ID code: '2LK3' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' A A 6 alpha beta 164 186 170 167 202 C1' G A 7 alpha beta 197 220 203 200 236 C1' A A 8 alpha beta 231 253 237 234 269 C1' U A 9 alpha beta 264 284 270 267 299 C1' C A 10 alpha beta 294 314 300 297 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' G A 12 alpha beta 358 381 364 361 397 C1' A A 13 alpha beta 392 414 398 395 430 C1' A A 14 alpha beta 425 447 431 428 463 C1' A A 15 alpha beta 458 480 464 461 496 C1' U A 16 alpha beta 491 511 497 494 526 C1' G A 17 alpha beta 521 544 527 524 560 C1' A A 18 alpha beta 555 577 561 558 593 C1' U A 19 alpha beta 588 608 594 591 623 C1' C A 20 alpha beta 618 638 624 621 654 C1' A A 21 alpha beta 649 671 655 652 687 C1' G A 22 alpha beta 682 705 688 685 721 C1' C A 23 alpha beta 716 736 722 719 752 C1' C A 24 alpha beta 747 768 753 750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' U A 5 OK OK 139 135 152 138 167 C2' A A 6 OK OK 169 165 184 168 200 C2' G A 7 OK OK 202 198 218 201 234 C2' A A 8 OK OK 236 232 251 235 267 C2' U A 9 OK OK 269 265 282 268 297 C2' C A 10 OK OK 299 295 312 298 328 C2' A A 11 OK OK 330 326 345 329 361 C2' G A 12 OK OK 363 359 379 362 395 C2' A A 13 OK OK 397 393 412 396 428 C2' A A 14 OK OK 430 426 445 429 461 C2' A A 15 OK OK 463 459 478 462 494 C2' U A 16 OK OK 496 492 509 495 524 C2' G A 17 OK OK 526 522 542 525 558 C2' A A 18 OK OK 560 556 575 559 591 C2' U A 19 OK OK 593 589 606 592 621 C2' C A 20 OK OK 623 619 636 622 652 C2' A A 21 OK OK 654 650 669 653 685 C2' G A 22 OK OK 687 683 703 686 719 C2' C A 23 OK OK 721 717 734 720 750 C2' C A 24 OK OK 752 748 766 751 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' U A 5 OK OK 133 151 136 137 165 C3' A A 6 OK OK 163 183 166 167 198 C3' G A 7 OK OK 196 217 199 200 232 C3' A A 8 OK OK 230 250 233 234 265 C3' U A 9 OK OK 263 281 266 267 295 C3' C A 10 OK OK 293 311 296 297 326 C3' A A 11 OK OK 324 344 327 328 359 C3' G A 12 OK OK 357 378 360 361 393 C3' A A 13 OK OK 391 411 394 395 426 C3' A A 14 OK OK 424 444 427 428 459 C3' A A 15 OK OK 457 477 460 461 492 C3' U A 16 OK OK 490 508 493 494 522 C3' G A 17 OK OK 520 541 523 524 556 C3' A A 18 OK OK 554 574 557 558 589 C3' U A 19 OK OK 587 605 590 591 619 C3' C A 20 OK OK 617 635 620 621 650 C3' A A 21 OK OK 648 668 651 652 683 C3' G A 22 OK OK 681 702 684 685 717 C3' C A 23 OK OK 715 733 718 719 748 C3' C A 24 OK OK 746 764 749 750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' U A 5 OK OK 135 150 132 134 163 C4' A A 6 OK OK 165 182 162 164 196 C4' G A 7 OK OK 198 216 195 197 230 C4' A A 8 OK OK 232 249 229 231 263 C4' U A 9 OK OK 265 280 262 264 293 C4' C A 10 OK OK 295 310 292 294 324 C4' A A 11 OK OK 326 343 323 325 357 C4' G A 12 OK OK 359 377 356 358 391 C4' A A 13 OK OK 393 410 390 392 424 C4' A A 14 OK OK 426 443 423 425 457 C4' A A 15 OK OK 459 476 456 458 490 C4' U A 16 OK OK 492 507 489 491 520 C4' G A 17 OK OK 522 540 519 521 554 C4' A A 18 OK OK 556 573 553 555 587 C4' U A 19 OK OK 589 604 586 588 617 C4' C A 20 OK OK 619 634 616 618 648 C4' A A 21 OK OK 650 667 647 649 681 C4' G A 22 OK OK 683 701 680 682 715 C4' C A 23 OK OK 717 732 714 716 746 C4' C A 24 OK OK 748 763 745 747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' U A 5 OK OK 131 148 149 133 162 C5' A A 6 OK OK 161 180 181 163 195 C5' G A 7 OK OK 194 214 215 196 229 C5' A A 8 OK OK 228 247 248 230 262 C5' U A 9 OK OK 261 278 279 263 292 C5' C A 10 OK OK 291 308 309 293 323 C5' A A 11 OK OK 322 341 342 324 356 C5' G A 12 OK OK 355 375 376 357 390 C5' A A 13 OK OK 389 408 409 391 423 C5' A A 14 OK OK 422 441 442 424 456 C5' A A 15 OK OK 455 474 475 457 489 C5' U A 16 OK OK 488 505 506 490 519 C5' G A 17 OK OK 518 538 539 520 553 C5' A A 18 OK OK 552 571 572 554 586 C5' U A 19 OK OK 585 602 603 587 616 C5' C A 20 OK OK 615 632 633 617 647 C5' A A 21 OK OK 646 665 666 648 680 C5' G A 22 OK OK 679 699 700 681 714 C5' C A 23 OK OK 713 730 731 715 745 C5' C A 24 OK OK 744 761 762 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P U A 5 distorted distorted 106 129 130 131 158 P A A 6 distorted distorted 136 159 160 161 191 P G A 7 distorted distorted 166 192 193 194 225 P A A 8 distorted distorted 199 226 227 228 258 P U A 9 distorted distorted 233 259 260 261 288 P C A 10 distorted distorted 266 289 290 291 319 P A A 11 distorted distorted 296 320 321 322 352 P G A 12 distorted distorted 327 353 354 355 386 P A A 13 distorted distorted 360 387 388 389 419 P A A 14 distorted distorted 394 420 421 422 452 P A A 15 distorted distorted 427 453 454 455 485 P U A 16 distorted distorted 460 486 487 488 515 P G A 17 distorted distorted 493 516 517 518 549 P A A 18 distorted distorted 523 550 551 552 582 P U A 19 distorted distorted 557 583 584 585 612 P C A 20 distorted distorted 590 613 614 615 643 P A A 21 distorted distorted 620 644 645 646 676 P G A 22 distorted distorted 651 677 678 679 710 P C A 23 distorted distorted 684 711 712 713 741 P C A 24 distorted distorted 718 742 743 744 ---------------------------------------------------------------------------------