ID code: '1HHW' 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' DC A 1 alpha beta 4 23 9 7 38 C1' DT A 2 alpha beta 34 48 39 37 70 C1' DG A 3 alpha beta 66 88 71 69 103 C1' DA A 4 alpha beta 99 120 104 102 132 C1' TLN A 5 alpha beta 131 149 133 143 169 C1' DA A 6 alpha beta 165 186 170 168 201 C1' DT A 7 alpha beta 197 210 202 200 233 C1' DG A 8 alpha beta 229 251 234 232 266 C1' DC A 9 alpha beta 262 281 267 265 296 C1' G B 10 alpha beta 291 314 297 294 331 C1' C B 11 alpha beta 326 346 332 329 362 C1' A B 12 alpha beta 357 379 363 360 395 C1' U B 13 alpha beta 390 410 396 393 425 C1' A B 14 alpha beta 420 442 426 423 458 C1' U B 15 alpha beta 453 473 459 456 488 C1' C B 16 alpha beta 483 503 489 486 519 C1' A B 17 alpha beta 514 536 520 517 552 C1' G B 18 alpha beta 547 570 553 550 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 37 C2' DT A 2 OK OK 38 35 49 50 69 C2' DG A 3 OK OK 70 67 86 87 102 C2' DA A 4 OK OK 103 100 118 119 143 C2' TLN A 5 OK OK 132 142 156 144 168 C2' DA A 6 OK OK 169 166 184 185 200 C2' DT A 7 OK OK 201 198 211 212 232 C2' DG A 8 OK OK 233 230 249 250 265 C2' DC A 9 OK OK 266 263 279 280 294 C2' G B 10 OK OK 296 292 312 295 329 C2' C B 11 OK OK 331 327 344 330 360 C2' A B 12 OK OK 362 358 377 361 393 C2' U B 13 OK OK 395 391 408 394 423 C2' A B 14 OK OK 425 421 440 424 456 C2' U B 15 OK OK 458 454 471 457 486 C2' C B 16 OK OK 488 484 501 487 517 C2' A B 17 OK OK 519 515 534 518 550 C2' G B 18 OK OK 552 548 568 551 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 35 C3' DT A 2 OK OK 33 52 36 37 67 C3' DG A 3 OK OK 65 85 68 69 100 C3' DA A 4 OK OK 98 117 101 102 142 C3' TLN A 5 OK OK 130 155 145 143 166 C3' DA A 6 OK OK 164 183 167 168 198 C3' DT A 7 OK OK 196 214 199 200 230 C3' DG A 8 OK OK 228 248 231 232 263 C3' DC A 9 OK OK 261 278 264 265 292 C3' G B 10 OK OK 290 311 293 294 327 C3' C B 11 OK OK 325 343 328 329 358 C3' A B 12 OK OK 356 376 359 360 391 C3' U B 13 OK OK 389 407 392 393 421 C3' A B 14 OK OK 419 439 422 423 454 C3' U B 15 OK OK 452 470 455 456 484 C3' C B 16 OK OK 482 500 485 486 515 C3' A B 17 OK OK 513 533 516 517 548 C3' G B 18 OK OK 546 567 549 550 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 33 C4' DT A 2 OK OK 35 53 32 34 65 C4' DG A 3 OK OK 67 84 64 66 98 C4' DA A 4 OK OK 100 116 97 99 130 C4' TLN A 5 OK 142 129 131 164 C4' DA A 6 OK OK 166 182 163 165 196 C4' DT A 7 OK OK 198 215 195 197 228 C4' DG A 8 OK OK 230 247 227 229 261 C4' DC A 9 OK OK 263 277 260 262 290 C4' G B 10 OK OK 292 310 289 291 325 C4' C B 11 OK OK 327 342 324 326 356 C4' A B 12 OK OK 358 375 355 357 389 C4' U B 13 OK OK 391 406 388 390 419 C4' A B 14 OK OK 421 438 418 420 452 C4' U B 15 OK OK 454 469 451 453 482 C4' C B 16 OK OK 484 499 481 483 513 C4' A B 17 OK OK 515 532 512 514 546 C4' G B 18 OK OK 548 566 545 547 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 distorted distorted 1 17 18 3 32 C5' DT A 2 OK OK 31 54 55 33 64 C5' DG A 3 distorted distorted 63 82 83 65 97 C5' DA A 4 OK OK 96 114 115 98 129 C5' TLN A 5 OK OK 128 147 148 130 163 C5' DA A 6 OK OK 162 180 181 164 195 C5' DT A 7 OK OK 194 216 217 196 227 C5' DG A 8 distorted distorted 226 245 246 228 260 C5' DC A 9 OK OK 259 275 276 261 289 C5' G B 10 OK OK 288 308 309 290 324 C5' C B 11 OK OK 323 340 341 325 355 C5' A B 12 OK OK 354 373 374 356 388 C5' U B 13 OK OK 387 404 405 389 418 C5' A B 14 distorted distorted 417 436 437 419 451 C5' U B 15 OK OK 450 467 468 452 481 C5' C B 16 OK OK 480 497 498 482 512 C5' A B 17 distorted distorted 511 530 531 513 545 C5' G B 18 OK OK 544 564 565 546 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 28 P DT A 2 distorted distorted 6 29 30 31 60 P DG A 3 distorted distorted 36 61 62 63 93 P DA A 4 distorted distorted 68 94 95 96 125 P TLN A 5 distorted distorted 101 126 127 128 159 P DA A 6 distorted distorted 145 160 161 162 191 P DT A 7 distorted distorted 167 192 193 194 223 P DG A 8 distorted distorted 199 224 225 226 256 P DC A 9 distorted distorted 231 257 258 259 320 P C B 11 distorted distorted 293 321 322 323 351 P A B 12 distorted distorted 328 352 353 354 384 P U B 13 distorted distorted 359 385 386 387 414 P A B 14 distorted distorted 392 415 416 417 447 P U B 15 distorted distorted 422 448 449 450 477 P C B 16 distorted distorted 455 478 479 480 508 P A B 17 distorted distorted 485 509 510 511 541 P G B 18 distorted distorted 516 542 543 544 ---------------------------------------------------------------------------------