ID code: '3E2E' 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' --------------------------------------------------------------------------------- 6598 C1' G R 1 beta 6593 6599 6596 6621 C1' G R 2 beta 6616 6622 6619 6644 C1' G R 3 beta 6639 6645 6642 6667 C1' A R 4 beta 6662 6668 6665 6689 C1' G R 5 beta 6684 6690 6687 6712 C1' U R 6 beta 6707 6713 6710 6732 C1' G R 7 beta 6727 6733 6730 6755 C1' DA T 1 beta 6751 6756 6754 6776 C1' DG T 2 beta 6772 6777 6775 6798 C1' DC T 3 beta 6794 6799 6797 6817 C1' DC T 4 beta 6813 6818 6816 6836 C1' DG T 5 beta 6832 6837 6835 6858 C1' DT T 6 beta 6854 6859 6857 6878 C1' DG T 7 beta 6874 6879 6877 6900 C1' DC T 8 beta 6896 6901 6899 6919 C1' DG T 9 beta 6915 6920 6918 6941 C1' DC T 10 beta 6937 6942 6940 6960 C1' DA T 11 beta 6956 6961 6959 6981 C1' DC T 12 beta 6977 6982 6980 7000 C1' DT T 13 beta 6996 7001 6999 7020 C1' DC T 14 beta 7016 7021 7019 7039 C1' DC T 15 beta 7035 7040 7038 7058 C1' DC T 16 beta 7054 7059 7057 7077 C1' DT T 19 beta 7073 7078 7076 7097 C1' DA T 20 beta 7093 7098 7096 7118 C1' DG T 21 beta 7114 7119 7117 7140 C1' DT T 22 beta 7136 7141 7139 7160 C1' DG T 23 beta 7156 7161 7159 7182 C1' DA T 24 beta 7178 7183 7181 7203 C1' DG T 25 beta 7199 7204 7202 7225 C1' DT T 26 beta 7221 7226 7224 7245 C1' DC T 27 beta 7241 7246 7244 7264 C1' DG T 28 beta 7260 7265 7263 7286 C1' DT T 29 beta 7282 7287 7285 7306 C1' DA T 30 beta 7302 7307 7305 7327 C1' DT T 31 beta 7323 7328 7326 7347 C1' DT T 32 beta 7343 7348 7346 7367 C1' DA T 33 beta 7363 7368 7366 7385 C1' DT N 101 beta 7381 7386 7384 7405 C1' DA N 102 beta 7401 7406 7404 7426 C1' DA N 103 beta 7422 7427 7425 7447 C1' DT N 104 beta 7443 7448 7446 7467 C1' DA N 105 beta 7463 7468 7466 7488 C1' DC N 106 beta 7484 7489 7487 7507 C1' DG N 107 beta 7503 7508 7506 7529 C1' DA N 108 beta 7525 7530 7528 7550 C1' DC N 109 beta 7546 7551 7549 7569 C1' DT N 110 beta 7565 7570 7568 7589 C1' DC N 111 beta 7585 7590 7588 7608 C1' DA N 112 beta 7604 7609 7607 7629 C1' DC N 113 beta 7625 7630 7628 7648 C1' DT N 119 beta 7644 7649 7647 7668 C1' DT N 120 beta 7664 7669 7667 7688 C1' DC N 121 beta 7684 7689 7687 7707 C1' DT N 122 beta 7703 7708 7706 7727 C1' DG N 123 beta 7723 7728 7726 7749 C1' DG N 124 beta 7745 7750 7748 7771 C1' DC N 125 beta 7767 7772 7770 7790 C1' DG N 126 beta 7786 7791 7789 7812 C1' DC N 127 beta 7808 7813 7811 7831 C1' DA N 128 beta 7827 7832 7830 7852 C1' DC N 129 beta 7848 7853 7851 7871 C1' DG N 130 beta 7867 7872 7870 7893 C1' DG N 131 beta 7889 7894 7892 7915 C1' DC N 132 beta 7911 7916 7914 7934 C1' DT N 133 beta 7930 7935 7933 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6596 C2' G R 1 OK 6598 6594 6597 6619 C2' G R 2 OK 6621 6617 6620 6642 C2' G R 3 OK 6644 6640 6643 6665 C2' A R 4 OK 6667 6663 6666 6687 C2' G R 5 OK 6689 6685 6688 6710 C2' U R 6 OK 6712 6708 6711 6730 C2' G R 7 OK 6732 6728 6731 6754 C2' DA T 1 6755 6752 6775 C2' DG T 2 6776 6773 6797 C2' DC T 3 6798 6795 6816 C2' DC T 4 6817 6814 6835 C2' DG T 5 6836 6833 6857 C2' DT T 6 6858 6855 6877 C2' DG T 7 6878 6875 6899 C2' DC T 8 6900 6897 6918 C2' DG T 9 6919 6916 6940 C2' DC T 10 6941 6938 6959 C2' DA T 11 6960 6957 6980 C2' DC T 12 6981 6978 6999 C2' DT T 13 7000 6997 7019 C2' DC T 14 7020 7017 7038 C2' DC T 15 7039 7036 7057 C2' DC T 16 7058 7055 7076 C2' DT T 19 7077 7074 7096 C2' DA T 20 7097 7094 7117 C2' DG T 21 7118 7115 7139 C2' DT T 22 7140 7137 7159 C2' DG T 23 7160 7157 7181 C2' DA T 24 7182 7179 7202 C2' DG T 25 7203 7200 7224 C2' DT T 26 7225 7222 7244 C2' DC T 27 7245 7242 7263 C2' DG T 28 7264 7261 7285 C2' DT T 29 7286 7283 7305 C2' DA T 30 7306 7303 7326 C2' DT T 31 7327 7324 7346 C2' DT T 32 7347 7344 7366 C2' DA T 33 7367 7364 7384 C2' DT N 101 7385 7382 7404 C2' DA N 102 7405 7402 7425 C2' DA N 103 7426 7423 7446 C2' DT N 104 7447 7444 7466 C2' DA N 105 7467 7464 7487 C2' DC N 106 7488 7485 7506 C2' DG N 107 7507 7504 7528 C2' DA N 108 7529 7526 7549 C2' DC N 109 7550 7547 7568 C2' DT N 110 7569 7566 7588 C2' DC N 111 7589 7586 7607 C2' DA N 112 7608 7605 7628 C2' DC N 113 7629 7626 7647 C2' DT N 119 7648 7645 7667 C2' DT N 120 7668 7665 7687 C2' DC N 121 7688 7685 7706 C2' DT N 122 7707 7704 7726 C2' DG N 123 7727 7724 7748 C2' DG N 124 7749 7746 7770 C2' DC N 125 7771 7768 7789 C2' DG N 126 7790 7787 7811 C2' DC N 127 7812 7809 7830 C2' DA N 128 7831 7828 7851 C2' DC N 129 7852 7849 7870 C2' DG N 130 7871 7868 7892 C2' DG N 131 7893 7890 7914 C2' DC N 132 7915 7912 7933 C2' DT N 133 7934 7931 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6594 C3' G R 1 OK 6592 6595 6596 6617 C3' G R 2 OK 6615 6618 6619 6640 C3' G R 3 OK 6638 6641 6642 6663 C3' A R 4 OK 6661 6664 6665 6685 C3' G R 5 OK 6683 6686 6687 6708 C3' U R 6 OK 6706 6709 6710 6728 C3' G R 7 OK 6726 6729 6730 6752 C3' DA T 1 OK 6750 6753 6754 6773 C3' DG T 2 OK 6771 6774 6775 6795 C3' DC T 3 OK 6793 6796 6797 6814 C3' DC T 4 OK 6812 6815 6816 6833 C3' DG T 5 OK 6831 6834 6835 6855 C3' DT T 6 OK 6853 6856 6857 6875 C3' DG T 7 OK 6873 6876 6877 6897 C3' DC T 8 OK 6895 6898 6899 6916 C3' DG T 9 OK 6914 6917 6918 6938 C3' DC T 10 OK 6936 6939 6940 6957 C3' DA T 11 OK 6955 6958 6959 6978 C3' DC T 12 OK 6976 6979 6980 6997 C3' DT T 13 OK 6995 6998 6999 7017 C3' DC T 14 OK 7015 7018 7019 7036 C3' DC T 15 OK 7034 7037 7038 7055 C3' DC T 16 OK 7053 7056 7057 7074 C3' DT T 19 OK 7072 7075 7076 7094 C3' DA T 20 OK 7092 7095 7096 7115 C3' DG T 21 OK 7113 7116 7117 7137 C3' DT T 22 OK 7135 7138 7139 7157 C3' DG T 23 OK 7155 7158 7159 7179 C3' DA T 24 OK 7177 7180 7181 7200 C3' DG T 25 OK 7198 7201 7202 7222 C3' DT T 26 OK 7220 7223 7224 7242 C3' DC T 27 OK 7240 7243 7244 7261 C3' DG T 28 OK 7259 7262 7263 7283 C3' DT T 29 OK 7281 7284 7285 7303 C3' DA T 30 OK 7301 7304 7305 7324 C3' DT T 31 OK 7322 7325 7326 7344 C3' DT T 32 OK 7342 7345 7346 7364 C3' DA T 33 OK 7362 7365 7366 7382 C3' DT N 101 OK 7380 7383 7384 7402 C3' DA N 102 OK 7400 7403 7404 7423 C3' DA N 103 OK 7421 7424 7425 7444 C3' DT N 104 OK 7442 7445 7446 7464 C3' DA N 105 OK 7462 7465 7466 7485 C3' DC N 106 OK 7483 7486 7487 7504 C3' DG N 107 OK 7502 7505 7506 7526 C3' DA N 108 OK 7524 7527 7528 7547 C3' DC N 109 OK 7545 7548 7549 7566 C3' DT N 110 OK 7564 7567 7568 7586 C3' DC N 111 OK 7584 7587 7588 7605 C3' DA N 112 OK 7603 7606 7607 7626 C3' DC N 113 OK 7624 7627 7628 7645 C3' DT N 119 OK 7643 7646 7647 7665 C3' DT N 120 OK 7663 7666 7667 7685 C3' DC N 121 OK 7683 7686 7687 7704 C3' DT N 122 OK 7702 7705 7706 7724 C3' DG N 123 OK 7722 7725 7726 7746 C3' DG N 124 OK 7744 7747 7748 7768 C3' DC N 125 OK 7766 7769 7770 7787 C3' DG N 126 OK 7785 7788 7789 7809 C3' DC N 127 OK 7807 7810 7811 7828 C3' DA N 128 OK 7826 7829 7830 7849 C3' DC N 129 OK 7847 7850 7851 7868 C3' DG N 130 OK 7866 7869 7870 7890 C3' DG N 131 OK 7888 7891 7892 7912 C3' DC N 132 OK 7910 7913 7914 7931 C3' DT N 133 OK 7929 7932 7933 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6592 C4' G R 1 OK 6594 6591 6593 6615 C4' G R 2 OK 6617 6614 6616 6638 C4' G R 3 OK 6640 6637 6639 6661 C4' A R 4 OK 6663 6660 6662 6683 C4' G R 5 OK 6685 6682 6684 6706 C4' U R 6 OK 6708 6705 6707 6726 C4' G R 7 OK 6728 6725 6727 6750 C4' DA T 1 OK 6752 6749 6751 6771 C4' DG T 2 OK 6773 6770 6772 6793 C4' DC T 3 OK 6795 6792 6794 6812 C4' DC T 4 OK 6814 6811 6813 6831 C4' DG T 5 OK 6833 6830 6832 6853 C4' DT T 6 OK 6855 6852 6854 6873 C4' DG T 7 OK 6875 6872 6874 6895 C4' DC T 8 OK 6897 6894 6896 6914 C4' DG T 9 OK 6916 6913 6915 6936 C4' DC T 10 OK 6938 6935 6937 6955 C4' DA T 11 OK 6957 6954 6956 6976 C4' DC T 12 OK 6978 6975 6977 6995 C4' DT T 13 OK 6997 6994 6996 7015 C4' DC T 14 OK 7017 7014 7016 7034 C4' DC T 15 OK 7036 7033 7035 7053 C4' DC T 16 OK 7055 7052 7054 7072 C4' DT T 19 OK 7074 7071 7073 7092 C4' DA T 20 OK 7094 7091 7093 7113 C4' DG T 21 OK 7115 7112 7114 7135 C4' DT T 22 OK 7137 7134 7136 7155 C4' DG T 23 OK 7157 7154 7156 7177 C4' DA T 24 OK 7179 7176 7178 7198 C4' DG T 25 OK 7200 7197 7199 7220 C4' DT T 26 OK 7222 7219 7221 7240 C4' DC T 27 OK 7242 7239 7241 7259 C4' DG T 28 OK 7261 7258 7260 7281 C4' DT T 29 OK 7283 7280 7282 7301 C4' DA T 30 OK 7303 7300 7302 7322 C4' DT T 31 OK 7324 7321 7323 7342 C4' DT T 32 OK 7344 7341 7343 7362 C4' DA T 33 OK 7364 7361 7363 7380 C4' DT N 101 OK 7382 7379 7381 7400 C4' DA N 102 OK 7402 7399 7401 7421 C4' DA N 103 OK 7423 7420 7422 7442 C4' DT N 104 OK 7444 7441 7443 7462 C4' DA N 105 OK 7464 7461 7463 7483 C4' DC N 106 OK 7485 7482 7484 7502 C4' DG N 107 OK 7504 7501 7503 7524 C4' DA N 108 OK 7526 7523 7525 7545 C4' DC N 109 OK 7547 7544 7546 7564 C4' DT N 110 OK 7566 7563 7565 7584 C4' DC N 111 OK 7586 7583 7585 7603 C4' DA N 112 OK 7605 7602 7604 7624 C4' DC N 113 OK 7626 7623 7625 7643 C4' DT N 119 OK 7645 7642 7644 7663 C4' DT N 120 OK 7665 7662 7664 7683 C4' DC N 121 OK 7685 7682 7684 7702 C4' DT N 122 OK 7704 7701 7703 7722 C4' DG N 123 OK 7724 7721 7723 7744 C4' DG N 124 OK 7746 7743 7745 7766 C4' DC N 125 OK 7768 7765 7767 7785 C4' DG N 126 OK 7787 7784 7786 7807 C4' DC N 127 OK 7809 7806 7808 7826 C4' DA N 128 OK 7828 7825 7827 7847 C4' DC N 129 OK 7849 7846 7848 7866 C4' DG N 130 OK 7868 7865 7867 7888 C4' DG N 131 OK 7890 7887 7889 7910 C4' DC N 132 OK 7912 7909 7911 7929 C4' DT N 133 OK 7931 7928 7930 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6591 C5' G R 1 6592 6614 C5' G R 2 6613 6615 6637 C5' G R 3 6636 6638 6660 C5' A R 4 6659 6661 6682 C5' G R 5 6681 6683 6705 C5' U R 6 6704 6706 6725 C5' G R 7 6724 6726 6749 C5' DA T 1 6748 6750 6770 C5' DG T 2 6769 6771 6792 C5' DC T 3 6791 6793 6811 C5' DC T 4 6810 6812 6830 C5' DG T 5 6829 6831 6852 C5' DT T 6 6851 6853 6872 C5' DG T 7 6871 6873 6894 C5' DC T 8 6893 6895 6913 C5' DG T 9 6912 6914 6935 C5' DC T 10 6934 6936 6954 C5' DA T 11 6953 6955 6975 C5' DC T 12 6974 6976 6994 C5' DT T 13 6993 6995 7014 C5' DC T 14 7013 7015 7033 C5' DC T 15 7032 7034 7052 C5' DC T 16 7051 7053 7071 C5' DT T 19 7070 7072 7091 C5' DA T 20 7090 7092 7112 C5' DG T 21 7111 7113 7134 C5' DT T 22 7133 7135 7154 C5' DG T 23 7153 7155 7176 C5' DA T 24 7175 7177 7197 C5' DG T 25 7196 7198 7219 C5' DT T 26 7218 7220 7239 C5' DC T 27 7238 7240 7258 C5' DG T 28 7257 7259 7280 C5' DT T 29 7279 7281 7300 C5' DA T 30 7299 7301 7321 C5' DT T 31 7320 7322 7341 C5' DT T 32 7340 7342 7361 C5' DA T 33 7360 7362 7379 C5' DT N 101 7380 7399 C5' DA N 102 7398 7400 7420 C5' DA N 103 7419 7421 7441 C5' DT N 104 7440 7442 7461 C5' DA N 105 7460 7462 7482 C5' DC N 106 7481 7483 7501 C5' DG N 107 7500 7502 7523 C5' DA N 108 7522 7524 7544 C5' DC N 109 7543 7545 7563 C5' DT N 110 7562 7564 7583 C5' DC N 111 7582 7584 7602 C5' DA N 112 7601 7603 7623 C5' DC N 113 7622 7624 7642 C5' DT N 119 7641 7643 7662 C5' DT N 120 7661 7663 7682 C5' DC N 121 7681 7683 7701 C5' DT N 122 7700 7702 7721 C5' DG N 123 7720 7722 7743 C5' DG N 124 7742 7744 7765 C5' DC N 125 7764 7766 7784 C5' DG N 126 7783 7785 7806 C5' DC N 127 7805 7807 7825 C5' DA N 128 7824 7826 7846 C5' DC N 129 7845 7847 7865 C5' DG N 130 7864 7866 7887 C5' DG N 131 7886 7888 7909 C5' DC N 132 7908 7910 7928 C5' DT N 133 7927 7929 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6610 P G R 2 distorted distorted 6595 6611 6612 6613 6633 P G R 3 distorted distorted 6618 6634 6635 6636 6656 P A R 4 distorted distorted 6641 6657 6658 6659 6678 P G R 5 distorted distorted 6664 6679 6680 6681 6701 P U R 6 distorted distorted 6686 6702 6703 6704 6721 P G R 7 distorted distorted 6709 6722 6723 6724 6745 P DA T 1 distorted distorted 6746 6747 6748 6766 P DG T 2 distorted distorted 6753 6767 6768 6769 6788 P DC T 3 distorted distorted 6774 6789 6790 6791 6807 P DC T 4 distorted distorted 6796 6808 6809 6810 6826 P DG T 5 distorted distorted 6815 6827 6828 6829 6848 P DT T 6 distorted distorted 6834 6849 6850 6851 6868 P DG T 7 distorted distorted 6856 6869 6870 6871 6890 P DC T 8 distorted distorted 6876 6891 6892 6893 6909 P DG T 9 distorted distorted 6898 6910 6911 6912 6931 P DC T 10 distorted distorted 6917 6932 6933 6934 6950 P DA T 11 distorted distorted 6939 6951 6952 6953 6971 P DC T 12 distorted distorted 6958 6972 6973 6974 6990 P DT T 13 distorted distorted 6979 6991 6992 6993 7010 P DC T 14 distorted distorted 6998 7011 7012 7013 7029 P DC T 15 distorted distorted 7018 7030 7031 7032 7048 P DC T 16 distorted distorted 7037 7049 7050 7051 7067 P DT T 19 OK OK 7068 7069 7070 7087 P DA T 20 distorted distorted 7075 7088 7089 7090 7108 P DG T 21 distorted distorted 7095 7109 7110 7111 7130 P DT T 22 distorted distorted 7116 7131 7132 7133 7150 P DG T 23 distorted distorted 7138 7151 7152 7153 7172 P DA T 24 distorted distorted 7158 7173 7174 7175 7193 P DG T 25 distorted distorted 7180 7194 7195 7196 7215 P DT T 26 distorted distorted 7201 7216 7217 7218 7235 P DC T 27 distorted distorted 7223 7236 7237 7238 7254 P DG T 28 distorted distorted 7243 7255 7256 7257 7276 P DT T 29 distorted distorted 7262 7277 7278 7279 7296 P DA T 30 distorted distorted 7284 7297 7298 7299 7317 P DT T 31 distorted distorted 7304 7318 7319 7320 7337 P DT T 32 distorted distorted 7325 7338 7339 7340 7357 P DA T 33 distorted distorted 7345 7358 7359 7360 7395 P DA N 102 distorted distorted 7383 7396 7397 7398 7416 P DA N 103 distorted distorted 7403 7417 7418 7419 7437 P DT N 104 distorted distorted 7424 7438 7439 7440 7457 P DA N 105 distorted distorted 7445 7458 7459 7460 7478 P DC N 106 distorted distorted 7465 7479 7480 7481 7497 P DG N 107 distorted distorted 7486 7498 7499 7500 7519 P DA N 108 distorted distorted 7505 7520 7521 7522 7540 P DC N 109 distorted distorted 7527 7541 7542 7543 7559 P DT N 110 distorted distorted 7548 7560 7561 7562 7579 P DC N 111 distorted distorted 7567 7580 7581 7582 7598 P DA N 112 distorted distorted 7587 7599 7600 7601 7619 P DC N 113 distorted distorted 7606 7620 7621 7622 7638 P DT N 119 distorted distorted 7639 7640 7641 7658 P DT N 120 distorted distorted 7646 7659 7660 7661 7678 P DC N 121 distorted distorted 7666 7679 7680 7681 7697 P DT N 122 distorted distorted 7686 7698 7699 7700 7717 P DG N 123 distorted distorted 7705 7718 7719 7720 7739 P DG N 124 distorted distorted 7725 7740 7741 7742 7761 P DC N 125 distorted distorted 7747 7762 7763 7764 7780 P DG N 126 distorted distorted 7769 7781 7782 7783 7802 P DC N 127 distorted distorted 7788 7803 7804 7805 7821 P DA N 128 distorted distorted 7810 7822 7823 7824 7842 P DC N 129 distorted distorted 7829 7843 7844 7845 7861 P DG N 130 distorted distorted 7850 7862 7863 7864 7883 P DG N 131 distorted distorted 7869 7884 7885 7886 7905 P DC N 132 distorted distorted 7891 7906 7907 7908 7924 P DT N 133 distorted distorted 7913 7925 7926 7927 ---------------------------------------------------------------------------------