ID code: '4FJN' 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' --------------------------------------------------------------------------------- 7379 C1' DA T 3 beta 7375 7380 7378 7400 C1' DA T 4 beta 7396 7401 7399 7421 C1' DG T 5 beta 7417 7422 7420 7443 C1' DT T 6 beta 7439 7444 7442 7463 C1' DA T 7 beta 7459 7464 7462 7484 C1' DA T 8 beta 7480 7485 7483 7505 C1' DG T 9 beta 7501 7506 7504 7527 C1' DC T 10 beta 7523 7528 7526 7546 C1' DA T 11 beta 7542 7547 7545 7567 C1' DG T 12 beta 7563 7568 7566 7589 C1' DT T 13 beta 7585 7590 7588 7609 C1' DC T 14 beta 7605 7610 7608 7628 C1' DC T 15 beta 7624 7629 7627 7647 C1' DG T 16 beta 7643 7648 7646 7669 C1' DC T 17 beta 7665 7670 7668 7688 C1' DG T 18 beta 7684 7689 7687 7708 C1' DG P 103 beta 7704 7709 7707 7730 C1' DC P 104 beta 7726 7731 7729 7749 C1' DG P 105 beta 7745 7750 7748 7771 C1' DG P 106 beta 7767 7772 7770 7793 C1' DA P 107 beta 7789 7794 7792 7814 C1' DC P 108 beta 7810 7815 7813 7833 C1' DT P 109 beta 7829 7834 7832 7853 C1' DG P 110 beta 7849 7854 7852 7875 C1' DC P 111 beta 7871 7876 7874 7894 C1' DT P 112 beta 7890 7895 7893 7914 C1' DT P 113 beta 7910 7915 7913 7934 C1' DA P 114 beta 7930 7935 7933 7953 C1' DOC P 115 beta 7957 7945 7954 7983 C1' TTP A1001 beta 7979 7984 7982 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7378 C2' DA T 3 7379 7376 7399 C2' DA T 4 7400 7397 7420 C2' DG T 5 7421 7418 7442 C2' DT T 6 7443 7440 7462 C2' DA T 7 7463 7460 7483 C2' DA T 8 7484 7481 7504 C2' DG T 9 7505 7502 7526 C2' DC T 10 7527 7524 7545 C2' DA T 11 7546 7543 7566 C2' DG T 12 7567 7564 7588 C2' DT T 13 7589 7586 7608 C2' DC T 14 7609 7606 7627 C2' DC T 15 7628 7625 7646 C2' DG T 16 7647 7644 7668 C2' DC T 17 7669 7666 7687 C2' DG T 18 7688 7685 7707 C2' DG P 103 7708 7705 7729 C2' DC P 104 7730 7727 7748 C2' DG P 105 7749 7746 7770 C2' DG P 106 7771 7768 7792 C2' DA P 107 7793 7790 7813 C2' DC P 108 7814 7811 7832 C2' DT P 109 7833 7830 7852 C2' DG P 110 7853 7850 7874 C2' DC P 111 7875 7872 7893 C2' DT P 112 7894 7891 7913 C2' DT P 113 7914 7911 7933 C2' DA P 114 7934 7931 7954 C2' DOC P 115 7953 7955 7982 C2' TTP A1001 7983 7980 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7376 C3' DA T 3 OK 7374 7377 7378 7397 C3' DA T 4 OK 7395 7398 7399 7418 C3' DG T 5 OK 7416 7419 7420 7440 C3' DT T 6 OK 7438 7441 7442 7460 C3' DA T 7 OK 7458 7461 7462 7481 C3' DA T 8 OK 7479 7482 7483 7502 C3' DG T 9 OK 7500 7503 7504 7524 C3' DC T 10 OK 7522 7525 7526 7543 C3' DA T 11 OK 7541 7544 7545 7564 C3' DG T 12 OK 7562 7565 7566 7586 C3' DT T 13 OK 7584 7587 7588 7606 C3' DC T 14 OK 7604 7607 7608 7625 C3' DC T 15 OK 7623 7626 7627 7644 C3' DG T 16 OK 7642 7645 7646 7666 C3' DC T 17 OK 7664 7667 7668 7685 C3' DG T 18 OK 7683 7686 7687 7705 C3' DG P 103 OK 7703 7706 7707 7727 C3' DC P 104 OK 7725 7728 7729 7746 C3' DG P 105 OK 7744 7747 7748 7768 C3' DG P 106 OK 7766 7769 7770 7790 C3' DA P 107 OK 7788 7791 7792 7811 C3' DC P 108 OK 7809 7812 7813 7830 C3' DT P 109 OK 7828 7831 7832 7850 C3' DG P 110 OK 7848 7851 7852 7872 C3' DC P 111 OK 7870 7873 7874 7891 C3' DT P 112 OK 7889 7892 7893 7911 C3' DT P 113 OK 7909 7912 7913 7931 C3' DA P 114 OK 7929 7932 7933 7955 C3' DOC P 115 7956 7954 7980 C3' TTP A1001 OK 7978 7981 7982 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7374 C4' DA T 3 OK 7376 7373 7375 7395 C4' DA T 4 OK 7397 7394 7396 7416 C4' DG T 5 OK 7418 7415 7417 7438 C4' DT T 6 OK 7440 7437 7439 7458 C4' DA T 7 OK 7460 7457 7459 7479 C4' DA T 8 OK 7481 7478 7480 7500 C4' DG T 9 OK 7502 7499 7501 7522 C4' DC T 10 OK 7524 7521 7523 7541 C4' DA T 11 OK 7543 7540 7542 7562 C4' DG T 12 OK 7564 7561 7563 7584 C4' DT T 13 OK 7586 7583 7585 7604 C4' DC T 14 OK 7606 7603 7605 7623 C4' DC T 15 OK 7625 7622 7624 7642 C4' DG T 16 OK 7644 7641 7643 7664 C4' DC T 17 OK 7666 7663 7665 7683 C4' DG T 18 OK 7685 7682 7684 7703 C4' DG P 103 OK 7705 7702 7704 7725 C4' DC P 104 OK 7727 7724 7726 7744 C4' DG P 105 OK 7746 7743 7745 7766 C4' DG P 106 OK 7768 7765 7767 7788 C4' DA P 107 OK 7790 7787 7789 7809 C4' DC P 108 OK 7811 7808 7810 7828 C4' DT P 109 OK 7830 7827 7829 7848 C4' DG P 110 OK 7850 7847 7849 7870 C4' DC P 111 OK 7872 7869 7871 7889 C4' DT P 112 OK 7891 7888 7890 7909 C4' DT P 113 OK 7911 7908 7910 7929 C4' DA P 114 OK 7931 7928 7930 7956 C4' DOC P 115 OK 7955 7958 7957 7978 C4' TTP A1001 OK 7980 7977 7979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7373 C5' DA T 3 7372 7374 7394 C5' DA T 4 7393 7395 7415 C5' DG T 5 7414 7416 7437 C5' DT T 6 7436 7438 7457 C5' DA T 7 7456 7458 7478 C5' DA T 8 7477 7479 7499 C5' DG T 9 7498 7500 7521 C5' DC T 10 7520 7522 7540 C5' DA T 11 7539 7541 7561 C5' DG T 12 7560 7562 7583 C5' DT T 13 7582 7584 7603 C5' DC T 14 7602 7604 7622 C5' DC T 15 7621 7623 7641 C5' DG T 16 7640 7642 7663 C5' DC T 17 7662 7664 7682 C5' DG T 18 7681 7683 7702 C5' DG P 103 7701 7703 7724 C5' DC P 104 7723 7725 7743 C5' DG P 105 7742 7744 7765 C5' DG P 106 7764 7766 7787 C5' DA P 107 7786 7788 7808 C5' DC P 108 7807 7809 7827 C5' DT P 109 7826 7828 7847 C5' DG P 110 7846 7848 7869 C5' DC P 111 7868 7870 7888 C5' DT P 112 7887 7889 7908 C5' DT P 113 7907 7909 7928 C5' DA P 114 7927 7929 7958 C5' DOC P 115 7959 7956 7977 C5' TTP A1001 7976 7978 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7369 P DA T 3 distorted distorted 7370 7371 7372 7390 P DA T 4 distorted distorted 7377 7391 7392 7393 7411 P DG T 5 distorted distorted 7398 7412 7413 7414 7433 P DT T 6 distorted distorted 7419 7434 7435 7436 7453 P DA T 7 distorted distorted 7441 7454 7455 7456 7474 P DA T 8 distorted distorted 7461 7475 7476 7477 7495 P DG T 9 distorted distorted 7482 7496 7497 7498 7517 P DC T 10 distorted distorted 7503 7518 7519 7520 7536 P DA T 11 distorted distorted 7525 7537 7538 7539 7557 P DG T 12 distorted distorted 7544 7558 7559 7560 7579 P DT T 13 distorted distorted 7565 7580 7581 7582 7599 P DC T 14 distorted distorted 7587 7600 7601 7602 7618 P DC T 15 distorted distorted 7607 7619 7620 7621 7637 P DG T 16 distorted distorted 7626 7638 7639 7640 7659 P DC T 17 distorted distorted 7645 7660 7661 7662 7678 P DG T 18 distorted distorted 7667 7679 7680 7681 7720 P DC P 104 distorted distorted 7706 7721 7722 7723 7739 P DG P 105 distorted distorted 7728 7740 7741 7742 7761 P DG P 106 distorted distorted 7747 7762 7763 7764 7783 P DA P 107 distorted distorted 7769 7784 7785 7786 7804 P DC P 108 distorted distorted 7791 7805 7806 7807 7823 P DT P 109 distorted distorted 7812 7824 7825 7826 7843 P DG P 110 distorted distorted 7831 7844 7845 7846 7865 P DC P 111 distorted distorted 7851 7866 7867 7868 7884 P DT P 112 distorted distorted 7873 7885 7886 7887 7904 P DT P 113 distorted distorted 7892 7905 7906 7907 7924 P DA P 114 distorted distorted 7912 7925 7926 7927 7960 P DOC P 115 distorted distorted 7932 7961 7962 7959 ---------------------------------------------------------------------------------