ID code: '4DU4' 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' --------------------------------------------------------------------------------- 7383 C1' DC T 2 beta 7379 7384 7382 7402 C1' DG T 3 beta 7398 7403 7401 7424 C1' DT T 4 beta 7420 7425 7423 7444 C1' DG T 5 beta 7440 7445 7443 7466 C1' DT T 6 beta 7462 7467 7465 7486 C1' DT T 7 beta 7482 7487 7485 7506 C1' DA T 8 beta 7502 7507 7505 7527 C1' DG T 9 beta 7523 7528 7526 7549 C1' DC T 10 beta 7545 7550 7548 7568 C1' DA T 11 beta 7564 7569 7567 7589 C1' DG T 12 beta 7585 7590 7588 7611 C1' DT T 13 beta 7607 7612 7610 7631 C1' DC T 14 beta 7627 7632 7630 7650 C1' DC T 15 beta 7646 7651 7649 7669 C1' DG T 16 beta 7665 7670 7668 7691 C1' DC T 17 beta 7687 7692 7690 7710 C1' DG T 18 beta 7706 7711 7709 7730 C1' DG P 103 beta 7726 7731 7729 7752 C1' DC P 104 beta 7748 7753 7751 7771 C1' DG P 105 beta 7767 7772 7770 7793 C1' DG P 106 beta 7789 7794 7792 7815 C1' DA P 107 beta 7811 7816 7814 7836 C1' DC P 108 beta 7832 7837 7835 7855 C1' DT P 109 beta 7851 7856 7854 7875 C1' DG P 110 beta 7871 7876 7874 7897 C1' DC P 111 beta 7893 7898 7896 7916 C1' DT P 112 beta 7912 7917 7915 7935 C1' 4DU P 113 beta 7936 7937 7934 7957 C1' DA P 114 beta 7953 7958 7956 7976 C1' DOC P 115 beta 7980 7968 7977 8006 C1' DTP A1001 beta 8002 8007 8005 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7382 C2' DC T 2 7383 7380 7401 C2' DG T 3 7402 7399 7423 C2' DT T 4 7424 7421 7443 C2' DG T 5 7444 7441 7465 C2' DT T 6 7466 7463 7485 C2' DT T 7 7486 7483 7505 C2' DA T 8 7506 7503 7526 C2' DG T 9 7527 7524 7548 C2' DC T 10 7549 7546 7567 C2' DA T 11 7568 7565 7588 C2' DG T 12 7589 7586 7610 C2' DT T 13 7611 7608 7630 C2' DC T 14 7631 7628 7649 C2' DC T 15 7650 7647 7668 C2' DG T 16 7669 7666 7690 C2' DC T 17 7691 7688 7709 C2' DG T 18 7710 7707 7729 C2' DG P 103 7730 7727 7751 C2' DC P 104 7752 7749 7770 C2' DG P 105 7771 7768 7792 C2' DG P 106 7793 7790 7814 C2' DA P 107 7815 7812 7835 C2' DC P 108 7836 7833 7854 C2' DT P 109 7855 7852 7874 C2' DG P 110 7875 7872 7896 C2' DC P 111 7897 7894 7915 C2' DT P 112 7916 7913 7934 C2' 4DU P 113 7935 7932 7956 C2' DA P 114 7957 7954 7977 C2' DOC P 115 7976 7978 8005 C2' DTP A1001 8006 8003 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7380 C3' DC T 2 OK 7378 7381 7382 7399 C3' DG T 3 OK 7397 7400 7401 7421 C3' DT T 4 OK 7419 7422 7423 7441 C3' DG T 5 OK 7439 7442 7443 7463 C3' DT T 6 OK 7461 7464 7465 7483 C3' DT T 7 OK 7481 7484 7485 7503 C3' DA T 8 OK 7501 7504 7505 7524 C3' DG T 9 OK 7522 7525 7526 7546 C3' DC T 10 OK 7544 7547 7548 7565 C3' DA T 11 OK 7563 7566 7567 7586 C3' DG T 12 OK 7584 7587 7588 7608 C3' DT T 13 OK 7606 7609 7610 7628 C3' DC T 14 OK 7626 7629 7630 7647 C3' DC T 15 OK 7645 7648 7649 7666 C3' DG T 16 OK 7664 7667 7668 7688 C3' DC T 17 OK 7686 7689 7690 7707 C3' DG T 18 OK 7705 7708 7709 7727 C3' DG P 103 OK 7725 7728 7729 7749 C3' DC P 104 OK 7747 7750 7751 7768 C3' DG P 105 OK 7766 7769 7770 7790 C3' DG P 106 OK 7788 7791 7792 7812 C3' DA P 107 OK 7810 7813 7814 7833 C3' DC P 108 OK 7831 7834 7835 7852 C3' DT P 109 OK 7850 7853 7854 7872 C3' DG P 110 OK 7870 7873 7874 7894 C3' DC P 111 OK 7892 7895 7896 7913 C3' DT P 112 OK 7911 7914 7915 7932 C3' 4DU P 113 OK 7931 7933 7934 7954 C3' DA P 114 OK 7952 7955 7956 7978 C3' DOC P 115 7979 7977 8003 C3' DTP A1001 OK 8001 8004 8005 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7378 C4' DC T 2 OK 7380 7377 7379 7397 C4' DG T 3 OK 7399 7396 7398 7419 C4' DT T 4 OK 7421 7418 7420 7439 C4' DG T 5 OK 7441 7438 7440 7461 C4' DT T 6 OK 7463 7460 7462 7481 C4' DT T 7 OK 7483 7480 7482 7501 C4' DA T 8 OK 7503 7500 7502 7522 C4' DG T 9 OK 7524 7521 7523 7544 C4' DC T 10 OK 7546 7543 7545 7563 C4' DA T 11 OK 7565 7562 7564 7584 C4' DG T 12 OK 7586 7583 7585 7606 C4' DT T 13 OK 7608 7605 7607 7626 C4' DC T 14 OK 7628 7625 7627 7645 C4' DC T 15 OK 7647 7644 7646 7664 C4' DG T 16 OK 7666 7663 7665 7686 C4' DC T 17 OK 7688 7685 7687 7705 C4' DG T 18 OK 7707 7704 7706 7725 C4' DG P 103 OK 7727 7724 7726 7747 C4' DC P 104 OK 7749 7746 7748 7766 C4' DG P 105 OK 7768 7765 7767 7788 C4' DG P 106 OK 7790 7787 7789 7810 C4' DA P 107 OK 7812 7809 7811 7831 C4' DC P 108 OK 7833 7830 7832 7850 C4' DT P 109 OK 7852 7849 7851 7870 C4' DG P 110 OK 7872 7869 7871 7892 C4' DC P 111 OK 7894 7891 7893 7911 C4' DT P 112 OK 7913 7910 7912 7931 C4' 4DU P 113 OK 7932 7930 7936 7952 C4' DA P 114 OK 7954 7951 7953 7979 C4' DOC P 115 OK 7978 7981 7980 8001 C4' DTP A1001 OK 8003 8000 8002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7377 C5' DC T 2 7376 7378 7396 C5' DG T 3 7395 7397 7418 C5' DT T 4 7417 7419 7438 C5' DG T 5 7437 7439 7460 C5' DT T 6 7459 7461 7480 C5' DT T 7 7479 7481 7500 C5' DA T 8 7499 7501 7521 C5' DG T 9 7520 7522 7543 C5' DC T 10 7542 7544 7562 C5' DA T 11 7561 7563 7583 C5' DG T 12 7582 7584 7605 C5' DT T 13 7604 7606 7625 C5' DC T 14 7624 7626 7644 C5' DC T 15 7643 7645 7663 C5' DG T 16 7662 7664 7685 C5' DC T 17 7684 7686 7704 C5' DG T 18 7703 7705 7724 C5' DG P 103 7723 7725 7746 C5' DC P 104 7745 7747 7765 C5' DG P 105 7764 7766 7787 C5' DG P 106 7786 7788 7809 C5' DA P 107 7808 7810 7830 C5' DC P 108 7829 7831 7849 C5' DT P 109 7848 7850 7869 C5' DG P 110 7868 7870 7891 C5' DC P 111 7890 7892 7910 C5' DT P 112 7909 7911 7930 C5' 4DU P 113 7929 7931 7951 C5' DA P 114 7950 7952 7981 C5' DOC P 115 7982 7979 8000 C5' DTP A1001 7999 8001 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7373 P DC T 2 distorted distorted 7374 7375 7376 7392 P DG T 3 distorted distorted 7381 7393 7394 7395 7414 P DT T 4 distorted distorted 7400 7415 7416 7417 7434 P DG T 5 distorted distorted 7422 7435 7436 7437 7456 P DT T 6 distorted distorted 7442 7457 7458 7459 7476 P DT T 7 distorted distorted 7464 7477 7478 7479 7496 P DA T 8 distorted distorted 7484 7497 7498 7499 7517 P DG T 9 distorted distorted 7504 7518 7519 7520 7539 P DC T 10 distorted distorted 7525 7540 7541 7542 7558 P DA T 11 distorted distorted 7547 7559 7560 7561 7579 P DG T 12 distorted distorted 7566 7580 7581 7582 7601 P DT T 13 distorted distorted 7587 7602 7603 7604 7621 P DC T 14 distorted distorted 7609 7622 7623 7624 7640 P DC T 15 distorted distorted 7629 7641 7642 7643 7659 P DG T 16 distorted distorted 7648 7660 7661 7662 7681 P DC T 17 distorted distorted 7667 7682 7683 7684 7700 P DG T 18 distorted distorted 7689 7701 7702 7703 7742 P DC P 104 distorted distorted 7728 7743 7744 7745 7761 P DG P 105 distorted distorted 7750 7762 7763 7764 7783 P DG P 106 distorted distorted 7769 7784 7785 7786 7805 P DA P 107 distorted distorted 7791 7806 7807 7808 7826 P DC P 108 distorted distorted 7813 7827 7828 7829 7845 P DT P 109 distorted distorted 7834 7846 7847 7848 7865 P DG P 110 distorted distorted 7853 7866 7867 7868 7887 P DC P 111 distorted distorted 7873 7888 7889 7890 7906 P DT P 112 distorted distorted 7895 7907 7908 7909 7927 P 4DU P 113 OK OK 7914 7928 7926 7929 7947 P DA P 114 distorted distorted 7933 7948 7949 7950 7983 P DOC P 115 distorted distorted 7955 7984 7985 7982 ---------------------------------------------------------------------------------