ID code: '4FJM' 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' --------------------------------------------------------------------------------- 7357 C1' DC T 2 beta 7353 7358 7356 7376 C1' DG T 3 beta 7372 7377 7375 7398 C1' DA T 4 beta 7394 7399 7397 7419 C1' DG T 5 beta 7415 7420 7418 7441 C1' DT T 6 beta 7437 7442 7440 7461 C1' DA T 7 beta 7457 7462 7460 7482 C1' DA T 8 beta 7478 7483 7481 7503 C1' DG T 9 beta 7499 7504 7502 7525 C1' DC T 10 beta 7521 7526 7524 7544 C1' DA T 11 beta 7540 7545 7543 7565 C1' DG T 12 beta 7561 7566 7564 7587 C1' DT T 13 beta 7583 7588 7586 7607 C1' DC T 14 beta 7603 7608 7606 7626 C1' DC T 15 beta 7622 7627 7625 7645 C1' DG T 16 beta 7641 7646 7644 7667 C1' DC T 17 beta 7663 7668 7666 7686 C1' DG T 18 beta 7682 7687 7685 7706 C1' DG P 103 beta 7702 7707 7705 7728 C1' DC P 104 beta 7724 7729 7727 7747 C1' DG P 105 beta 7743 7748 7746 7769 C1' DG P 106 beta 7765 7770 7768 7791 C1' DA P 107 beta 7787 7792 7790 7812 C1' DC P 108 beta 7808 7813 7811 7831 C1' DT P 109 beta 7827 7832 7830 7851 C1' DG P 110 beta 7847 7852 7850 7873 C1' DC P 111 beta 7869 7874 7872 7892 C1' DT P 112 beta 7888 7893 7891 7912 C1' DT P 113 beta 7908 7913 7911 7932 C1' DA P 114 beta 7928 7933 7931 7951 C1' DOC P 115 beta 7955 7943 7952 7970 C1' DCP A1001 beta 7974 7962 7971 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7356 C2' DC T 2 7357 7354 7375 C2' DG T 3 7376 7373 7397 C2' DA T 4 7398 7395 7418 C2' DG T 5 7419 7416 7440 C2' DT T 6 7441 7438 7460 C2' DA T 7 7461 7458 7481 C2' DA T 8 7482 7479 7502 C2' DG T 9 7503 7500 7524 C2' DC T 10 7525 7522 7543 C2' DA T 11 7544 7541 7564 C2' DG T 12 7565 7562 7586 C2' DT T 13 7587 7584 7606 C2' DC T 14 7607 7604 7625 C2' DC T 15 7626 7623 7644 C2' DG T 16 7645 7642 7666 C2' DC T 17 7667 7664 7685 C2' DG T 18 7686 7683 7705 C2' DG P 103 7706 7703 7727 C2' DC P 104 7728 7725 7746 C2' DG P 105 7747 7744 7768 C2' DG P 106 7769 7766 7790 C2' DA P 107 7791 7788 7811 C2' DC P 108 7812 7809 7830 C2' DT P 109 7831 7828 7850 C2' DG P 110 7851 7848 7872 C2' DC P 111 7873 7870 7891 C2' DT P 112 7892 7889 7911 C2' DT P 113 7912 7909 7931 C2' DA P 114 7932 7929 7952 C2' DOC P 115 7951 7953 7971 C2' DCP A1001 7970 7972 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7354 C3' DC T 2 OK 7352 7355 7356 7373 C3' DG T 3 OK 7371 7374 7375 7395 C3' DA T 4 OK 7393 7396 7397 7416 C3' DG T 5 OK 7414 7417 7418 7438 C3' DT T 6 OK 7436 7439 7440 7458 C3' DA T 7 OK 7456 7459 7460 7479 C3' DA T 8 OK 7477 7480 7481 7500 C3' DG T 9 OK 7498 7501 7502 7522 C3' DC T 10 OK 7520 7523 7524 7541 C3' DA T 11 OK 7539 7542 7543 7562 C3' DG T 12 OK 7560 7563 7564 7584 C3' DT T 13 OK 7582 7585 7586 7604 C3' DC T 14 OK 7602 7605 7606 7623 C3' DC T 15 OK 7621 7624 7625 7642 C3' DG T 16 OK 7640 7643 7644 7664 C3' DC T 17 OK 7662 7665 7666 7683 C3' DG T 18 OK 7681 7684 7685 7703 C3' DG P 103 OK 7701 7704 7705 7725 C3' DC P 104 OK 7723 7726 7727 7744 C3' DG P 105 OK 7742 7745 7746 7766 C3' DG P 106 OK 7764 7767 7768 7788 C3' DA P 107 OK 7786 7789 7790 7809 C3' DC P 108 OK 7807 7810 7811 7828 C3' DT P 109 OK 7826 7829 7830 7848 C3' DG P 110 OK 7846 7849 7850 7870 C3' DC P 111 OK 7868 7871 7872 7889 C3' DT P 112 OK 7887 7890 7891 7909 C3' DT P 113 OK 7907 7910 7911 7929 C3' DA P 114 OK 7927 7930 7931 7953 C3' DOC P 115 7954 7952 7972 C3' DCP A1001 OK 7973 7975 7971 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7352 C4' DC T 2 OK 7354 7351 7353 7371 C4' DG T 3 OK 7373 7370 7372 7393 C4' DA T 4 OK 7395 7392 7394 7414 C4' DG T 5 OK 7416 7413 7415 7436 C4' DT T 6 OK 7438 7435 7437 7456 C4' DA T 7 OK 7458 7455 7457 7477 C4' DA T 8 OK 7479 7476 7478 7498 C4' DG T 9 OK 7500 7497 7499 7520 C4' DC T 10 OK 7522 7519 7521 7539 C4' DA T 11 OK 7541 7538 7540 7560 C4' DG T 12 OK 7562 7559 7561 7582 C4' DT T 13 OK 7584 7581 7583 7602 C4' DC T 14 OK 7604 7601 7603 7621 C4' DC T 15 OK 7623 7620 7622 7640 C4' DG T 16 OK 7642 7639 7641 7662 C4' DC T 17 OK 7664 7661 7663 7681 C4' DG T 18 OK 7683 7680 7682 7701 C4' DG P 103 OK 7703 7700 7702 7723 C4' DC P 104 OK 7725 7722 7724 7742 C4' DG P 105 OK 7744 7741 7743 7764 C4' DG P 106 OK 7766 7763 7765 7786 C4' DA P 107 OK 7788 7785 7787 7807 C4' DC P 108 OK 7809 7806 7808 7826 C4' DT P 109 OK 7828 7825 7827 7846 C4' DG P 110 OK 7848 7845 7847 7868 C4' DC P 111 OK 7870 7867 7869 7887 C4' DT P 112 OK 7889 7886 7888 7907 C4' DT P 113 OK 7909 7906 7908 7927 C4' DA P 114 OK 7929 7926 7928 7954 C4' DOC P 115 OK 7953 7956 7955 7973 C4' DCP A1001 OK 7972 7976 7974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7351 C5' DC T 2 7350 7352 7370 C5' DG T 3 7369 7371 7392 C5' DA T 4 7391 7393 7413 C5' DG T 5 7412 7414 7435 C5' DT T 6 7434 7436 7455 C5' DA T 7 7454 7456 7476 C5' DA T 8 7475 7477 7497 C5' DG T 9 7496 7498 7519 C5' DC T 10 7518 7520 7538 C5' DA T 11 7537 7539 7559 C5' DG T 12 7558 7560 7581 C5' DT T 13 7580 7582 7601 C5' DC T 14 7600 7602 7620 C5' DC T 15 7619 7621 7639 C5' DG T 16 7638 7640 7661 C5' DC T 17 7660 7662 7680 C5' DG T 18 7679 7681 7700 C5' DG P 103 7699 7701 7722 C5' DC P 104 7721 7723 7741 C5' DG P 105 7740 7742 7763 C5' DG P 106 7762 7764 7785 C5' DA P 107 7784 7786 7806 C5' DC P 108 7805 7807 7825 C5' DT P 109 7824 7826 7845 C5' DG P 110 7844 7846 7867 C5' DC P 111 7866 7868 7886 C5' DT P 112 7885 7887 7906 C5' DT P 113 7905 7907 7926 C5' DA P 114 7925 7927 7956 C5' DOC P 115 7957 7954 7976 C5' DCP A1001 7977 7973 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7347 P DC T 2 distorted distorted 7348 7349 7350 7366 P DG T 3 distorted distorted 7355 7367 7368 7369 7388 P DA T 4 distorted distorted 7374 7389 7390 7391 7409 P DG T 5 distorted distorted 7396 7410 7411 7412 7431 P DT T 6 distorted distorted 7417 7432 7433 7434 7451 P DA T 7 distorted distorted 7439 7452 7453 7454 7472 P DA T 8 distorted distorted 7459 7473 7474 7475 7493 P DG T 9 distorted distorted 7480 7494 7495 7496 7515 P DC T 10 distorted distorted 7501 7516 7517 7518 7534 P DA T 11 distorted distorted 7523 7535 7536 7537 7555 P DG T 12 distorted distorted 7542 7556 7557 7558 7577 P DT T 13 distorted distorted 7563 7578 7579 7580 7597 P DC T 14 distorted distorted 7585 7598 7599 7600 7616 P DC T 15 distorted distorted 7605 7617 7618 7619 7635 P DG T 16 distorted distorted 7624 7636 7637 7638 7657 P DC T 17 distorted distorted 7643 7658 7659 7660 7676 P DG T 18 distorted distorted 7665 7677 7678 7679 7718 P DC P 104 distorted distorted 7704 7719 7720 7721 7737 P DG P 105 distorted distorted 7726 7738 7739 7740 7759 P DG P 106 distorted distorted 7745 7760 7761 7762 7781 P DA P 107 distorted distorted 7767 7782 7783 7784 7802 P DC P 108 distorted distorted 7789 7803 7804 7805 7821 P DT P 109 distorted distorted 7810 7822 7823 7824 7841 P DG P 110 distorted distorted 7829 7842 7843 7844 7863 P DC P 111 distorted distorted 7849 7864 7865 7866 7882 P DT P 112 distorted distorted 7871 7883 7884 7885 7902 P DT P 113 distorted distorted 7890 7903 7904 7905 7922 P DA P 114 distorted distorted 7910 7923 7924 7925 7958 P DOC P 115 distorted distorted 7930 7959 7960 7957 ---------------------------------------------------------------------------------