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Assignment of DNA conformers

The server assigns 18 conformers based on the values of their backbone torsion angles.

  • Table defining the conformers is below and Cartesian coordinates of their representative samples can be downloaded.
  • The conformers consist of three BI-forms, two BII-forms, three A-forms, three Z-forms, four mixed A/B forms, and three conformers with bases in the syn orientation.
  • Conformationally extreme conformers are not assigned to any of the above; these steps formally represent the 19th conformer.
  • More information about the conformers and the ways how the conformers were identified can be found in the paper by Svozil et al., Nucleic Acids Research, 36, 3690 (2008).

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.


or


Nucleotide conformers (ntC) used for the assignment of steps. Conformers are identified by numbers as in Svozil et al. Nucleic Acids Research, 36, 3690 (2008).

ntC Description δ ε ζ α+1 β+1 γ+1 δ+1 χ χ+1
8 "canonical" A-DNA 83 205 287 294 174 54 83 199 203
13 A-DNA, BI-like χ 89 201 275 294 162 54 89 244 244
19 A-DNA, α+1/γ+1 crank 84 194 290 149 192 182 88 205 188
41 A-to-B, δ>C3'-, δ+1 C2'-endo 90 196 280 299 179 55 142 222 256
32 BI-to-A, δ+1 O4'-endo 129 186 264 295 170 52 98 247 233
109 BII-to-A, δ+1>C3'-endo 142 213 181 297 139 52 90 273 207
110 as 109 plus α+1/γ+1 crank, high β+1 146 257 186 60 224 196 90 260 200
54 "canonical" BI 136 183 259 303 181 44 138 252 259
50 BI variant 129 181 265 300 177 50 123 246 245
86 BII variant 140 201 216 314 154 46 140 262 253
96 BII variant 143 245 170 297 141 46 141 271 257
116 BI, α+1/γ+1 crank, α/γ normal 140 194 247 31 197 296 150 253 253
119 BI, 5'-mismatch, χ syn, α/γ crank 144 189 266 303 167 53 138 70 259
121 3'-mismatch, χ+1 syn, δ O4'-endo 99 209 278 295 174 54 128 243 67
122 as 121 plus α+1/γ+1 crank 136 196 225 33 187 295 145 257 70
123 Z, Y/R step 147 264 76 66 186 179 95 205 61
124 Z, R/Y step, ZI 96 242 294 209 231 55 144 63 205
126 Z, R/Y step, ZII 95 187 62 169 162 44 144 58 213
NN Not Assigned

The assignment is performed in the torsional space by the k-nearest neighbors algorithm [Čech et. al, BMC Bioinformatics, (2013), to be published].

© Jiří Černý & Bohdan Schneider