 270 235 30 4.7 5.1
B form with extremely low values of α, β, ɣ, and low ε and ζ miB BB10 901 1.6 0 0.0 50 138 196 192 22 106 19 129 257 258 26 4.4 4.9
BI like with α/ɣ switch (260/170), low β 70, χ2 A like miB BB12 456 0.8 0 0.0 90 140 196 280 257 76 171 140 269 205 24 3.9 4.2
BI like with α/ɣ switch (220/160), low β 70, χ2 A like miB BB13 242 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 161 0.3 0 0.0 33 110 104 305 220 255 83 133 259 265 29 4.3 4.9
BI like with high α (340) and ɣ near 0 miB BB15 520 0.9 2 0.0 37 144 189 257 345 189 350 148 250 262 22 4.4 5.0
B like pucker, χ2 A like, unusual combination of ε, ζ, α, ɣ, χ2 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 16 0.0 211 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 6 0.0 86 0.2 36 82 222 279 299 225 52 143 201 244 2 7.7 7.8
A-B backbone, parallel distant bases can be intercalated, α/ɣ switch (70/300), χ2 B like ICL IC03 1 0.0 30 0.1 17 81 239 256 69 178 302 145 200 265 359 7.5 7.8
A-B backbone, parallel distant bases can be intercalated, α/ɣ switch (190/180), χ1 B like ICL IC04 10 0.0 34 0.1 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 29 0.1 7 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, χ A like ICL IC06 63 0.1 13 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 27 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 89 0.2 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 39 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 0.0 224 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 0.0 299 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 31 0.1 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, α, β, bases distant, low rise OPN OP06 0 0.0 45 0.1 25 82 213 143 301 172 48 81 204 201 243 10.1 9.0
A pucker and χ torsions, unusual combination of ε, ζ, α, β, low rise OPN OP07 0 0.0 67 0.1 22 82 247 194 293 149 44 81 196 188 324 7.8 7.5
A pucker and χ torsions, unusual combination of ε, ζ, α, β, bases parallel, low rise OPN OP08 0 0.0 106 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, α, β, bases distant, angled OPN OP09 0 0.0 75 0.1 38 82 198 269 203 146 51 148 203 250 163 7.8 6.7
B-A pucker and χ torsions, unusual combination of ε, ζ, α, β, bases distant, parallel OPN OP10 2 0.0 83 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, α, β, bases distant, perpendicular OPN OP11 6 0.0 281 0.5 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, α, β, bases distant, angled OPN OP12 8 0.0 238 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, α, β, bases distant, perpendicular OPN OP13 0 0.0 51 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, α, β, bases distant, angled OPN OP14 0 0.0 57 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, α, β, bases can pair with each other OPN OP15 12 0.0 169 0.3 45 149 201 151 292 149 41 86 265 188 22 6.9 6.6
B-A pucker and χ torsions, unusual combination of ε, ζ, α, β, bases distant, perpendicular OPN OP16 0 0.0 33 0.1 21 147 268 150 309 178 47 80 229 195 101 8.9 7.4
B-A pucker and χ torsions, unusual combination of ε, ζ, α, β, bases distant, angled OPN OP17 0 0.0 24 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, α, β, bases distant, angled. Similar to OPS1 OPN OP18 1 0.0 49 0.1 34 149 291 106 66 198 55 147 225 242 230 8.6 6.5
B pucker and χ torsions, unusual combination of ε, ζ, α, β, 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, α, β, bases distant in 4-way junction OPN OP20 39 0.1 78 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, α, β, bases distant in 5'-end dsDNA OPN OP21 26 0.0 58 0.1 21 149 242 80 67 177 62 144 228 244 245 10.3 8.2
B pucker and χ torsions, unusual combination of ε, ζ, α, β, bases distant angled OPN OP22 44 0.1 64 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 56 0.1 21 147 260 168 272 80 175 149 221 259 60 7.0 5.5
B-like open, low χ2, perpendicular bases OPN OP24 1 0.0 92 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 28 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, α, β, bases can pair with each other OPN OP26 1 0.0 63 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, α, β, 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, α, β, bases distant, angled OPN OP28 0 0.0 37 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 40 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 14 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, α, β, bases distant angled OPN OP31 0 0.0 38 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, α, β, bases perpendicular, first base syn OPN OPS1 5 0.0 78 0.1 23 146 263 289 283 184 53 82 63 192 94 8.2 7.5
B pucker, unusual combination of ε, ζ, α, β, bases angled, second base 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 2 0.0 125 0.2 52 79 221 301 291 171 59 81 15 196 45 4.4 5.3
A-B, second base 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, second base syn SYN AB2S 4 0.0 66 0.1 36 84 220 287 307 171 53 140 203 69 11 4.8 5.7
BI like, unusual β and ɣ, second base syn SYN BB1S 29 0.1 0 0.0 24 139 199 281 306 258 308 151 237 66 357 6.5 6.6
BI like, α 50, ɣ 290,second base 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, first base syn SYN BBS1 307 0.5 0 0.0 38 146 187 274 296 172 52 135 64 260 45 3.9 4.5
Z like conformer similar to ZZS2, both bases anti ZZZ ZZ01 4 0.0 303 0.5 237 81 210 49 166 150 49 147 208 226 306 4.6 6.0
Z like conformer similar to ZZ1S with α/ɣ 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, δ2 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 100 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 10 919 18.9 15 062 26.4 0
Annotation CANA NtC 57 634 100.0 57 011 100.0 6 870 δ1 ε1 ζ1 α2 β2 γ2 δ2 χ1 χ2 μ NN C'C'
# % # % GS, #    
DNA RNA 1 2 3 4 5 6 7 8 9 10 11 12
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).