ID code: '4DTU' 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' --------------------------------------------------------------------------------- 7410 C1' DT T 1 beta 7406 7411 7409 7430 C1' DC T 2 beta 7426 7431 7429 7449 C1' DG T 3 beta 7445 7450 7448 7469 C1' 3DR T 4 7468 7465 7482 C1' DG T 5 beta 7478 7483 7481 7504 C1' DT T 6 beta 7500 7505 7503 7524 C1' DA T 7 beta 7520 7525 7523 7545 C1' DA T 8 beta 7541 7546 7544 7566 C1' DG T 9 beta 7562 7567 7565 7588 C1' DC T 10 beta 7584 7589 7587 7607 C1' DA T 11 beta 7603 7608 7606 7628 C1' DG T 12 beta 7624 7629 7627 7650 C1' DT T 13 beta 7646 7651 7649 7670 C1' DC T 14 beta 7666 7671 7669 7689 C1' DC T 15 beta 7685 7690 7688 7708 C1' DG T 16 beta 7704 7709 7707 7730 C1' DC T 17 beta 7726 7731 7729 7749 C1' DG T 18 beta 7745 7750 7748 7769 C1' DG P 103 beta 7765 7770 7768 7791 C1' DC P 104 beta 7787 7792 7790 7810 C1' DG P 105 beta 7806 7811 7809 7832 C1' DG P 106 beta 7828 7833 7831 7854 C1' DA P 107 beta 7850 7855 7853 7875 C1' DC P 108 beta 7871 7876 7874 7894 C1' DT P 109 beta 7890 7895 7893 7914 C1' DG P 110 beta 7910 7915 7913 7936 C1' DC P 111 beta 7932 7937 7935 7955 C1' DT P 112 beta 7951 7956 7954 7975 C1' DT P 113 beta 7971 7976 7974 7995 C1' DA P 114 beta 7991 7996 7994 8014 C1' DOC P 115 beta 8018 8006 8015 8044 C1' DGT A1001 beta 8040 8045 8043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7409 C2' DT T 1 7410 7407 7429 C2' DC T 2 7430 7427 7448 C2' DG T 3 7449 7446 7465 C2' 3DR T 4 7469 7470 7481 C2' DG T 5 7482 7479 7503 C2' DT T 6 7504 7501 7523 C2' DA T 7 7524 7521 7544 C2' DA T 8 7545 7542 7565 C2' DG T 9 7566 7563 7587 C2' DC T 10 7588 7585 7606 C2' DA T 11 7607 7604 7627 C2' DG T 12 7628 7625 7649 C2' DT T 13 7650 7647 7669 C2' DC T 14 7670 7667 7688 C2' DC T 15 7689 7686 7707 C2' DG T 16 7708 7705 7729 C2' DC T 17 7730 7727 7748 C2' DG T 18 7749 7746 7768 C2' DG P 103 7769 7766 7790 C2' DC P 104 7791 7788 7809 C2' DG P 105 7810 7807 7831 C2' DG P 106 7832 7829 7853 C2' DA P 107 7854 7851 7874 C2' DC P 108 7875 7872 7893 C2' DT P 109 7894 7891 7913 C2' DG P 110 7914 7911 7935 C2' DC P 111 7936 7933 7954 C2' DT P 112 7955 7952 7974 C2' DT P 113 7975 7972 7994 C2' DA P 114 7995 7992 8015 C2' DOC P 115 8014 8016 8043 C2' DGT A1001 8044 8041 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7407 C3' DT T 1 OK 7405 7408 7409 7427 C3' DC T 2 OK 7425 7428 7429 7446 C3' DG T 3 OK 7444 7447 7448 7470 C3' 3DR T 4 OK 7467 7471 7465 7479 C3' DG T 5 OK 7477 7480 7481 7501 C3' DT T 6 OK 7499 7502 7503 7521 C3' DA T 7 OK 7519 7522 7523 7542 C3' DA T 8 OK 7540 7543 7544 7563 C3' DG T 9 OK 7561 7564 7565 7585 C3' DC T 10 OK 7583 7586 7587 7604 C3' DA T 11 OK 7602 7605 7606 7625 C3' DG T 12 OK 7623 7626 7627 7647 C3' DT T 13 OK 7645 7648 7649 7667 C3' DC T 14 OK 7665 7668 7669 7686 C3' DC T 15 OK 7684 7687 7688 7705 C3' DG T 16 OK 7703 7706 7707 7727 C3' DC T 17 OK 7725 7728 7729 7746 C3' DG T 18 OK 7744 7747 7748 7766 C3' DG P 103 OK 7764 7767 7768 7788 C3' DC P 104 OK 7786 7789 7790 7807 C3' DG P 105 OK 7805 7808 7809 7829 C3' DG P 106 OK 7827 7830 7831 7851 C3' DA P 107 OK 7849 7852 7853 7872 C3' DC P 108 OK 7870 7873 7874 7891 C3' DT P 109 OK 7889 7892 7893 7911 C3' DG P 110 OK 7909 7912 7913 7933 C3' DC P 111 OK 7931 7934 7935 7952 C3' DT P 112 OK 7950 7953 7954 7972 C3' DT P 113 OK 7970 7973 7974 7992 C3' DA P 114 OK 7990 7993 7994 8016 C3' DOC P 115 8017 8015 8041 C3' DGT A1001 OK 8039 8042 8043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7405 C4' DT T 1 OK 7407 7404 7406 7425 C4' DC T 2 OK 7427 7424 7426 7444 C4' DG T 3 OK 7446 7443 7445 7467 C4' 3DR T 4 OK 7470 7466 7468 7477 C4' DG T 5 OK 7479 7476 7478 7499 C4' DT T 6 OK 7501 7498 7500 7519 C4' DA T 7 OK 7521 7518 7520 7540 C4' DA T 8 OK 7542 7539 7541 7561 C4' DG T 9 OK 7563 7560 7562 7583 C4' DC T 10 OK 7585 7582 7584 7602 C4' DA T 11 OK 7604 7601 7603 7623 C4' DG T 12 OK 7625 7622 7624 7645 C4' DT T 13 OK 7647 7644 7646 7665 C4' DC T 14 OK 7667 7664 7666 7684 C4' DC T 15 OK 7686 7683 7685 7703 C4' DG T 16 OK 7705 7702 7704 7725 C4' DC T 17 OK 7727 7724 7726 7744 C4' DG T 18 OK 7746 7743 7745 7764 C4' DG P 103 OK 7766 7763 7765 7786 C4' DC P 104 OK 7788 7785 7787 7805 C4' DG P 105 OK 7807 7804 7806 7827 C4' DG P 106 OK 7829 7826 7828 7849 C4' DA P 107 OK 7851 7848 7850 7870 C4' DC P 108 OK 7872 7869 7871 7889 C4' DT P 109 OK 7891 7888 7890 7909 C4' DG P 110 OK 7911 7908 7910 7931 C4' DC P 111 OK 7933 7930 7932 7950 C4' DT P 112 OK 7952 7949 7951 7970 C4' DT P 113 OK 7972 7969 7971 7990 C4' DA P 114 OK 7992 7989 7991 8017 C4' DOC P 115 OK 8016 8019 8018 8039 C4' DGT A1001 OK 8041 8038 8040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7404 C5' DT T 1 7403 7405 7424 C5' DC T 2 7423 7425 7443 C5' DG T 3 7442 7444 7466 C5' 3DR T 4 7461 7467 7476 C5' DG T 5 7475 7477 7498 C5' DT T 6 7497 7499 7518 C5' DA T 7 7517 7519 7539 C5' DA T 8 7538 7540 7560 C5' DG T 9 7559 7561 7582 C5' DC T 10 7581 7583 7601 C5' DA T 11 7600 7602 7622 C5' DG T 12 7621 7623 7644 C5' DT T 13 7643 7645 7664 C5' DC T 14 7663 7665 7683 C5' DC T 15 7682 7684 7702 C5' DG T 16 7701 7703 7724 C5' DC T 17 7723 7725 7743 C5' DG T 18 7742 7744 7763 C5' DG P 103 7762 7764 7785 C5' DC P 104 7784 7786 7804 C5' DG P 105 7803 7805 7826 C5' DG P 106 7825 7827 7848 C5' DA P 107 7847 7849 7869 C5' DC P 108 7868 7870 7888 C5' DT P 109 7887 7889 7908 C5' DG P 110 7907 7909 7930 C5' DC P 111 7929 7931 7949 C5' DT P 112 7948 7950 7969 C5' DT P 113 7968 7970 7989 C5' DA P 114 7988 7990 8019 C5' DOC P 115 8020 8017 8038 C5' DGT A1001 8037 8039 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7420 P DC T 2 distorted distorted 7408 7421 7422 7423 7439 P DG T 3 distorted distorted 7428 7440 7441 7442 7462 P 3DR T 4 OK OK 7447 7463 7464 7461 7472 P DG T 5 distorted distorted 7471 7473 7474 7475 7494 P DT T 6 distorted distorted 7480 7495 7496 7497 7514 P DA T 7 distorted distorted 7502 7515 7516 7517 7535 P DA T 8 distorted distorted 7522 7536 7537 7538 7556 P DG T 9 distorted distorted 7543 7557 7558 7559 7578 P DC T 10 distorted distorted 7564 7579 7580 7581 7597 P DA T 11 distorted distorted 7586 7598 7599 7600 7618 P DG T 12 distorted distorted 7605 7619 7620 7621 7640 P DT T 13 distorted distorted 7626 7641 7642 7643 7660 P DC T 14 distorted distorted 7648 7661 7662 7663 7679 P DC T 15 distorted distorted 7668 7680 7681 7682 7698 P DG T 16 distorted distorted 7687 7699 7700 7701 7720 P DC T 17 distorted distorted 7706 7721 7722 7723 7739 P DG T 18 distorted distorted 7728 7740 7741 7742 7781 P DC P 104 distorted distorted 7767 7782 7783 7784 7800 P DG P 105 distorted distorted 7789 7801 7802 7803 7822 P DG P 106 distorted distorted 7808 7823 7824 7825 7844 P DA P 107 distorted distorted 7830 7845 7846 7847 7865 P DC P 108 distorted distorted 7852 7866 7867 7868 7884 P DT P 109 distorted distorted 7873 7885 7886 7887 7904 P DG P 110 distorted distorted 7892 7905 7906 7907 7926 P DC P 111 distorted distorted 7912 7927 7928 7929 7945 P DT P 112 distorted distorted 7934 7946 7947 7948 7965 P DT P 113 distorted distorted 7953 7966 7967 7968 7985 P DA P 114 distorted distorted 7973 7986 7987 7988 8021 P DOC P 115 distorted distorted 7993 8022 8023 8020 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