ID code: '3IN5' 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' --------------------------------------------------------------------------------- 6766 C1' DG P 3 beta 6762 6767 6765 6788 C1' DG P 4 beta 6784 6789 6787 6810 C1' DG P 5 beta 6806 6811 6809 6832 C1' DA P 6 beta 6828 6833 6831 6853 C1' DA P 7 beta 6849 6854 6852 6874 C1' DG P 8 beta 6870 6875 6873 6896 C1' DG P 9 beta 6892 6897 6895 6918 C1' DA P 10 beta 6914 6919 6917 6939 C1' DC P 11 beta 6935 6940 6938 6958 C1' DT P 12 beta 6954 6959 6957 6976 C1' DOC P 13 beta 6980 6968 6977 6994 C1' DC T 2 beta 6990 6995 6993 7013 C1' DT T 3 beta 7009 7014 7012 7033 C1' DA T 4 beta 7029 7034 7032 7054 C1' 8OG T 5 beta 7050 7055 7053 7077 C1' DG T 6 beta 7073 7078 7076 7099 C1' DA T 7 beta 7095 7100 7098 7120 C1' DG T 8 beta 7116 7121 7119 7142 C1' DT T 9 beta 7138 7143 7141 7162 C1' DC T 10 beta 7158 7163 7161 7181 C1' DC T 11 beta 7177 7182 7180 7200 C1' DT T 12 beta 7196 7201 7199 7220 C1' DT T 13 beta 7216 7221 7219 7240 C1' DC T 14 beta 7236 7241 7239 7259 C1' DC T 15 beta 7255 7260 7258 7278 C1' DC T 16 beta 7274 7279 7277 7295 C1' DG Q 2 beta 7291 7296 7294 7317 C1' DG Q 3 beta 7313 7318 7316 7339 C1' DG Q 4 beta 7335 7340 7338 7361 C1' DG Q 5 beta 7357 7362 7360 7383 C1' DA Q 6 beta 7379 7384 7382 7404 C1' DA Q 7 beta 7400 7405 7403 7425 C1' DG Q 8 beta 7421 7426 7424 7447 C1' DG Q 9 beta 7443 7448 7446 7469 C1' DA Q 10 beta 7465 7470 7468 7490 C1' DC Q 11 beta 7486 7491 7489 7509 C1' DT Q 12 beta 7505 7510 7508 7527 C1' DOC Q 13 beta 7531 7519 7528 7545 C1' DA U 4 beta 7541 7546 7544 7566 C1' 8OG U 5 beta 7562 7567 7565 7589 C1' DG U 6 beta 7585 7590 7588 7611 C1' DA U 7 beta 7607 7612 7610 7632 C1' DG U 8 beta 7628 7633 7631 7654 C1' DT U 9 beta 7650 7655 7653 7674 C1' DC U 10 beta 7670 7675 7673 7693 C1' DC U 11 beta 7689 7694 7692 7712 C1' DT U 12 beta 7708 7713 7711 7732 C1' DT U 13 beta 7728 7733 7731 7752 C1' DC U 14 beta 7748 7753 7751 7771 C1' DC U 15 beta 7767 7772 7770 7790 C1' DC U 16 beta 7786 7791 7789 7809 C1' DC U 17 beta 7805 7810 7808 7838 C1' ATP A 1 beta 7834 7839 7837 7870 C1' ATP B 2 beta 7866 7871 7869 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6765 C2' DG P 3 6766 6763 6787 C2' DG P 4 6788 6785 6809 C2' DG P 5 6810 6807 6831 C2' DA P 6 6832 6829 6852 C2' DA P 7 6853 6850 6873 C2' DG P 8 6874 6871 6895 C2' DG P 9 6896 6893 6917 C2' DA P 10 6918 6915 6938 C2' DC P 11 6939 6936 6957 C2' DT P 12 6958 6955 6977 C2' DOC P 13 6976 6978 6993 C2' DC T 2 6994 6991 7012 C2' DT T 3 7013 7010 7032 C2' DA T 4 7033 7030 7053 C2' 8OG T 5 7054 7051 7076 C2' DG T 6 7077 7074 7098 C2' DA T 7 7099 7096 7119 C2' DG T 8 7120 7117 7141 C2' DT T 9 7142 7139 7161 C2' DC T 10 7162 7159 7180 C2' DC T 11 7181 7178 7199 C2' DT T 12 7200 7197 7219 C2' DT T 13 7220 7217 7239 C2' DC T 14 7240 7237 7258 C2' DC T 15 7259 7256 7277 C2' DC T 16 7278 7275 7294 C2' DG Q 2 7295 7292 7316 C2' DG Q 3 7317 7314 7338 C2' DG Q 4 7339 7336 7360 C2' DG Q 5 7361 7358 7382 C2' DA Q 6 7383 7380 7403 C2' DA Q 7 7404 7401 7424 C2' DG Q 8 7425 7422 7446 C2' DG Q 9 7447 7444 7468 C2' DA Q 10 7469 7466 7489 C2' DC Q 11 7490 7487 7508 C2' DT Q 12 7509 7506 7528 C2' DOC Q 13 7527 7529 7544 C2' DA U 4 7545 7542 7565 C2' 8OG U 5 7566 7563 7588 C2' DG U 6 7589 7586 7610 C2' DA U 7 7611 7608 7631 C2' DG U 8 7632 7629 7653 C2' DT U 9 7654 7651 7673 C2' DC U 10 7674 7671 7692 C2' DC U 11 7693 7690 7711 C2' DT U 12 7712 7709 7731 C2' DT U 13 7732 7729 7751 C2' DC U 14 7752 7749 7770 C2' DC U 15 7771 7768 7789 C2' DC U 16 7790 7787 7808 C2' DC U 17 7809 7806 7837 C2' ATP A 1 7838 7835 7869 C2' ATP B 2 7870 7867 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6763 C3' DG P 3 OK 6761 6764 6765 6785 C3' DG P 4 OK 6783 6786 6787 6807 C3' DG P 5 OK 6805 6808 6809 6829 C3' DA P 6 OK 6827 6830 6831 6850 C3' DA P 7 OK 6848 6851 6852 6871 C3' DG P 8 OK 6869 6872 6873 6893 C3' DG P 9 OK 6891 6894 6895 6915 C3' DA P 10 OK 6913 6916 6917 6936 C3' DC P 11 OK 6934 6937 6938 6955 C3' DT P 12 OK 6953 6956 6957 6978 C3' DOC P 13 6979 6977 6991 C3' DC T 2 OK 6989 6992 6993 7010 C3' DT T 3 OK 7008 7011 7012 7030 C3' DA T 4 OK 7028 7031 7032 7051 C3' 8OG T 5 OK 7049 7052 7053 7074 C3' DG T 6 OK 7072 7075 7076 7096 C3' DA T 7 OK 7094 7097 7098 7117 C3' DG T 8 OK 7115 7118 7119 7139 C3' DT T 9 OK 7137 7140 7141 7159 C3' DC T 10 OK 7157 7160 7161 7178 C3' DC T 11 OK 7176 7179 7180 7197 C3' DT T 12 OK 7195 7198 7199 7217 C3' DT T 13 OK 7215 7218 7219 7237 C3' DC T 14 OK 7235 7238 7239 7256 C3' DC T 15 OK 7254 7257 7258 7275 C3' DC T 16 OK 7273 7276 7277 7292 C3' DG Q 2 OK 7290 7293 7294 7314 C3' DG Q 3 OK 7312 7315 7316 7336 C3' DG Q 4 OK 7334 7337 7338 7358 C3' DG Q 5 OK 7356 7359 7360 7380 C3' DA Q 6 OK 7378 7381 7382 7401 C3' DA Q 7 OK 7399 7402 7403 7422 C3' DG Q 8 OK 7420 7423 7424 7444 C3' DG Q 9 OK 7442 7445 7446 7466 C3' DA Q 10 OK 7464 7467 7468 7487 C3' DC Q 11 OK 7485 7488 7489 7506 C3' DT Q 12 OK 7504 7507 7508 7529 C3' DOC Q 13 7530 7528 7542 C3' DA U 4 OK 7540 7543 7544 7563 C3' 8OG U 5 OK 7561 7564 7565 7586 C3' DG U 6 OK 7584 7587 7588 7608 C3' DA U 7 OK 7606 7609 7610 7629 C3' DG U 8 OK 7627 7630 7631 7651 C3' DT U 9 OK 7649 7652 7653 7671 C3' DC U 10 OK 7669 7672 7673 7690 C3' DC U 11 OK 7688 7691 7692 7709 C3' DT U 12 OK 7707 7710 7711 7729 C3' DT U 13 OK 7727 7730 7731 7749 C3' DC U 14 OK 7747 7750 7751 7768 C3' DC U 15 OK 7766 7769 7770 7787 C3' DC U 16 OK 7785 7788 7789 7806 C3' DC U 17 OK 7804 7807 7808 7835 C3' ATP A 1 OK 7833 7836 7837 7867 C3' ATP B 2 OK 7865 7868 7869 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6761 C4' DG P 3 OK 6763 6760 6762 6783 C4' DG P 4 OK 6785 6782 6784 6805 C4' DG P 5 OK 6807 6804 6806 6827 C4' DA P 6 OK 6829 6826 6828 6848 C4' DA P 7 OK 6850 6847 6849 6869 C4' DG P 8 OK 6871 6868 6870 6891 C4' DG P 9 OK 6893 6890 6892 6913 C4' DA P 10 OK 6915 6912 6914 6934 C4' DC P 11 OK 6936 6933 6935 6953 C4' DT P 12 OK 6955 6952 6954 6979 C4' DOC P 13 OK 6978 6981 6980 6989 C4' DC T 2 OK 6991 6988 6990 7008 C4' DT T 3 OK 7010 7007 7009 7028 C4' DA T 4 OK 7030 7027 7029 7049 C4' 8OG T 5 OK 7051 7048 7050 7072 C4' DG T 6 OK 7074 7071 7073 7094 C4' DA T 7 OK 7096 7093 7095 7115 C4' DG T 8 OK 7117 7114 7116 7137 C4' DT T 9 OK 7139 7136 7138 7157 C4' DC T 10 OK 7159 7156 7158 7176 C4' DC T 11 OK 7178 7175 7177 7195 C4' DT T 12 OK 7197 7194 7196 7215 C4' DT T 13 OK 7217 7214 7216 7235 C4' DC T 14 OK 7237 7234 7236 7254 C4' DC T 15 OK 7256 7253 7255 7273 C4' DC T 16 OK 7275 7272 7274 7290 C4' DG Q 2 OK 7292 7289 7291 7312 C4' DG Q 3 OK 7314 7311 7313 7334 C4' DG Q 4 OK 7336 7333 7335 7356 C4' DG Q 5 OK 7358 7355 7357 7378 C4' DA Q 6 OK 7380 7377 7379 7399 C4' DA Q 7 OK 7401 7398 7400 7420 C4' DG Q 8 OK 7422 7419 7421 7442 C4' DG Q 9 OK 7444 7441 7443 7464 C4' DA Q 10 OK 7466 7463 7465 7485 C4' DC Q 11 OK 7487 7484 7486 7504 C4' DT Q 12 OK 7506 7503 7505 7530 C4' DOC Q 13 OK 7529 7532 7531 7540 C4' DA U 4 OK 7542 7539 7541 7561 C4' 8OG U 5 OK 7563 7560 7562 7584 C4' DG U 6 OK 7586 7583 7585 7606 C4' DA U 7 OK 7608 7605 7607 7627 C4' DG U 8 OK 7629 7626 7628 7649 C4' DT U 9 OK 7651 7648 7650 7669 C4' DC U 10 OK 7671 7668 7670 7688 C4' DC U 11 OK 7690 7687 7689 7707 C4' DT U 12 OK 7709 7706 7708 7727 C4' DT U 13 OK 7729 7726 7728 7747 C4' DC U 14 OK 7749 7746 7748 7766 C4' DC U 15 OK 7768 7765 7767 7785 C4' DC U 16 OK 7787 7784 7786 7804 C4' DC U 17 OK 7806 7803 7805 7833 C4' ATP A 1 OK 7835 7832 7834 7865 C4' ATP B 2 OK 7867 7864 7866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6760 C5' DG P 3 6759 6761 6782 C5' DG P 4 6781 6783 6804 C5' DG P 5 6803 6805 6826 C5' DA P 6 6825 6827 6847 C5' DA P 7 6846 6848 6868 C5' DG P 8 6867 6869 6890 C5' DG P 9 6889 6891 6912 C5' DA P 10 6911 6913 6933 C5' DC P 11 6932 6934 6952 C5' DT P 12 6951 6953 6981 C5' DOC P 13 6982 6979 6988 C5' DC T 2 6987 6989 7007 C5' DT T 3 7006 7008 7027 C5' DA T 4 7026 7028 7048 C5' 8OG T 5 7047 7049 7071 C5' DG T 6 7070 7072 7093 C5' DA T 7 7092 7094 7114 C5' DG T 8 7113 7115 7136 C5' DT T 9 7135 7137 7156 C5' DC T 10 7155 7157 7175 C5' DC T 11 7174 7176 7194 C5' DT T 12 7193 7195 7214 C5' DT T 13 7213 7215 7234 C5' DC T 14 7233 7235 7253 C5' DC T 15 7252 7254 7272 C5' DC T 16 7271 7273 7289 C5' DG Q 2 7288 7290 7311 C5' DG Q 3 7310 7312 7333 C5' DG Q 4 7332 7334 7355 C5' DG Q 5 7354 7356 7377 C5' DA Q 6 7376 7378 7398 C5' DA Q 7 7397 7399 7419 C5' DG Q 8 7418 7420 7441 C5' DG Q 9 7440 7442 7463 C5' DA Q 10 7462 7464 7484 C5' DC Q 11 7483 7485 7503 C5' DT Q 12 7502 7504 7532 C5' DOC Q 13 7533 7530 7539 C5' DA U 4 7538 7540 7560 C5' 8OG U 5 7559 7561 7583 C5' DG U 6 7582 7584 7605 C5' DA U 7 7604 7606 7626 C5' DG U 8 7625 7627 7648 C5' DT U 9 7647 7649 7668 C5' DC U 10 7667 7669 7687 C5' DC U 11 7686 7688 7706 C5' DT U 12 7705 7707 7726 C5' DT U 13 7725 7727 7746 C5' DC U 14 7745 7747 7765 C5' DC U 15 7764 7766 7784 C5' DC U 16 7783 7785 7803 C5' DC U 17 7802 7804 7832 C5' ATP A 1 7831 7833 7864 C5' ATP B 2 7863 7865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6778 P DG P 4 distorted distorted 6764 6779 6780 6781 6800 P DG P 5 distorted distorted 6786 6801 6802 6803 6822 P DA P 6 distorted distorted 6808 6823 6824 6825 6843 P DA P 7 distorted distorted 6830 6844 6845 6846 6864 P DG P 8 distorted distorted 6851 6865 6866 6867 6886 P DG P 9 distorted distorted 6872 6887 6888 6889 6908 P DA P 10 distorted distorted 6894 6909 6910 6911 6929 P DC P 11 distorted distorted 6916 6930 6931 6932 6948 P DT P 12 distorted distorted 6937 6949 6950 6951 6983 P DOC P 13 distorted distorted 6956 6984 6985 6982 7003 P DT T 3 distorted distorted 6992 7004 7005 7006 7023 P DA T 4 distorted distorted 7011 7024 7025 7026 7044 P 8OG T 5 distorted distorted 7031 7045 7046 7047 7067 P DG T 6 distorted distorted 7052 7068 7069 7070 7089 P DA T 7 distorted distorted 7075 7090 7091 7092 7110 P DG T 8 distorted distorted 7097 7111 7112 7113 7132 P DT T 9 distorted distorted 7118 7133 7134 7135 7152 P DC T 10 distorted distorted 7140 7153 7154 7155 7171 P DC T 11 distorted distorted 7160 7172 7173 7174 7190 P DT T 12 distorted distorted 7179 7191 7192 7193 7210 P DT T 13 distorted distorted 7198 7211 7212 7213 7230 P DC T 14 distorted distorted 7218 7231 7232 7233 7249 P DC T 15 distorted distorted 7238 7250 7251 7252 7268 P DC T 16 distorted distorted 7257 7269 7270 7271 7307 P DG Q 3 distorted distorted 7293 7308 7309 7310 7329 P DG Q 4 distorted distorted 7315 7330 7331 7332 7351 P DG Q 5 distorted distorted 7337 7352 7353 7354 7373 P DA Q 6 distorted distorted 7359 7374 7375 7376 7394 P DA Q 7 distorted distorted 7381 7395 7396 7397 7415 P DG Q 8 distorted distorted 7402 7416 7417 7418 7437 P DG Q 9 distorted distorted 7423 7438 7439 7440 7459 P DA Q 10 distorted distorted 7445 7460 7461 7462 7480 P DC Q 11 distorted distorted 7467 7481 7482 7483 7499 P DT Q 12 distorted distorted 7488 7500 7501 7502 7534 P DOC Q 13 distorted distorted 7507 7535 7536 7533 7556 P 8OG U 5 distorted distorted 7543 7557 7558 7559 7579 P DG U 6 distorted distorted 7564 7580 7581 7582 7601 P DA U 7 distorted distorted 7587 7602 7603 7604 7622 P DG U 8 distorted distorted 7609 7623 7624 7625 7644 P DT U 9 distorted distorted 7630 7645 7646 7647 7664 P DC U 10 distorted distorted 7652 7665 7666 7667 7683 P DC U 11 distorted distorted 7672 7684 7685 7686 7702 P DT U 12 distorted distorted 7691 7703 7704 7705 7722 P DT U 13 distorted distorted 7710 7723 7724 7725 7742 P DC U 14 distorted distorted 7730 7743 7744 7745 7761 P DC U 15 distorted distorted 7750 7762 7763 7764 7780 P DC U 16 distorted distorted 7769 7781 7782 7783 7799 P DC U 17 distorted distorted 7788 7800 7801 7802 ---------------------------------------------------------------------------------