ID code: '3GLP' 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 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' U A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' U A 6 beta 110 116 113 135 C1' G A 7 beta 130 136 133 158 C1' C A 8 beta 153 159 156 178 C1' G B 1 beta 171 179 176 282 C1' G B 4 beta 276 283 280 350 C1' U B 6 beta 345 351 348 370 C1' G B 7 beta 365 371 368 393 C1' C B 8 beta 388 394 391 411 C1' G C 1 beta 406 412 409 434 C1' C C 2 beta 429 435 432 454 C1' U C 3 beta 449 455 452 479 C1' G C 4 470 480 513 C1' C C 5 514 573 C1' G C 7 beta 568 574 571 596 C1' C C 8 beta 591 597 594 614 C1' G D 1 beta 609 615 612 637 C1' C D 2 beta 632 638 635 657 C1' U D 3 beta 652 658 655 677 C1' G D 4 beta 672 678 675 700 C1' C D 5 beta 695 701 698 720 C1' U D 6 beta 715 721 718 740 C1' G D 7 beta 735 741 738 763 C1' C D 8 beta 758 764 761 781 C1' G E 1 beta 776 782 779 804 C1' C E 2 beta 799 805 802 824 C1' U E 3 beta 819 825 822 844 C1' G E 4 beta 839 845 842 867 C1' C E 5 beta 862 868 865 887 C1' U E 6 beta 882 888 885 907 C1' G E 7 beta 902 908 905 930 C1' C E 8 beta 925 931 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' U A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' U A 6 OK 115 111 114 133 C2' G A 7 OK 135 131 134 156 C2' C A 8 OK 158 154 157 176 C2' G B 1 178 177 280 C2' G B 4 OK 282 277 281 348 C2' U B 6 OK 350 346 349 368 C2' G B 7 OK 370 366 369 391 C2' C B 8 OK 393 389 392 409 C2' G C 1 OK 411 407 410 432 C2' C C 2 OK 434 430 433 452 C2' U C 3 OK 454 450 453 571 C2' G C 7 OK 573 569 572 594 C2' C C 8 OK 596 592 595 612 C2' G D 1 OK 614 610 613 635 C2' C D 2 OK 637 633 636 655 C2' U D 3 OK 657 653 656 675 C2' G D 4 OK 677 673 676 698 C2' C D 5 OK 700 696 699 718 C2' U D 6 OK 720 716 719 738 C2' G D 7 OK 740 736 739 761 C2' C D 8 OK 763 759 762 779 C2' G E 1 OK 781 777 780 802 C2' C E 2 OK 804 800 803 822 C2' U E 3 OK 824 820 823 842 C2' G E 4 OK 844 840 843 865 C2' C E 5 OK 867 863 866 885 C2' U E 6 OK 887 883 886 905 C2' G E 7 OK 907 903 906 928 C2' C E 8 OK 930 926 929 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' U A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' U A 6 OK 109 112 113 131 C3' G A 7 OK 129 132 133 154 C3' C A 8 OK 152 155 156 277 C3' G B 4 275 280 346 C3' U B 6 OK 344 347 348 366 C3' G B 7 OK 364 367 368 389 C3' C B 8 OK 387 390 391 407 C3' G C 1 OK 405 408 409 430 C3' C C 2 OK 428 431 432 450 C3' U C 3 OK 448 451 452 569 C3' G C 7 OK 567 570 571 592 C3' C C 8 OK 590 593 594 610 C3' G D 1 OK 608 611 612 633 C3' C D 2 OK 631 634 635 653 C3' U D 3 OK 651 654 655 673 C3' G D 4 OK 671 674 675 696 C3' C D 5 OK 694 697 698 716 C3' U D 6 OK 714 717 718 736 C3' G D 7 OK 734 737 738 759 C3' C D 8 OK 757 760 761 777 C3' G E 1 OK 775 778 779 800 C3' C E 2 OK 798 801 802 820 C3' U E 3 OK 818 821 822 840 C3' G E 4 OK 838 841 842 863 C3' C E 5 OK 861 864 865 883 C3' U E 6 OK 881 884 885 903 C3' G E 7 OK 901 904 905 926 C3' C E 8 OK 924 927 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' U A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' U A 6 OK 111 108 110 129 C4' G A 7 OK 131 128 130 152 C4' C A 8 OK 154 151 153 170 C4' G B 1 169 171 275 C4' G B 4 OK 277 274 276 344 C4' U B 6 346 345 364 C4' G B 7 OK 366 363 365 387 C4' C B 8 OK 389 386 388 405 C4' G C 1 OK 407 404 406 428 C4' C C 2 OK 430 427 429 448 C4' U C 3 OK 450 447 449 567 C4' G C 7 OK 569 566 568 590 C4' C C 8 OK 592 589 591 608 C4' G D 1 OK 610 607 609 631 C4' C D 2 OK 633 630 632 651 C4' U D 3 OK 653 650 652 671 C4' G D 4 OK 673 670 672 694 C4' C D 5 OK 696 693 695 714 C4' U D 6 OK 716 713 715 734 C4' G D 7 OK 736 733 735 757 C4' C D 8 OK 759 756 758 775 C4' G E 1 OK 777 774 776 798 C4' C E 2 OK 800 797 799 818 C4' U E 3 OK 820 817 819 838 C4' G E 4 OK 840 837 839 861 C4' C E 5 OK 863 860 862 881 C4' U E 6 OK 883 880 882 901 C4' G E 7 OK 903 900 902 924 C4' C E 8 OK 926 923 925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' U A 3 44 46 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' U A 6 107 109 128 C5' G A 7 127 129 151 C5' C A 8 150 152 169 C5' G B 1 168 170 274 C5' G B 4 273 275 363 C5' G B 7 362 364 386 C5' C B 8 385 387 404 C5' G C 1 403 405 427 C5' C C 2 426 428 447 C5' U C 3 446 448 467 C5' G C 4 466 566 C5' G C 7 565 567 589 C5' C C 8 588 590 607 C5' G D 1 606 608 630 C5' C D 2 629 631 650 C5' U D 3 649 651 670 C5' G D 4 669 671 693 C5' C D 5 692 694 713 C5' U D 6 712 714 733 C5' G D 7 732 734 756 C5' C D 8 755 757 774 C5' G E 1 773 775 797 C5' C E 2 796 798 817 C5' U E 3 816 818 837 C5' G E 4 836 838 860 C5' C E 5 859 861 880 C5' U E 6 879 881 900 C5' G E 7 899 901 923 C5' C E 8 922 924 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P U A 3 distorted distorted 29 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P U A 6 distorted distorted 92 105 106 107 124 P G A 7 distorted distorted 112 125 126 127 147 P C A 8 distorted distorted 132 148 149 150 190 P C B 2 191 P C B 2 230 P U B 3 231 P U B 3 270 P G B 4 distorted distorted 271 272 273 294 P C B 5 295 P C B 5 334 P U B 6 335 P U B 6 359 P G B 7 distorted distorted 347 360 361 362 382 P C B 8 distorted distorted 367 383 384 385 423 P C C 2 distorted distorted 408 424 425 426 443 P U C 3 distorted distorted 431 444 445 446 463 P G C 4 distorted distorted 451 464 465 466 491 P C C 5 492 P C C 5 522 P U C 6 523 P U C 6 562 P G C 7 distorted distorted 563 564 565 585 P C C 8 distorted distorted 570 586 587 588 626 P C D 2 distorted distorted 611 627 628 629 646 P U D 3 distorted distorted 634 647 648 649 666 P G D 4 distorted distorted 654 667 668 669 689 P C D 5 distorted distorted 674 690 691 692 709 P U D 6 distorted distorted 697 710 711 712 729 P G D 7 distorted distorted 717 730 731 732 752 P C D 8 distorted distorted 737 753 754 755 793 P C E 2 distorted distorted 778 794 795 796 813 P U E 3 distorted distorted 801 814 815 816 833 P G E 4 distorted distorted 821 834 835 836 856 P C E 5 distorted distorted 841 857 858 859 876 P U E 6 distorted distorted 864 877 878 879 896 P G E 7 distorted distorted 884 897 898 899 919 P C E 8 distorted distorted 904 920 921 922 ---------------------------------------------------------------------------------