ID code: '3SQ0' 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' --------------------------------------------------------------------------------- 7386 C1' DT T 1 beta 7382 7387 7385 7406 C1' DC T 2 beta 7402 7407 7405 7425 C1' DA T 3 beta 7421 7426 7424 7446 C1' DA T 4 beta 7442 7447 7445 7467 C1' DG T 5 beta 7463 7468 7466 7489 C1' DT T 6 beta 7485 7490 7488 7509 C1' DA T 7 beta 7505 7510 7508 7530 C1' DA T 8 beta 7526 7531 7529 7551 C1' DG T 9 beta 7547 7552 7550 7573 C1' DC T 10 beta 7569 7574 7572 7592 C1' DA T 11 beta 7588 7593 7591 7613 C1' DG T 12 beta 7609 7614 7612 7635 C1' DT T 13 beta 7631 7636 7634 7655 C1' DC T 14 beta 7651 7656 7654 7674 C1' DC T 15 beta 7670 7675 7673 7693 C1' DG T 16 beta 7689 7694 7692 7715 C1' DC T 17 beta 7711 7716 7714 7734 C1' DG T 18 beta 7730 7735 7733 7754 C1' DG P 103 beta 7750 7755 7753 7776 C1' DC P 104 beta 7772 7777 7775 7795 C1' DG P 105 beta 7791 7796 7794 7817 C1' DG P 106 beta 7813 7818 7816 7839 C1' DA P 107 beta 7835 7840 7838 7860 C1' DC P 108 beta 7856 7861 7859 7879 C1' DT P 109 beta 7875 7880 7878 7899 C1' DG P 110 beta 7895 7900 7898 7921 C1' DC P 111 beta 7917 7922 7920 7940 C1' DT P 112 beta 7936 7941 7939 7960 C1' DT P 113 beta 7956 7961 7959 7980 C1' DA P 114 beta 7976 7981 7979 7999 C1' DOC P 115 beta 8003 7991 8000 8018 C1' DUP A 904 beta 8022 8017 8019 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7385 C2' DT T 1 7386 7383 7405 C2' DC T 2 7406 7403 7424 C2' DA T 3 7425 7422 7445 C2' DA T 4 7446 7443 7466 C2' DG T 5 7467 7464 7488 C2' DT T 6 7489 7486 7508 C2' DA T 7 7509 7506 7529 C2' DA T 8 7530 7527 7550 C2' DG T 9 7551 7548 7572 C2' DC T 10 7573 7570 7591 C2' DA T 11 7592 7589 7612 C2' DG T 12 7613 7610 7634 C2' DT T 13 7635 7632 7654 C2' DC T 14 7655 7652 7673 C2' DC T 15 7674 7671 7692 C2' DG T 16 7693 7690 7714 C2' DC T 17 7715 7712 7733 C2' DG T 18 7734 7731 7753 C2' DG P 103 7754 7751 7775 C2' DC P 104 7776 7773 7794 C2' DG P 105 7795 7792 7816 C2' DG P 106 7817 7814 7838 C2' DA P 107 7839 7836 7859 C2' DC P 108 7860 7857 7878 C2' DT P 109 7879 7876 7898 C2' DG P 110 7899 7896 7920 C2' DC P 111 7921 7918 7939 C2' DT P 112 7940 7937 7959 C2' DT P 113 7960 7957 7979 C2' DA P 114 7980 7977 8000 C2' DOC P 115 7999 8001 8019 C2' DUP A 904 8018 8020 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7383 C3' DT T 1 OK 7381 7384 7385 7403 C3' DC T 2 OK 7401 7404 7405 7422 C3' DA T 3 OK 7420 7423 7424 7443 C3' DA T 4 OK 7441 7444 7445 7464 C3' DG T 5 OK 7462 7465 7466 7486 C3' DT T 6 OK 7484 7487 7488 7506 C3' DA T 7 OK 7504 7507 7508 7527 C3' DA T 8 OK 7525 7528 7529 7548 C3' DG T 9 OK 7546 7549 7550 7570 C3' DC T 10 OK 7568 7571 7572 7589 C3' DA T 11 OK 7587 7590 7591 7610 C3' DG T 12 OK 7608 7611 7612 7632 C3' DT T 13 OK 7630 7633 7634 7652 C3' DC T 14 OK 7650 7653 7654 7671 C3' DC T 15 OK 7669 7672 7673 7690 C3' DG T 16 OK 7688 7691 7692 7712 C3' DC T 17 OK 7710 7713 7714 7731 C3' DG T 18 OK 7729 7732 7733 7751 C3' DG P 103 OK 7749 7752 7753 7773 C3' DC P 104 OK 7771 7774 7775 7792 C3' DG P 105 OK 7790 7793 7794 7814 C3' DG P 106 OK 7812 7815 7816 7836 C3' DA P 107 OK 7834 7837 7838 7857 C3' DC P 108 OK 7855 7858 7859 7876 C3' DT P 109 OK 7874 7877 7878 7896 C3' DG P 110 OK 7894 7897 7898 7918 C3' DC P 111 OK 7916 7919 7920 7937 C3' DT P 112 OK 7935 7938 7939 7957 C3' DT P 113 OK 7955 7958 7959 7977 C3' DA P 114 OK 7975 7978 7979 8001 C3' DOC P 115 8002 8000 8020 C3' DUP A 904 OK 8023 8021 8019 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7381 C4' DT T 1 OK 7383 7380 7382 7401 C4' DC T 2 OK 7403 7400 7402 7420 C4' DA T 3 OK 7422 7419 7421 7441 C4' DA T 4 OK 7443 7440 7442 7462 C4' DG T 5 OK 7464 7461 7463 7484 C4' DT T 6 OK 7486 7483 7485 7504 C4' DA T 7 OK 7506 7503 7505 7525 C4' DA T 8 OK 7527 7524 7526 7546 C4' DG T 9 OK 7548 7545 7547 7568 C4' DC T 10 OK 7570 7567 7569 7587 C4' DA T 11 OK 7589 7586 7588 7608 C4' DG T 12 OK 7610 7607 7609 7630 C4' DT T 13 OK 7632 7629 7631 7650 C4' DC T 14 OK 7652 7649 7651 7669 C4' DC T 15 OK 7671 7668 7670 7688 C4' DG T 16 OK 7690 7687 7689 7710 C4' DC T 17 OK 7712 7709 7711 7729 C4' DG T 18 OK 7731 7728 7730 7749 C4' DG P 103 OK 7751 7748 7750 7771 C4' DC P 104 OK 7773 7770 7772 7790 C4' DG P 105 OK 7792 7789 7791 7812 C4' DG P 106 OK 7814 7811 7813 7834 C4' DA P 107 OK 7836 7833 7835 7855 C4' DC P 108 OK 7857 7854 7856 7874 C4' DT P 109 OK 7876 7873 7875 7894 C4' DG P 110 OK 7896 7893 7895 7916 C4' DC P 111 OK 7918 7915 7917 7935 C4' DT P 112 OK 7937 7934 7936 7955 C4' DT P 113 OK 7957 7954 7956 7975 C4' DA P 114 OK 7977 7974 7976 8002 C4' DOC P 115 OK 8001 8004 8003 8023 C4' DUP A 904 OK 8020 8024 8022 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7380 C5' DT T 1 7379 7381 7400 C5' DC T 2 7399 7401 7419 C5' DA T 3 7418 7420 7440 C5' DA T 4 7439 7441 7461 C5' DG T 5 7460 7462 7483 C5' DT T 6 7482 7484 7503 C5' DA T 7 7502 7504 7524 C5' DA T 8 7523 7525 7545 C5' DG T 9 7544 7546 7567 C5' DC T 10 7566 7568 7586 C5' DA T 11 7585 7587 7607 C5' DG T 12 7606 7608 7629 C5' DT T 13 7628 7630 7649 C5' DC T 14 7648 7650 7668 C5' DC T 15 7667 7669 7687 C5' DG T 16 7686 7688 7709 C5' DC T 17 7708 7710 7728 C5' DG T 18 7727 7729 7748 C5' DG P 103 7747 7749 7770 C5' DC P 104 7769 7771 7789 C5' DG P 105 7788 7790 7811 C5' DG P 106 7810 7812 7833 C5' DA P 107 7832 7834 7854 C5' DC P 108 7853 7855 7873 C5' DT P 109 7872 7874 7893 C5' DG P 110 7892 7894 7915 C5' DC P 111 7914 7916 7934 C5' DT P 112 7933 7935 7954 C5' DT P 113 7953 7955 7974 C5' DA P 114 7973 7975 8004 C5' DOC P 115 8005 8002 8024 C5' DUP A 904 8025 8023 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7396 P DC T 2 distorted distorted 7384 7397 7398 7399 7415 P DA T 3 distorted distorted 7404 7416 7417 7418 7436 P DA T 4 distorted distorted 7423 7437 7438 7439 7457 P DG T 5 distorted distorted 7444 7458 7459 7460 7479 P DT T 6 distorted distorted 7465 7480 7481 7482 7499 P DA T 7 distorted distorted 7487 7500 7501 7502 7520 P DA T 8 distorted distorted 7507 7521 7522 7523 7541 P DG T 9 distorted distorted 7528 7542 7543 7544 7563 P DC T 10 distorted distorted 7549 7564 7565 7566 7582 P DA T 11 distorted distorted 7571 7583 7584 7585 7603 P DG T 12 distorted distorted 7590 7604 7605 7606 7625 P DT T 13 distorted distorted 7611 7626 7627 7628 7645 P DC T 14 distorted distorted 7633 7646 7647 7648 7664 P DC T 15 distorted distorted 7653 7665 7666 7667 7683 P DG T 16 distorted distorted 7672 7684 7685 7686 7705 P DC T 17 distorted distorted 7691 7706 7707 7708 7724 P DG T 18 distorted distorted 7713 7725 7726 7727 7766 P DC P 104 distorted distorted 7752 7767 7768 7769 7785 P DG P 105 distorted distorted 7774 7786 7787 7788 7807 P DG P 106 distorted distorted 7793 7808 7809 7810 7829 P DA P 107 distorted distorted 7815 7830 7831 7832 7850 P DC P 108 distorted distorted 7837 7851 7852 7853 7869 P DT P 109 distorted distorted 7858 7870 7871 7872 7889 P DG P 110 distorted distorted 7877 7890 7891 7892 7911 P DC P 111 distorted distorted 7897 7912 7913 7914 7930 P DT P 112 distorted distorted 7919 7931 7932 7933 7950 P DT P 113 distorted distorted 7938 7951 7952 7953 7970 P DA P 114 distorted distorted 7958 7971 7972 7973 8006 P DOC P 115 distorted distorted 7978 8007 8008 8005 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