Assignment of DNA conformers (DNATCO v2.3)

Tutorial

Test run (PDB ID 1bna)

The server assigns 44 DNA conformers based on the values of their 9 backbone torsion angles.

  • 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. "NS" lables steps with Not Stacked 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 45th conformer.
  • The webserver in version 2 is described in Černý et al., Nucleic Acids Research, 44, W284 (2016).
  • More information about the conformers and the ways how the conformers were identified will be published but the current assignement improves the conformers described 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*).
  • 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.


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News and changes:

  • v2.3:
    • the improved assignment protocol involves known δ/psudorotation 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/B/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).

Nucleotide conformers (NtC) used for the structural assignment of steps. Their detailed description will be published but the current assignment improves the conformers described in Svozil et al. Nucleic Acids Research, 36, 3690 (2008).
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. "NS" lables steps with Not Stacked bases. "S" at 3rd or 4th position means that the 1st or 2nd base is in syn orientation.

CANANtCAnnotationδεζα1β1γ1δ1χχ1count
AAA AA00 The most frequent, "canonical" A-DNA (identical to A-RNA) 83 206 287 293 174 55 83 199 202 296
AAA AA01 A-DNA with α1/γ1 crank (150/180) 82 194 291 149 193 182 87 205 188 55
AAA AA02 A-DNA with BI-like χ/χ1 88 203 275 294 161 54 88 244 245 168
AAA AA03 A-DNA similar to AA01, high α1 83 214 273 330 165 26 86 202 215 9
AAA AA04 A-DNA similar to AA01, low α1 80 198 301 255 175 91 83 202 192 14
A-B AB01 A-to-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A/B pattern 86 193 283 299 180 55 142 221 255 100
A-B AB02 A-to-B: δ~O4'-endo, extremely low ε, χ/χ1 are B-like 92 61 59 208 185 64 133 237 253 18
A-B AB03 A-to-B: similar to AB01 with high α1 and low ζ, β1, γ1 96 195 253 344 151 33 131 220 250 11
B1A BA01 BI-to-A complex conformer with δ1 from C3' to O4'-endo, χ/χ1 are B-like 133 190 259 292 169 51 89 247 230 54
B1A BA05 BI-to-A complex conformer with δ1 from C3' to O4'-endo, χ/χ1 are B-like 130 184 266 295 171 53 101 249 235 107
B1A BA09 BI-to-A: β1~60, α1/γ1 crank (250/170), χ1 A-like 135 199 287 254 71 168 86 265 187 13
B1A BA10 B-to-A complex cluster: α1~100, γ1~180, χ1 A-like 135 201 217 103 229 195 88 258 195 43
B2A BA08 BII-to-A: β1~120, χ1 A-like 141 212 188 302 129 55 85 271 211 12
B2A BA13 BII-to-A complex cluster: α1~60, γ1~180, χ1 A-like 142 231 197 74 232 197 89 266 199 57
B2A BA16 BII-to-A: χ1 A-like 145 255 187 63 226 196 87 260 201 7
B2A BA17 BII-to-A: δ1~O4'-endo, β1~120 148 255 177 294 130 44 96 272 234 27
BBB BB00 The most frequent DNA conformer, "canonical" B form, also called BI 138 183 259 303 180 44 138 252 258 1,958
2B1 BB01 Less populated variant of BI form 132 181 265 301 177 49 121 248 244 142
3B1 BB02 BI with α1/γ1 crank (30/300) 140 194 246 32 194 297 150 252 253 134
3B1 BB03 BI with α1/γ1 crank (170/170) 145 176 276 166 164 173 146 239 232 31
B12 BB04 BI-to-BII conformer 140 201 214 315 153 46 140 263 253 243
B12 BB05 BI-to-BII with α1/γ1 crank (70/230), χ1 A-like 143 220 202 67 231 221 124 268 209 20
BB2 BB07 BII form, typical by ε/ζ switch compared to BI 144 245 171 297 141 46 141 270 259 371
BB2 BB08 BII form, variant, α1/γ1 crank (60/210) 142 248 195 64 230 210 142 262 230 19
miB BB10 B form with extremely low values of α1, β1, γ1 139 195 191 23 106 19 129 257 258 49
miB BB11 B form with α1/γ1 crank (120/180) 144 200 199 121 226 189 143 258 222 22
miB BB12 BI with α1/γ1 crank (250/170), low β1 70, χ1 A-like 140 196 287 248 73 172 144 263 212 18
miB BB13 BI with α1/γ1 crank (210/160), low β1 100, χ1 A-like 143 186 291 216 104 161 147 252 219 17
miB BB14 B-form with extremely low ε 121 104 303 229 260 73 132 264 263 8
miB BB15 BI with high α1 and γ1 near 0 149 187 261 341 192 354 148 250 261 17
miB BB16 Complex cluster of B-like conformers: A-like χ, bases may be unstacked to incorporate intercalated drug, occurs where backbone accommodates deformation (metal ion near, strand crossing in Holliday junctions, ends of duplexes) 145 227 281 288 173 51 142 197 267 117
SQX AB1S A-to-B-like but χ1 syn, mostly in duplexes 91 214 280 295 176 56 139 238 67 14
SQX BBS1 BI-like but χ syn, may be in duplex but many G-G in quadruplexes 146 189 275 294 174 52 135 62 261 47
SQX BB1S G-G in quadruplexes, unusual β1, γ1, χ1 syn 140 202 282 307 258 304 151 236 65 17
SQX BB2S BI-like but χ1 syn, mostly G-G in quadruplexes, α1 g+, γ1 g- 137 196 225 33 187 295 145 257 70 8
SQX NS1S Partially unstacked T-G/G-T in quadruplexes, χ1 syn, unusual ζ, α1, γ1 143 206 61 82 204 192 146 242 68 13
SQX NS02 Start of loop in quadruplex or hairpin, G-X, untypical ζ, α1, γ1 145 225 67 74 189 191 137 264 258 14
SQX NS03 Partially unstacked T-T in quadruplexes, unusual combination of ε, ζ, α1, γ1, χ1 143 294 111 153 197 53 151 262 185 13
SQX NS04 Unstacked, in 4-way junction, ε, ζ high values 140 275 279 304 191 56 150 266 210 12
SQX NS05 5'-end of dsDNA, base open (unstacked), ζ, α1 ~60 154 242 77 63 177 64 137 237 249 10
ZZZ ZZ1S Z form, Y-R step 148 264 76 66 186 179 95 205 60 20
ZZZ ZZ2S Z form, Y-R step, δ1 C2'-endo 141 263 71 78 179 185 148 208 77 41
ZZZ ZZS1 ZI form, R-Y step 97 242 294 209 230 55 144 63 205 48
ZZZ ZZS2 ZII form, R-Y step 95 186 63 169 162 44 144 58 213 17

The assignment is performed in the torsional space by the modified k-nearest neighbors algorithm according to Čech et al. BMC Bioinformatics, 2013, doi: 10.1186/1471-2105-14 -205

Download

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

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

© Jiří Černý & Bohdan Schneider