ID code: '1NBR' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' C A 7 alpha beta 204 224 210 207 240 C1' U A 8 alpha beta 235 255 241 238 270 C1' U A 9 alpha beta 265 285 271 268 300 C1' C A 10 alpha beta 295 315 301 298 331 C1' A A 11 alpha beta 326 348 332 329 364 C1' A A 12 alpha beta 359 381 365 362 397 C1' C A 13 alpha beta 392 412 398 395 428 C1' A A 14 alpha beta 423 445 429 426 461 C1' G A 15 alpha beta 456 479 462 459 495 C1' U A 16 alpha beta 490 510 496 493 525 C1' G A 17 alpha beta 520 543 526 523 559 C1' C A 18 alpha beta 554 574 560 557 590 C1' U A 19 alpha beta 585 605 591 588 620 C1' U A 20 alpha beta 615 635 621 618 650 C1' G A 21 alpha beta 645 668 651 648 684 C1' G A 22 alpha beta 679 702 685 682 718 C1' A A 23 alpha beta 713 735 719 716 751 C1' C A 24 alpha beta 746 766 752 749 782 C1' G A 25 alpha beta 777 800 783 780 816 C1' C A 26 alpha beta 811 831 817 814 847 C1' U A 27 alpha beta 842 862 848 845 877 C1' C A 28 alpha beta 872 892 878 875 908 C1' C A 29 alpha beta 903 924 909 906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' G A 6 OK OK 175 171 191 174 207 C2' C A 7 OK OK 209 205 222 208 238 C2' U A 8 OK OK 240 236 253 239 268 C2' U A 9 OK OK 270 266 283 269 298 C2' C A 10 OK OK 300 296 313 299 329 C2' A A 11 OK OK 331 327 346 330 362 C2' A A 12 OK OK 364 360 379 363 395 C2' C A 13 OK OK 397 393 410 396 426 C2' A A 14 OK OK 428 424 443 427 459 C2' G A 15 OK OK 461 457 477 460 493 C2' U A 16 OK OK 495 491 508 494 523 C2' G A 17 OK OK 525 521 541 524 557 C2' C A 18 OK OK 559 555 572 558 588 C2' U A 19 OK OK 590 586 603 589 618 C2' U A 20 OK OK 620 616 633 619 648 C2' G A 21 OK OK 650 646 666 649 682 C2' G A 22 OK OK 684 680 700 683 716 C2' A A 23 OK OK 718 714 733 717 749 C2' C A 24 OK OK 751 747 764 750 780 C2' G A 25 OK OK 782 778 798 781 814 C2' C A 26 OK OK 816 812 829 815 845 C2' U A 27 OK OK 847 843 860 846 875 C2' C A 28 OK OK 877 873 890 876 906 C2' C A 29 OK OK 908 904 922 907 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' G A 6 OK OK 169 190 172 173 205 C3' C A 7 OK OK 203 221 206 207 236 C3' U A 8 OK OK 234 252 237 238 266 C3' U A 9 OK OK 264 282 267 268 296 C3' C A 10 OK OK 294 312 297 298 327 C3' A A 11 OK OK 325 345 328 329 360 C3' A A 12 OK OK 358 378 361 362 393 C3' C A 13 OK OK 391 409 394 395 424 C3' A A 14 OK OK 422 442 425 426 457 C3' G A 15 OK OK 455 476 458 459 491 C3' U A 16 OK OK 489 507 492 493 521 C3' G A 17 OK OK 519 540 522 523 555 C3' C A 18 OK OK 553 571 556 557 586 C3' U A 19 OK OK 584 602 587 588 616 C3' U A 20 OK OK 614 632 617 618 646 C3' G A 21 OK OK 644 665 647 648 680 C3' G A 22 OK OK 678 699 681 682 714 C3' A A 23 OK OK 712 732 715 716 747 C3' C A 24 OK OK 745 763 748 749 778 C3' G A 25 OK OK 776 797 779 780 812 C3' C A 26 OK OK 810 828 813 814 843 C3' U A 27 OK OK 841 859 844 845 873 C3' C A 28 OK OK 871 889 874 875 904 C3' C A 29 OK OK 902 920 905 906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' G A 6 OK OK 171 189 168 170 203 C4' C A 7 OK OK 205 220 202 204 234 C4' U A 8 OK OK 236 251 233 235 264 C4' U A 9 OK OK 266 281 263 265 294 C4' C A 10 OK OK 296 311 293 295 325 C4' A A 11 OK OK 327 344 324 326 358 C4' A A 12 OK OK 360 377 357 359 391 C4' C A 13 OK OK 393 408 390 392 422 C4' A A 14 OK OK 424 441 421 423 455 C4' G A 15 OK OK 457 475 454 456 489 C4' U A 16 OK OK 491 506 488 490 519 C4' G A 17 OK OK 521 539 518 520 553 C4' C A 18 OK OK 555 570 552 554 584 C4' U A 19 OK OK 586 601 583 585 614 C4' U A 20 OK OK 616 631 613 615 644 C4' G A 21 OK OK 646 664 643 645 678 C4' G A 22 OK OK 680 698 677 679 712 C4' A A 23 OK OK 714 731 711 713 745 C4' C A 24 OK OK 747 762 744 746 776 C4' G A 25 OK OK 778 796 775 777 810 C4' C A 26 OK OK 812 827 809 811 841 C4' U A 27 OK OK 843 858 840 842 871 C4' C A 28 OK OK 873 888 870 872 902 C4' C A 29 OK OK 904 919 901 903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' G A 6 OK OK 167 187 188 169 202 C5' C A 7 OK OK 201 218 219 203 233 C5' U A 8 OK OK 232 249 250 234 263 C5' U A 9 OK OK 262 279 280 264 293 C5' C A 10 OK OK 292 309 310 294 324 C5' A A 11 OK OK 323 342 343 325 357 C5' A A 12 OK OK 356 375 376 358 390 C5' C A 13 OK OK 389 406 407 391 421 C5' A A 14 OK OK 420 439 440 422 454 C5' G A 15 OK OK 453 473 474 455 488 C5' U A 16 OK OK 487 504 505 489 518 C5' G A 17 OK OK 517 537 538 519 552 C5' C A 18 OK OK 551 568 569 553 583 C5' U A 19 OK OK 582 599 600 584 613 C5' U A 20 OK OK 612 629 630 614 643 C5' G A 21 OK OK 642 662 663 644 677 C5' G A 22 OK OK 676 696 697 678 711 C5' A A 23 OK OK 710 729 730 712 744 C5' C A 24 OK OK 743 760 761 745 775 C5' G A 25 OK OK 774 794 795 776 809 C5' C A 26 OK OK 808 825 826 810 840 C5' U A 27 OK OK 839 856 857 841 870 C5' C A 28 OK OK 869 886 887 871 901 C5' C A 29 OK OK 900 917 918 902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P G A 6 distorted distorted 142 165 166 167 198 P C A 7 distorted distorted 172 199 200 201 229 P U A 8 distorted distorted 206 230 231 232 259 P U A 9 distorted distorted 237 260 261 262 289 P C A 10 distorted distorted 267 290 291 292 320 P A A 11 distorted distorted 297 321 322 323 353 P A A 12 distorted distorted 328 354 355 356 386 P C A 13 distorted distorted 361 387 388 389 417 P A A 14 distorted distorted 394 418 419 420 450 P G A 15 distorted distorted 425 451 452 453 484 P U A 16 distorted distorted 458 485 486 487 514 P G A 17 distorted distorted 492 515 516 517 548 P C A 18 distorted distorted 522 549 550 551 579 P U A 19 distorted distorted 556 580 581 582 609 P U A 20 distorted distorted 587 610 611 612 639 P G A 21 distorted distorted 617 640 641 642 673 P G A 22 distorted distorted 647 674 675 676 707 P A A 23 distorted distorted 681 708 709 710 740 P C A 24 distorted distorted 715 741 742 743 771 P G A 25 distorted distorted 748 772 773 774 805 P C A 26 distorted distorted 779 806 807 808 836 P U A 27 distorted distorted 813 837 838 839 866 P C A 28 distorted distorted 844 867 868 869 897 P C A 29 distorted distorted 874 898 899 900 ---------------------------------------------------------------------------------