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.

ntAntCAnnotationδεζα1β1γ1δ1χχ1count
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
A-B AB01 A-to-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A/B pattern 86 193 283 299 180 55 142 221 255 101
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 21
B1A BA01 BI-to-A complex conformer with δ1 from C3' to O4'-endo, χ/χ1 are B-like 135 188 253 303 159 53 87 258 225 20
B1A BA02 122 185 271 279 186 48 89 233 238 9
B1A BA03 130 194 263 282 178 48 89 238 236 15
B1A BA04 137 190 258 296 165 54 90 249 226 16
B1A BA05 128 183 257 297 169 52 97 243 222 14
B1A BA06 129 185 267 296 170 53 101 249 236 86
B1A BA07 137 181 271 289 177 53 107 256 242 19
B1A BA08 B-to-A: β1~120, χ1 A-like 141 212 188 302 129 55 85 271 211 12
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 129 189 223 131 219 184 94 252 198 13
B1A BA11 133 203 233 100 218 199 88 252 199 15
B1A BA12 141 208 202 89 244 199 85 267 191 21
B2A BA13 BII-to-A complex cluster: α1~60, γ1~180, χ1 A-like 142 224 191 80 237 196 92 271 197 20
B2A BA14 143 230 209 69 231 204 87 262 200 23
B2A BA15 142 240 187 75 227 189 88 267 201 19
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 1,960
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 46 140 263 253 244
B12 BB05 BI-to-BII with α1/γ1 crank (70/230), χ1 A-like 143 214 217 57 229 237 119 272 216 8
B12 BB06 143 223 193 73 233 212 126 265 205 14
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) 145 259 184 61 223 205 140 268 235 11
BB2 BB09 140 238 207 67 237 215 145 255 226 11
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 18
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) 144 215 301 278 180 42 144 194 281 11
miB BB17 141 249 288 287 155 47 137 201 286 13
miB BB18 147 226 274 286 168 53 145 199 278 30
miB BB19 145 218 274 295 182 55 142 191 245 38
miB BB20 142 233 295 294 165 50 139 188 257 7
miB BB21 143 237 283 283 173 47 143 207 276 18
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 c 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

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