ID code: '1SKW' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 11 C1' DC P 14 beta 7 12 10 30 C1' DA P 15 beta 26 31 29 51 C1' DG P 16 beta 47 52 50 73 C1' DT P 17 beta 69 74 72 93 C1' DG P 18 beta 89 94 92 115 C1' DC P 19 beta 111 116 114 134 C1' DC P 20 beta 130 135 133 160 C1' 2DT P 21 beta 159 147 156 173 C1' DA T 6 beta 169 174 172 194 C1' DG T 7 beta 190 195 193 216 C1' DG T 8 beta 212 217 215 238 C1' DC T 9 beta 234 239 237 257 C1' DA T 10 beta 253 258 256 278 C1' DC T 11 beta 274 279 277 297 C1' DT T 12 beta 293 298 296 317 C1' DG T 13 beta 313 318 316 339 C1' DG T 14 beta 335 340 338 361 C1' DC T 15 beta 357 362 360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DC P 14 11 8 29 C2' DA P 15 30 27 50 C2' DG P 16 51 48 72 C2' DT P 17 73 70 92 C2' DG P 18 93 90 114 C2' DC P 19 115 112 133 C2' DC P 20 134 131 156 C2' 2DT P 21 160 161 172 C2' DA T 6 173 170 193 C2' DG T 7 194 191 215 C2' DG T 8 216 213 237 C2' DC T 9 238 235 256 C2' DA T 10 257 254 277 C2' DC T 11 278 275 296 C2' DT T 12 297 294 316 C2' DG T 13 317 314 338 C2' DG T 14 339 336 360 C2' DC T 15 361 358 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DC P 14 OK 6 9 10 27 C3' DA P 15 OK 25 28 29 48 C3' DG P 16 OK 46 49 50 70 C3' DT P 17 OK 68 71 72 90 C3' DG P 18 OK 88 91 92 112 C3' DC P 19 OK 110 113 114 131 C3' DC P 20 OK 129 132 133 161 C3' 2DT P 21 158 156 170 C3' DA T 6 OK 168 171 172 191 C3' DG T 7 OK 189 192 193 213 C3' DG T 8 OK 211 214 215 235 C3' DC T 9 OK 233 236 237 254 C3' DA T 10 OK 252 255 256 275 C3' DC T 11 OK 273 276 277 294 C3' DT T 12 OK 292 295 296 314 C3' DG T 13 OK 312 315 316 336 C3' DG T 14 OK 334 337 338 358 C3' DC T 15 OK 356 359 360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DC P 14 OK 8 5 7 25 C4' DA P 15 OK 27 24 26 46 C4' DG P 16 OK 48 45 47 68 C4' DT P 17 OK 70 67 69 88 C4' DG P 18 OK 90 87 89 110 C4' DC P 19 OK 112 109 111 129 C4' DC P 20 OK 131 128 130 158 C4' 2DT P 21 OK 161 157 159 168 C4' DA T 6 OK 170 167 169 189 C4' DG T 7 OK 191 188 190 211 C4' DG T 8 OK 213 210 212 233 C4' DC T 9 OK 235 232 234 252 C4' DA T 10 OK 254 251 253 273 C4' DC T 11 OK 275 272 274 292 C4' DT T 12 OK 294 291 293 312 C4' DG T 13 OK 314 311 313 334 C4' DG T 14 OK 336 333 335 356 C4' DC T 15 OK 358 355 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DC P 14 4 6 24 C5' DA P 15 23 25 45 C5' DG P 16 44 46 67 C5' DT P 17 66 68 87 C5' DG P 18 86 88 109 C5' DC P 19 108 110 128 C5' DC P 20 127 129 157 C5' 2DT P 21 146 158 167 C5' DA T 6 166 168 188 C5' DG T 7 187 189 210 C5' DG T 8 209 211 232 C5' DC T 9 231 233 251 C5' DA T 10 250 252 272 C5' DC T 11 271 273 291 C5' DT T 12 290 292 311 C5' DG T 13 310 312 333 C5' DG T 14 332 334 355 C5' DC T 15 354 356 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DC P 14 OK OK 2 3 4 20 P DA P 15 distorted distorted 9 21 22 23 41 P DG P 16 distorted distorted 28 42 43 44 63 P DT P 17 distorted distorted 49 64 65 66 83 P DG P 18 distorted distorted 71 84 85 86 105 P DC P 19 distorted distorted 91 106 107 108 124 P DC P 20 distorted distorted 113 125 126 127 143 P 2DT P 21 distorted distorted 132 144 145 146 163 P DA T 6 OK OK 164 165 166 184 P DG T 7 distorted distorted 171 185 186 187 206 P DG T 8 distorted distorted 192 207 208 209 228 P DC T 9 distorted distorted 214 229 230 231 247 P DA T 10 distorted distorted 236 248 249 250 268 P DC T 11 distorted distorted 255 269 270 271 287 P DT T 12 distorted distorted 276 288 289 290 307 P DG T 13 distorted distorted 295 308 309 310 329 P DG T 14 distorted distorted 315 330 331 332 351 P DC T 15 distorted distorted 337 352 353 354 ---------------------------------------------------------------------------------