ID code: '4XNO' 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 beta 4 9 7 27 C1' DT A 2 beta 23 28 26 46 C1' BRU A 3 beta 51 37 47 67 C1' DA A 4 beta 63 68 66 88 C1' DT A 5 beta 84 89 87 110 C1' 1WA A 6 beta 115 109 111 132 C1' 1WA A 7 beta 137 131 133 154 C1' 1WA A 8 beta 159 153 155 174 C1' 1W5 A 9 179 175 196 C1' 1W5 A 10 201 197 218 C1' 1W5 A 11 223 219 240 C1' DA A 12 beta 236 241 239 261 C1' DT A 13 beta 257 262 260 281 C1' DA A 14 beta 277 282 280 302 C1' DA A 15 beta 298 303 301 323 C1' DG A 16 beta 319 324 322 343 C1' DC B 1 beta 339 344 342 362 C1' DT B 2 beta 358 363 361 381 C1' BRU B 3 beta 386 372 382 402 C1' DA B 4 beta 398 403 401 423 C1' DT B 5 beta 419 424 422 445 C1' 1WA B 6 beta 450 444 446 467 C1' 1WA B 7 beta 472 466 468 489 C1' 1WA B 8 beta 494 488 490 509 C1' 1W5 B 9 514 510 531 C1' 1W5 B 10 536 532 553 C1' 1W5 B 11 558 554 575 C1' DA B 12 beta 571 576 574 596 C1' DT B 13 beta 592 597 595 616 C1' DA B 14 beta 612 617 615 637 C1' DA B 15 beta 633 638 636 658 C1' DG B 16 beta 654 659 657 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 26 C2' DT A 2 27 24 47 C2' BRU A 3 46 48 66 C2' DA A 4 67 64 87 C2' DT A 5 88 85 111 C2' 1WA A 6 110 112 133 C2' 1WA A 7 132 134 155 C2' 1WA A 8 154 156 175 C2' 1W5 A 9 174 176 197 C2' 1W5 A 10 196 198 219 C2' 1W5 A 11 218 220 239 C2' DA A 12 240 237 260 C2' DT A 13 261 258 280 C2' DA A 14 281 278 301 C2' DA A 15 302 299 322 C2' DG A 16 323 320 342 C2' DC B 1 343 340 361 C2' DT B 2 362 359 382 C2' BRU B 3 381 383 401 C2' DA B 4 402 399 422 C2' DT B 5 423 420 446 C2' 1WA B 6 445 447 468 C2' 1WA B 7 467 469 490 C2' 1WA B 8 489 491 510 C2' 1W5 B 9 509 511 532 C2' 1W5 B 10 531 533 554 C2' 1W5 B 11 553 555 574 C2' DA B 12 575 572 595 C2' DT B 13 596 593 615 C2' DA B 14 616 613 636 C2' DA B 15 637 634 657 C2' DG B 16 658 655 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK 3 6 7 24 C3' DT A 2 OK 22 25 26 48 C3' BRU A 3 OK 49 50 47 64 C3' DA A 4 OK 62 65 66 85 C3' DT A 5 OK 83 86 87 112 C3' 1WA A 6 OK 114 113 111 134 C3' 1WA A 7 OK 136 135 133 156 C3' 1WA A 8 OK 158 157 155 176 C3' 1W5 A 9 OK 178 177 175 198 C3' 1W5 A 10 OK 200 199 197 220 C3' 1W5 A 11 OK 222 221 219 237 C3' DA A 12 OK 235 238 239 258 C3' DT A 13 OK 256 259 260 278 C3' DA A 14 OK 276 279 280 299 C3' DA A 15 OK 297 300 301 320 C3' DG A 16 OK 318 321 322 340 C3' DC B 1 OK 338 341 342 359 C3' DT B 2 OK 357 360 361 383 C3' BRU B 3 OK 384 385 382 399 C3' DA B 4 OK 397 400 401 420 C3' DT B 5 OK 418 421 422 447 C3' 1WA B 6 OK 449 448 446 469 C3' 1WA B 7 OK 471 470 468 491 C3' 1WA B 8 OK 493 492 490 511 C3' 1W5 B 9 OK 513 512 510 533 C3' 1W5 B 10 OK 535 534 532 555 C3' 1W5 B 11 OK 557 556 554 572 C3' DA B 12 OK 570 573 574 593 C3' DT B 13 OK 591 594 595 613 C3' DA B 14 OK 611 614 615 634 C3' DA B 15 OK 632 635 636 655 C3' DG B 16 OK 653 656 657 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK 5 2 4 22 C4' DT A 2 OK 24 21 23 49 C4' BRU A 3 OK 48 52 51 62 C4' DA A 4 OK 64 61 63 83 C4' DT A 5 OK 85 82 84 114 C4' 1WA A 6 OK 112 116 115 136 C4' 1WA A 7 OK 134 138 137 158 C4' 1WA A 8 OK 156 160 159 178 C4' 1W5 A 9 OK 176 180 179 200 C4' 1W5 A 10 OK 198 202 201 222 C4' 1W5 A 11 OK 220 224 223 235 C4' DA A 12 OK 237 234 236 256 C4' DT A 13 OK 258 255 257 276 C4' DA A 14 OK 278 275 277 297 C4' DA A 15 OK 299 296 298 318 C4' DG A 16 OK 320 317 319 338 C4' DC B 1 OK 340 337 339 357 C4' DT B 2 OK 359 356 358 384 C4' BRU B 3 OK 383 387 386 397 C4' DA B 4 OK 399 396 398 418 C4' DT B 5 OK 420 417 419 449 C4' 1WA B 6 OK 447 451 450 471 C4' 1WA B 7 OK 469 473 472 493 C4' 1WA B 8 OK 491 495 494 513 C4' 1W5 B 9 OK 511 515 514 535 C4' 1W5 B 10 OK 533 537 536 557 C4' 1W5 B 11 OK 555 559 558 570 C4' DA B 12 OK 572 569 571 591 C4' DT B 13 OK 593 590 592 611 C4' DA B 14 OK 613 610 612 632 C4' DA B 15 OK 634 631 633 653 C4' DG B 16 OK 655 652 654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 1 3 21 C5' DT A 2 20 22 52 C5' BRU A 3 53 49 61 C5' DA A 4 60 62 82 C5' DT A 5 81 83 116 C5' 1WA A 6 117 114 138 C5' 1WA A 7 139 136 160 C5' 1WA A 8 161 158 180 C5' 1W5 A 9 181 178 202 C5' 1W5 A 10 203 200 224 C5' 1W5 A 11 225 222 234 C5' DA A 12 233 235 255 C5' DT A 13 254 256 275 C5' DA A 14 274 276 296 C5' DA A 15 295 297 317 C5' DG A 16 316 318 337 C5' DC B 1 336 338 356 C5' DT B 2 355 357 387 C5' BRU B 3 388 384 396 C5' DA B 4 395 397 417 C5' DT B 5 416 418 451 C5' 1WA B 6 452 449 473 C5' 1WA B 7 474 471 495 C5' 1WA B 8 496 493 515 C5' 1W5 B 9 516 513 537 C5' 1W5 B 10 538 535 559 C5' 1W5 B 11 560 557 569 C5' DA B 12 568 570 590 C5' DT B 13 589 591 610 C5' DA B 14 609 611 631 C5' DA B 15 630 632 652 C5' DG B 16 651 653 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P DT A 2 distorted distorted 6 18 19 20 54 P BRU A 3 distorted distorted 25 55 56 53 57 P DA A 4 distorted distorted 50 58 59 60 78 P DT A 5 distorted distorted 65 79 80 81 98 P 1WA A 6 distorted distorted 86 118 119 117 120 P 1WA A 7 distorted distorted 113 140 141 139 142 P 1WA A 8 distorted distorted 135 162 163 161 165 P 1W5 A 9 distorted distorted 157 184 185 181 187 P 1W5 A 10 distorted distorted 177 206 207 203 209 P 1W5 A 11 distorted distorted 199 228 229 225 230 P DA A 12 distorted distorted 221 231 232 233 251 P DT A 13 distorted distorted 238 252 253 254 271 P DA A 14 distorted distorted 259 272 273 274 292 P DA A 15 distorted distorted 279 293 294 295 313 P DG A 16 distorted distorted 300 314 315 316 352 P DT B 2 distorted distorted 341 353 354 355 389 P BRU B 3 distorted distorted 360 390 391 388 392 P DA B 4 distorted distorted 385 393 394 395 413 P DT B 5 distorted distorted 400 414 415 416 433 P 1WA B 6 distorted distorted 421 453 454 452 455 P 1WA B 7 distorted distorted 448 475 476 474 477 P 1WA B 8 distorted distorted 470 497 498 496 500 P 1W5 B 9 distorted distorted 492 519 520 516 522 P 1W5 B 10 distorted distorted 512 541 542 538 544 P 1W5 B 11 distorted distorted 534 563 564 560 565 P DA B 12 distorted distorted 556 566 567 568 586 P DT B 13 distorted distorted 573 587 588 589 606 P DA B 14 distorted distorted 594 607 608 609 627 P DA B 15 distorted distorted 614 628 629 630 648 P DG B 16 distorted distorted 635 649 650 651 ---------------------------------------------------------------------------------