ID code: '3SQ4' 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' --------------------------------------------------------------------------------- 7385 C1' DC T 3 beta 7381 7386 7384 7404 C1' 2PR T 4 beta 7400 7405 7403 7425 C1' DT T 5 beta 7421 7426 7424 7445 C1' DC T 6 beta 7441 7446 7444 7464 C1' DG T 7 beta 7460 7465 7463 7486 C1' DC T 8 beta 7482 7487 7485 7505 C1' DC T 9 beta 7501 7506 7504 7524 C1' DG T 10 beta 7520 7525 7523 7546 C1' DC T 11 beta 7542 7547 7545 7565 C1' DC T 12 beta 7561 7566 7564 7584 C1' DG T 13 beta 7580 7585 7583 7606 C1' DC T 14 beta 7602 7607 7605 7625 C1' DG T 15 beta 7621 7626 7624 7647 C1' DC T 16 beta 7643 7648 7646 7666 C1' DG T 17 beta 7662 7667 7665 7688 C1' DG T 18 beta 7684 7689 7687 7708 C1' DC P 103 beta 7704 7709 7707 7727 C1' DG P 104 beta 7723 7728 7726 7749 C1' DC P 105 beta 7745 7750 7748 7768 C1' DG P 106 beta 7764 7769 7767 7790 C1' DC P 107 beta 7786 7791 7789 7809 C1' DG P 108 beta 7805 7810 7808 7831 C1' DG P 109 beta 7827 7832 7830 7853 C1' DC P 110 beta 7849 7854 7852 7872 C1' DG P 111 beta 7868 7873 7871 7894 C1' DG P 112 beta 7890 7895 7893 7916 C1' DC P 113 beta 7912 7917 7915 7935 C1' DG P 114 beta 7931 7936 7934 7956 C1' 2DA P 115 beta 7953 7957 7955 7987 C1' TTP A 903 beta 7983 7988 7986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7384 C2' DC T 3 7385 7382 7403 C2' 2PR T 4 7404 7401 7424 C2' DT T 5 7425 7422 7444 C2' DC T 6 7445 7442 7463 C2' DG T 7 7464 7461 7485 C2' DC T 8 7486 7483 7504 C2' DC T 9 7505 7502 7523 C2' DG T 10 7524 7521 7545 C2' DC T 11 7546 7543 7564 C2' DC T 12 7565 7562 7583 C2' DG T 13 7584 7581 7605 C2' DC T 14 7606 7603 7624 C2' DG T 15 7625 7622 7646 C2' DC T 16 7647 7644 7665 C2' DG T 17 7666 7663 7687 C2' DG T 18 7688 7685 7707 C2' DC P 103 7708 7705 7726 C2' DG P 104 7727 7724 7748 C2' DC P 105 7749 7746 7767 C2' DG P 106 7768 7765 7789 C2' DC P 107 7790 7787 7808 C2' DG P 108 7809 7806 7830 C2' DG P 109 7831 7828 7852 C2' DC P 110 7853 7850 7871 C2' DG P 111 7872 7869 7893 C2' DG P 112 7894 7891 7915 C2' DC P 113 7916 7913 7934 C2' DG P 114 7935 7932 7955 C2' 2DA P 115 7956 7954 7986 C2' TTP A 903 7987 7984 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7382 C3' DC T 3 OK 7380 7383 7384 7401 C3' 2PR T 4 OK 7399 7402 7403 7422 C3' DT T 5 OK 7420 7423 7424 7442 C3' DC T 6 OK 7440 7443 7444 7461 C3' DG T 7 OK 7459 7462 7463 7483 C3' DC T 8 OK 7481 7484 7485 7502 C3' DC T 9 OK 7500 7503 7504 7521 C3' DG T 10 OK 7519 7522 7523 7543 C3' DC T 11 OK 7541 7544 7545 7562 C3' DC T 12 OK 7560 7563 7564 7581 C3' DG T 13 OK 7579 7582 7583 7603 C3' DC T 14 OK 7601 7604 7605 7622 C3' DG T 15 OK 7620 7623 7624 7644 C3' DC T 16 OK 7642 7645 7646 7663 C3' DG T 17 OK 7661 7664 7665 7685 C3' DG T 18 OK 7683 7686 7687 7705 C3' DC P 103 OK 7703 7706 7707 7724 C3' DG P 104 OK 7722 7725 7726 7746 C3' DC P 105 OK 7744 7747 7748 7765 C3' DG P 106 OK 7763 7766 7767 7787 C3' DC P 107 OK 7785 7788 7789 7806 C3' DG P 108 OK 7804 7807 7808 7828 C3' DG P 109 OK 7826 7829 7830 7850 C3' DC P 110 OK 7848 7851 7852 7869 C3' DG P 111 OK 7867 7870 7871 7891 C3' DG P 112 OK 7889 7892 7893 7913 C3' DC P 113 OK 7911 7914 7915 7932 C3' DG P 114 OK 7930 7933 7934 7954 C3' 2DA P 115 7952 7955 7984 C3' TTP A 903 OK 7982 7985 7986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7380 C4' DC T 3 OK 7382 7379 7381 7399 C4' 2PR T 4 OK 7401 7398 7400 7420 C4' DT T 5 OK 7422 7419 7421 7440 C4' DC T 6 OK 7442 7439 7441 7459 C4' DG T 7 OK 7461 7458 7460 7481 C4' DC T 8 OK 7483 7480 7482 7500 C4' DC T 9 OK 7502 7499 7501 7519 C4' DG T 10 OK 7521 7518 7520 7541 C4' DC T 11 OK 7543 7540 7542 7560 C4' DC T 12 OK 7562 7559 7561 7579 C4' DG T 13 OK 7581 7578 7580 7601 C4' DC T 14 OK 7603 7600 7602 7620 C4' DG T 15 OK 7622 7619 7621 7642 C4' DC T 16 OK 7644 7641 7643 7661 C4' DG T 17 OK 7663 7660 7662 7683 C4' DG T 18 OK 7685 7682 7684 7703 C4' DC P 103 OK 7705 7702 7704 7722 C4' DG P 104 OK 7724 7721 7723 7744 C4' DC P 105 OK 7746 7743 7745 7763 C4' DG P 106 OK 7765 7762 7764 7785 C4' DC P 107 OK 7787 7784 7786 7804 C4' DG P 108 OK 7806 7803 7805 7826 C4' DG P 109 OK 7828 7825 7827 7848 C4' DC P 110 OK 7850 7847 7849 7867 C4' DG P 111 OK 7869 7866 7868 7889 C4' DG P 112 OK 7891 7888 7890 7911 C4' DC P 113 OK 7913 7910 7912 7930 C4' DG P 114 OK 7932 7929 7931 7952 C4' 2DA P 115 OK 7954 7951 7953 7982 C4' TTP A 903 OK 7984 7981 7983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7379 C5' DC T 3 7378 7380 7398 C5' 2PR T 4 7397 7399 7419 C5' DT T 5 7418 7420 7439 C5' DC T 6 7438 7440 7458 C5' DG T 7 7457 7459 7480 C5' DC T 8 7479 7481 7499 C5' DC T 9 7498 7500 7518 C5' DG T 10 7517 7519 7540 C5' DC T 11 7539 7541 7559 C5' DC T 12 7558 7560 7578 C5' DG T 13 7577 7579 7600 C5' DC T 14 7599 7601 7619 C5' DG T 15 7618 7620 7641 C5' DC T 16 7640 7642 7660 C5' DG T 17 7659 7661 7682 C5' DG T 18 7681 7683 7702 C5' DC P 103 7701 7703 7721 C5' DG P 104 7720 7722 7743 C5' DC P 105 7742 7744 7762 C5' DG P 106 7761 7763 7784 C5' DC P 107 7783 7785 7803 C5' DG P 108 7802 7804 7825 C5' DG P 109 7824 7826 7847 C5' DC P 110 7846 7848 7866 C5' DG P 111 7865 7867 7888 C5' DG P 112 7887 7889 7910 C5' DC P 113 7909 7911 7929 C5' DG P 114 7928 7930 7951 C5' 2DA P 115 7950 7952 7981 C5' TTP A 903 7980 7982 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7375 P DC T 3 distorted distorted 7376 7377 7378 7394 P 2PR T 4 OK OK 7383 7395 7396 7397 7415 P DT T 5 distorted distorted 7402 7416 7417 7418 7435 P DC T 6 distorted distorted 7423 7436 7437 7438 7454 P DG T 7 distorted distorted 7443 7455 7456 7457 7476 P DC T 8 distorted distorted 7462 7477 7478 7479 7495 P DC T 9 distorted distorted 7484 7496 7497 7498 7514 P DG T 10 distorted distorted 7503 7515 7516 7517 7536 P DC T 11 distorted distorted 7522 7537 7538 7539 7555 P DC T 12 distorted distorted 7544 7556 7557 7558 7574 P DG T 13 distorted distorted 7563 7575 7576 7577 7596 P DC T 14 distorted distorted 7582 7597 7598 7599 7615 P DG T 15 distorted distorted 7604 7616 7617 7618 7637 P DC T 16 distorted distorted 7623 7638 7639 7640 7656 P DG T 17 distorted distorted 7645 7657 7658 7659 7678 P DG T 18 distorted distorted 7664 7679 7680 7681 7717 P DG P 104 distorted distorted 7706 7718 7719 7720 7739 P DC P 105 distorted distorted 7725 7740 7741 7742 7758 P DG P 106 distorted distorted 7747 7759 7760 7761 7780 P DC P 107 distorted distorted 7766 7781 7782 7783 7799 P DG P 108 distorted distorted 7788 7800 7801 7802 7821 P DG P 109 distorted distorted 7807 7822 7823 7824 7843 P DC P 110 distorted distorted 7829 7844 7845 7846 7862 P DG P 111 distorted distorted 7851 7863 7864 7865 7884 P DG P 112 distorted distorted 7870 7885 7886 7887 7906 P DC P 113 distorted distorted 7892 7907 7908 7909 7925 P DG P 114 distorted distorted 7914 7926 7927 7928 7947 P 2DA P 115 distorted distorted 7933 7948 7949 7950 ---------------------------------------------------------------------------------