ID code: '1UUD' 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 B 17 alpha beta 4 26 10 7 43 C1' G B 18 alpha beta 38 61 44 41 77 C1' C B 19 alpha beta 72 92 78 75 108 C1' A B 20 alpha beta 103 125 109 106 141 C1' G B 21 alpha beta 136 159 142 139 175 C1' A B 22 alpha beta 170 192 176 173 208 C1' U B 23 alpha beta 203 223 209 206 238 C1' C B 24 alpha beta 233 253 239 236 269 C1' U B 25 alpha beta 264 284 270 267 299 C1' G B 26 alpha beta 294 317 300 297 333 C1' A B 27 alpha beta 328 350 334 331 366 C1' G B 28 alpha beta 361 384 367 364 400 C1' C B 29 alpha beta 395 415 401 398 431 C1' C B 30 alpha beta 426 446 432 429 462 C1' U B 31 alpha beta 457 477 463 460 492 C1' G B 32 alpha beta 487 510 493 490 526 C1' G B 33 alpha beta 521 544 527 524 560 C1' G B 34 alpha beta 555 578 561 558 594 C1' A B 35 alpha beta 589 611 595 592 627 C1' G B 36 alpha beta 622 645 628 625 661 C1' C B 37 alpha beta 656 676 662 659 692 C1' U B 38 alpha beta 687 707 693 690 722 C1' C B 39 alpha beta 717 737 723 720 753 C1' U B 40 alpha beta 748 768 754 751 783 C1' C B 41 alpha beta 778 798 784 781 814 C1' U B 42 alpha beta 809 829 815 812 844 C1' G B 43 alpha beta 839 862 845 842 878 C1' C B 44 alpha beta 873 893 879 876 909 C1' C B 45 alpha beta 904 924 910 907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 17 OK 9 5 8 41 C2' G B 18 OK OK 43 39 59 42 75 C2' C B 19 OK OK 77 73 90 76 106 C2' A B 20 OK OK 108 104 123 107 139 C2' G B 21 OK OK 141 137 157 140 173 C2' A B 22 OK OK 175 171 190 174 206 C2' U B 23 OK OK 208 204 221 207 236 C2' C B 24 OK OK 238 234 251 237 267 C2' U B 25 OK OK 269 265 282 268 297 C2' G B 26 OK OK 299 295 315 298 331 C2' A B 27 OK OK 333 329 348 332 364 C2' G B 28 OK OK 366 362 382 365 398 C2' C B 29 OK OK 400 396 413 399 429 C2' C B 30 OK OK 431 427 444 430 460 C2' U B 31 OK OK 462 458 475 461 490 C2' G B 32 OK OK 492 488 508 491 524 C2' G B 33 OK OK 526 522 542 525 558 C2' G B 34 OK OK 560 556 576 559 592 C2' A B 35 OK OK 594 590 609 593 625 C2' G B 36 OK OK 627 623 643 626 659 C2' C B 37 OK OK 661 657 674 660 690 C2' U B 38 OK OK 692 688 705 691 720 C2' C B 39 OK OK 722 718 735 721 751 C2' U B 40 OK OK 753 749 766 752 781 C2' C B 41 OK OK 783 779 796 782 812 C2' U B 42 OK OK 814 810 827 813 842 C2' G B 43 OK OK 844 840 860 843 876 C2' C B 44 OK OK 878 874 891 877 907 C2' C B 45 OK OK 909 905 922 908 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 17 OK OK 3 24 6 7 39 C3' G B 18 OK OK 37 58 40 41 73 C3' C B 19 OK OK 71 89 74 75 104 C3' A B 20 OK OK 102 122 105 106 137 C3' G B 21 OK OK 135 156 138 139 171 C3' A B 22 OK OK 169 189 172 173 204 C3' U B 23 OK OK 202 220 205 206 234 C3' C B 24 OK OK 232 250 235 236 265 C3' U B 25 OK OK 263 281 266 267 295 C3' G B 26 OK OK 293 314 296 297 329 C3' A B 27 OK OK 327 347 330 331 362 C3' G B 28 OK OK 360 381 363 364 396 C3' C B 29 OK OK 394 412 397 398 427 C3' C B 30 OK OK 425 443 428 429 458 C3' U B 31 OK OK 456 474 459 460 488 C3' G B 32 OK OK 486 507 489 490 522 C3' G B 33 OK OK 520 541 523 524 556 C3' G B 34 OK OK 554 575 557 558 590 C3' A B 35 OK OK 588 608 591 592 623 C3' G B 36 OK OK 621 642 624 625 657 C3' C B 37 OK OK 655 673 658 659 688 C3' U B 38 OK OK 686 704 689 690 718 C3' C B 39 OK OK 716 734 719 720 749 C3' U B 40 OK OK 747 765 750 751 779 C3' C B 41 OK OK 777 795 780 781 810 C3' U B 42 OK OK 808 826 811 812 840 C3' G B 43 OK OK 838 859 841 842 874 C3' C B 44 OK OK 872 890 875 876 905 C3' C B 45 OK OK 903 921 906 907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 17 OK OK 5 23 2 4 37 C4' G B 18 OK OK 39 57 36 38 71 C4' C B 19 OK OK 73 88 70 72 102 C4' A B 20 OK OK 104 121 101 103 135 C4' G B 21 OK OK 137 155 134 136 169 C4' A B 22 OK OK 171 188 168 170 202 C4' U B 23 OK OK 204 219 201 203 232 C4' C B 24 OK OK 234 249 231 233 263 C4' U B 25 OK OK 265 280 262 264 293 C4' G B 26 OK OK 295 313 292 294 327 C4' A B 27 OK OK 329 346 326 328 360 C4' G B 28 OK OK 362 380 359 361 394 C4' C B 29 OK OK 396 411 393 395 425 C4' C B 30 OK OK 427 442 424 426 456 C4' U B 31 OK OK 458 473 455 457 486 C4' G B 32 OK OK 488 506 485 487 520 C4' G B 33 OK OK 522 540 519 521 554 C4' G B 34 OK OK 556 574 553 555 588 C4' A B 35 OK OK 590 607 587 589 621 C4' G B 36 OK OK 623 641 620 622 655 C4' C B 37 OK OK 657 672 654 656 686 C4' U B 38 OK OK 688 703 685 687 716 C4' C B 39 OK OK 718 733 715 717 747 C4' U B 40 OK OK 749 764 746 748 777 C4' C B 41 OK OK 779 794 776 778 808 C4' U B 42 OK OK 810 825 807 809 838 C4' G B 43 OK OK 840 858 837 839 872 C4' C B 44 OK OK 874 889 871 873 903 C4' C B 45 OK OK 905 920 902 904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 17 OK OK 1 21 22 3 36 C5' G B 18 OK OK 35 55 56 37 70 C5' C B 19 distorted distorted 69 86 87 71 101 C5' A B 20 OK OK 100 119 120 102 134 C5' G B 21 distorted distorted 133 153 154 135 168 C5' A B 22 distorted distorted 167 186 187 169 201 C5' U B 23 OK OK 200 217 218 202 231 C5' C B 24 distorted distorted 230 247 248 232 262 C5' U B 25 OK OK 261 278 279 263 292 C5' G B 26 distorted distorted 291 311 312 293 326 C5' A B 27 distorted distorted 325 344 345 327 359 C5' G B 28 OK OK 358 378 379 360 393 C5' C B 29 distorted distorted 392 409 410 394 424 C5' C B 30 OK OK 423 440 441 425 455 C5' U B 31 OK OK 454 471 472 456 485 C5' G B 32 distorted distorted 484 504 505 486 519 C5' G B 33 distorted distorted 518 538 539 520 553 C5' G B 34 distorted distorted 552 572 573 554 587 C5' A B 35 OK OK 586 605 606 588 620 C5' G B 36 OK OK 619 639 640 621 654 C5' C B 37 OK OK 653 670 671 655 685 C5' U B 38 distorted distorted 684 701 702 686 715 C5' C B 39 distorted distorted 714 731 732 716 746 C5' U B 40 distorted distorted 745 762 763 747 776 C5' C B 41 distorted distorted 775 792 793 777 807 C5' U B 42 OK OK 806 823 824 808 837 C5' G B 43 OK OK 836 856 857 838 871 C5' C B 44 OK OK 870 887 888 872 902 C5' C B 45 OK OK 901 918 919 903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G B 18 distorted distorted 6 33 34 35 66 P C B 19 distorted distorted 40 67 68 69 97 P A B 20 distorted distorted 74 98 99 100 130 P G B 21 distorted distorted 105 131 132 133 164 P A B 22 distorted distorted 138 165 166 167 197 P U B 23 distorted distorted 172 198 199 200 227 P C B 24 distorted distorted 205 228 229 230 258 P U B 25 distorted distorted 235 259 260 261 288 P G B 26 distorted distorted 266 289 290 291 322 P A B 27 distorted distorted 296 323 324 325 355 P G B 28 distorted distorted 330 356 357 358 389 P C B 29 distorted distorted 363 390 391 392 420 P C B 30 distorted distorted 397 421 422 423 451 P U B 31 distorted distorted 428 452 453 454 481 P G B 32 distorted distorted 459 482 483 484 515 P G B 33 distorted distorted 489 516 517 518 549 P G B 34 distorted distorted 523 550 551 552 583 P A B 35 distorted distorted 557 584 585 586 616 P G B 36 distorted distorted 591 617 618 619 650 P C B 37 distorted distorted 624 651 652 653 681 P U B 38 distorted distorted 658 682 683 684 711 P C B 39 distorted distorted 689 712 713 714 742 P U B 40 distorted distorted 719 743 744 745 772 P C B 41 distorted distorted 750 773 774 775 803 P U B 42 distorted distorted 780 804 805 806 833 P G B 43 distorted distorted 811 834 835 836 867 P C B 44 distorted distorted 841 868 869 870 898 P C B 45 distorted distorted 875 899 900 901 ---------------------------------------------------------------------------------