ID code: '3KDE' 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' --------------------------------------------------------------------------------- 8 C1' DG A 1 beta 4 9 7 30 C1' DT A 2 beta 26 31 29 50 C1' DT A 3 beta 46 51 49 70 C1' DA A 4 beta 66 71 69 91 C1' DA A 5 beta 87 92 90 112 C1' DG A 6 beta 108 113 111 133 C1' BRU A 7 beta 138 124 134 154 C1' DG A 8 beta 150 155 153 176 C1' DG A 9 beta 172 177 175 198 C1' DA A 10 beta 194 199 197 219 C1' BRU B 11 beta 224 210 220 237 C1' DC B 12 beta 233 238 236 256 C1' DC B 13 beta 252 257 255 275 C1' DA B 14 beta 271 276 274 296 C1' DC B 15 beta 292 297 295 315 C1' DT B 16 beta 311 316 314 335 C1' DT B 17 beta 331 336 334 355 C1' DA B 18 beta 351 356 354 376 C1' DA B 19 beta 372 377 375 397 C1' DC B 20 beta 393 398 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 8 5 29 C2' DT A 2 30 27 49 C2' DT A 3 50 47 69 C2' DA A 4 70 67 90 C2' DA A 5 91 88 111 C2' DG A 6 112 109 134 C2' BRU A 7 133 135 153 C2' DG A 8 154 151 175 C2' DG A 9 176 173 197 C2' DA A 10 198 195 220 C2' BRU B 11 219 221 236 C2' DC B 12 237 234 255 C2' DC B 13 256 253 274 C2' DA B 14 275 272 295 C2' DC B 15 296 293 314 C2' DT B 16 315 312 334 C2' DT B 17 335 332 354 C2' DA B 18 355 352 375 C2' DA B 19 376 373 396 C2' DC B 20 397 394 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK 3 6 7 27 C3' DT A 2 OK 25 28 29 47 C3' DT A 3 OK 45 48 49 67 C3' DA A 4 OK 65 68 69 88 C3' DA A 5 OK 86 89 90 109 C3' DG A 6 OK 107 110 111 135 C3' BRU A 7 OK 136 137 134 151 C3' DG A 8 OK 149 152 153 173 C3' DG A 9 OK 171 174 175 195 C3' DA A 10 OK 193 196 197 221 C3' BRU B 11 OK 222 223 220 234 C3' DC B 12 OK 232 235 236 253 C3' DC B 13 OK 251 254 255 272 C3' DA B 14 OK 270 273 274 293 C3' DC B 15 OK 291 294 295 312 C3' DT B 16 OK 310 313 314 332 C3' DT B 17 OK 330 333 334 352 C3' DA B 18 OK 350 353 354 373 C3' DA B 19 OK 371 374 375 394 C3' DC B 20 OK 392 395 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK 5 2 4 25 C4' DT A 2 OK 27 24 26 45 C4' DT A 3 OK 47 44 46 65 C4' DA A 4 OK 67 64 66 86 C4' DA A 5 OK 88 85 87 107 C4' DG A 6 OK 109 106 108 136 C4' BRU A 7 OK 135 139 138 149 C4' DG A 8 OK 151 148 150 171 C4' DG A 9 OK 173 170 172 193 C4' DA A 10 OK 195 192 194 222 C4' BRU B 11 OK 221 225 224 232 C4' DC B 12 OK 234 231 233 251 C4' DC B 13 OK 253 250 252 270 C4' DA B 14 OK 272 269 271 291 C4' DC B 15 OK 293 290 292 310 C4' DT B 16 OK 312 309 311 330 C4' DT B 17 OK 332 329 331 350 C4' DA B 18 OK 352 349 351 371 C4' DA B 19 OK 373 370 372 392 C4' DC B 20 OK 394 391 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 1 3 24 C5' DT A 2 23 25 44 C5' DT A 3 43 45 64 C5' DA A 4 63 65 85 C5' DA A 5 84 86 106 C5' DG A 6 105 107 139 C5' BRU A 7 140 136 148 C5' DG A 8 147 149 170 C5' DG A 9 169 171 192 C5' DA A 10 191 193 225 C5' BRU B 11 226 222 231 C5' DC B 12 230 232 250 C5' DC B 13 249 251 269 C5' DA B 14 268 270 290 C5' DC B 15 289 291 309 C5' DT B 16 308 310 329 C5' DT B 17 328 330 349 C5' DA B 18 348 350 370 C5' DA B 19 369 371 391 C5' DC B 20 390 392 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DT A 2 distorted distorted 6 21 22 23 40 P DT A 3 distorted distorted 28 41 42 43 60 P DA A 4 distorted distorted 48 61 62 63 81 P DA A 5 distorted distorted 68 82 83 84 102 P DG A 6 distorted distorted 89 103 104 105 141 P BRU A 7 distorted distorted 110 142 143 140 144 P DG A 8 distorted distorted 137 145 146 147 166 P DG A 9 distorted distorted 152 167 168 169 188 P DA A 10 distorted distorted 174 189 190 191 227 P DC B 12 distorted distorted 223 228 229 230 246 P DC B 13 distorted distorted 235 247 248 249 265 P DA B 14 distorted distorted 254 266 267 268 286 P DC B 15 distorted distorted 273 287 288 289 305 P DT B 16 distorted distorted 294 306 307 308 325 P DT B 17 distorted distorted 313 326 327 328 345 P DA B 18 distorted distorted 333 346 347 348 366 P DA B 19 distorted distorted 353 367 368 369 387 P DC B 20 distorted distorted 374 388 389 390 ---------------------------------------------------------------------------------