ID code: '1QDG' 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' G A 1 alpha beta 4 24 9 7 42 C1' G A 2 alpha beta 38 58 43 41 75 C1' T A 3 beta alpha 71 91 76 74 107 C1' T A 4 alpha beta 103 123 108 106 139 C1' G A 5 alpha beta 135 155 140 138 172 C1' G A 6 alpha beta 168 188 173 171 205 C1' T A 7 alpha beta 201 221 206 204 237 C1' G A 8 alpha beta 233 253 238 236 270 C1' T A 9 alpha beta 266 286 271 269 302 C1' G A 10 alpha beta 298 318 303 301 335 C1' G A 11 alpha beta 331 351 336 334 368 C1' T A 12 beta alpha 364 384 369 367 400 C1' T A 13 alpha beta 396 416 401 399 432 C1' G A 14 alpha beta 428 448 433 431 465 C1' G A 15 alpha beta 461 482 466 464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 8 5 29 30 41 C2' G A 2 OK OK 42 39 63 64 74 C2' T A 3 OK OK 75 72 89 90 106 C2' T A 4 OK OK 107 104 121 122 138 C2' G A 5 OK OK 139 136 160 161 171 C2' G A 6 OK OK 172 169 193 194 204 C2' T A 7 OK OK 205 202 219 220 236 C2' G A 8 OK OK 237 234 258 259 269 C2' T A 9 OK OK 270 267 284 285 301 C2' G A 10 OK OK 302 299 323 324 334 C2' G A 11 OK OK 335 332 356 357 367 C2' T A 12 OK OK 368 365 382 383 399 C2' T A 13 OK OK 400 397 414 415 431 C2' G A 14 OK OK 432 429 453 454 464 C2' G A 15 OK OK 465 462 487 488 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 23 6 7 39 C3' G A 2 OK OK 37 57 40 41 72 C3' T A 3 distorted distorted 70 88 73 74 104 C3' T A 4 OK OK 102 120 105 106 136 C3' G A 5 OK OK 134 154 137 138 169 C3' G A 6 OK OK 167 187 170 171 202 C3' T A 7 OK OK 200 218 203 204 234 C3' G A 8 distorted distorted 232 252 235 236 267 C3' T A 9 OK OK 265 283 268 269 299 C3' G A 10 OK OK 297 317 300 301 332 C3' G A 11 OK OK 330 350 333 334 365 C3' T A 12 distorted distorted 363 381 366 367 397 C3' T A 13 OK OK 395 413 398 399 429 C3' G A 14 OK OK 427 447 430 431 462 C3' G A 15 OK OK 460 480 463 464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 22 2 4 37 C4' G A 2 OK OK 39 56 36 38 70 C4' T A 3 distorted distorted 72 87 69 71 102 C4' T A 4 OK OK 104 119 101 103 134 C4' G A 5 OK OK 136 153 133 135 167 C4' G A 6 OK OK 169 186 166 168 200 C4' T A 7 OK OK 202 217 199 201 232 C4' G A 8 OK OK 234 251 231 233 265 C4' T A 9 OK OK 267 282 264 266 297 C4' G A 10 OK OK 299 316 296 298 330 C4' G A 11 OK OK 332 349 329 331 363 C4' T A 12 distorted distorted 365 380 362 364 395 C4' T A 13 OK OK 397 412 394 396 427 C4' G A 14 OK OK 429 446 426 428 460 C4' G A 15 OK OK 462 479 459 461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 20 21 3 36 C5' G A 2 OK OK 35 54 55 37 69 C5' T A 3 OK OK 68 85 86 70 101 C5' T A 4 OK OK 100 117 118 102 133 C5' G A 5 OK OK 132 151 152 134 166 C5' G A 6 OK OK 165 184 185 167 199 C5' T A 7 OK OK 198 215 216 200 231 C5' G A 8 OK OK 230 249 250 232 264 C5' T A 9 OK OK 263 280 281 265 296 C5' G A 10 OK OK 295 314 315 297 329 C5' G A 11 OK OK 328 347 348 330 362 C5' T A 12 OK OK 361 378 379 363 394 C5' T A 13 OK OK 393 410 411 395 426 C5' G A 14 OK OK 425 444 445 427 459 C5' G A 15 OK OK 458 477 478 460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 65 P T A 3 distorted distorted 40 66 67 68 97 P T A 4 distorted distorted 73 98 99 100 129 P G A 5 distorted distorted 105 130 131 132 162 P G A 6 distorted distorted 137 163 164 165 195 P T A 7 distorted distorted 170 196 197 198 227 P G A 8 distorted distorted 203 228 229 230 260 P T A 9 distorted distorted 235 261 262 263 292 P G A 10 distorted distorted 268 293 294 295 325 P G A 11 distorted distorted 300 326 327 328 358 P T A 12 distorted distorted 333 359 360 361 390 P T A 13 distorted distorted 366 391 392 393 422 P G A 14 distorted distorted 398 423 424 425 455 P G A 15 distorted distorted 430 456 457 458 ---------------------------------------------------------------------------------