ID code: '4DB4' 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' --------------------------------------------------------------------------------- 6842 C1' G C -7 alpha beta 6837 6860 6843 6840 6877 C1' G C -6 alpha beta 6872 6895 6878 6875 6911 C1' G C -5 alpha beta 6906 6929 6912 6909 6945 C1' C C -4 alpha beta 6940 6960 6946 6943 6976 C1' G C -3 alpha beta 6971 6994 6977 6974 7010 C1' G C -2 alpha beta 7005 7028 7011 7008 7044 C1' G C -1 alpha beta 7039 7062 7045 7042 7077 C1' DC C 0 beta 7073 7078 7076 7096 C1' DC C 1 beta 7092 7097 7095 7115 C1' DC C 2 beta 7111 7116 7114 7134 C1' DG C 3 beta 7130 7135 7133 7156 C1' DC C 4 beta 7152 7157 7155 7175 C1' DC C 5 beta 7171 7176 7174 7194 C1' DC C 6 beta 7190 7195 7193 7212 C1' G D 7 alpha beta 7207 7230 7213 7210 7247 C1' G D 8 alpha beta 7242 7265 7248 7245 7281 C1' G D 9 alpha beta 7276 7299 7282 7279 7315 C1' C D 10 alpha beta 7310 7330 7316 7313 7346 C1' G D 11 alpha beta 7341 7364 7347 7344 7380 C1' G D 12 alpha beta 7375 7398 7381 7378 7414 C1' G D 13 alpha beta 7409 7432 7415 7412 7447 C1' DC D 14 beta 7443 7448 7446 7466 C1' DC D 15 beta 7462 7467 7465 7485 C1' DC D 16 beta 7481 7486 7484 7504 C1' DG D 17 beta 7500 7505 7503 7526 C1' DC D 18 beta 7522 7527 7525 7545 C1' DC D 19 beta 7541 7546 7544 7564 C1' DC D 20 beta 7560 7565 7563 7582 C1' G E 7 alpha beta 7577 7600 7583 7580 7617 C1' G E 8 alpha beta 7612 7635 7618 7615 7651 C1' G E 9 alpha beta 7646 7669 7652 7649 7685 C1' C E 10 alpha beta 7680 7700 7686 7683 7716 C1' G E 11 alpha beta 7711 7734 7717 7714 7750 C1' G E 12 alpha beta 7745 7768 7751 7748 7784 C1' G E 13 alpha beta 7779 7802 7785 7782 7817 C1' DC E 14 beta 7813 7818 7816 7836 C1' DC E 15 beta 7832 7837 7835 7855 C1' DC E 16 beta 7851 7856 7854 7874 C1' DG E 17 beta 7870 7875 7873 7896 C1' DC E 18 beta 7892 7897 7895 7915 C1' DC E 19 beta 7911 7916 7914 7934 C1' DC E 20 beta 7930 7935 7933 7952 C1' G F -7 alpha beta 7947 7970 7953 7950 7987 C1' G F -6 alpha beta 7982 8005 7988 7985 8021 C1' G F -5 alpha beta 8016 8039 8022 8019 8054 C1' C F -4 alpha beta 8049 8069 8055 8052 8085 C1' G F -3 alpha beta 8080 8103 8086 8083 8119 C1' G F -2 alpha beta 8114 8137 8120 8117 8153 C1' G F -1 alpha beta 8148 8171 8154 8151 8186 C1' DC F 0 beta 8182 8187 8185 8205 C1' DC F 1 beta 8201 8206 8204 8224 C1' DC F 2 beta 8220 8225 8223 8243 C1' DG F 3 beta 8239 8244 8242 8265 C1' DC F 4 beta 8261 8266 8264 8284 C1' DC F 5 beta 8280 8285 8283 8303 C1' DC F 6 beta 8299 8304 8302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6840 C2' G C -7 OK OK 6842 6838 6858 6841 6875 C2' G C -6 OK OK 6877 6873 6893 6876 6909 C2' G C -5 OK OK 6911 6907 6927 6910 6943 C2' C C -4 OK OK 6945 6941 6958 6944 6974 C2' G C -3 OK OK 6976 6972 6992 6975 7008 C2' G C -2 OK OK 7010 7006 7026 7009 7042 C2' G C -1 OK OK 7044 7040 7060 7043 7076 C2' DC C 0 7077 7074 7095 C2' DC C 1 7096 7093 7114 C2' DC C 2 7115 7112 7133 C2' DG C 3 7134 7131 7155 C2' DC C 4 7156 7153 7174 C2' DC C 5 7175 7172 7193 C2' DC C 6 7194 7191 7210 C2' G D 7 OK OK 7212 7208 7228 7211 7245 C2' G D 8 OK OK 7247 7243 7263 7246 7279 C2' G D 9 OK OK 7281 7277 7297 7280 7313 C2' C D 10 OK OK 7315 7311 7328 7314 7344 C2' G D 11 OK OK 7346 7342 7362 7345 7378 C2' G D 12 OK OK 7380 7376 7396 7379 7412 C2' G D 13 OK OK 7414 7410 7430 7413 7446 C2' DC D 14 7447 7444 7465 C2' DC D 15 7466 7463 7484 C2' DC D 16 7485 7482 7503 C2' DG D 17 7504 7501 7525 C2' DC D 18 7526 7523 7544 C2' DC D 19 7545 7542 7563 C2' DC D 20 7564 7561 7580 C2' G E 7 OK OK 7582 7578 7598 7581 7615 C2' G E 8 OK OK 7617 7613 7633 7616 7649 C2' G E 9 OK OK 7651 7647 7667 7650 7683 C2' C E 10 OK OK 7685 7681 7698 7684 7714 C2' G E 11 OK OK 7716 7712 7732 7715 7748 C2' G E 12 OK OK 7750 7746 7766 7749 7782 C2' G E 13 OK OK 7784 7780 7800 7783 7816 C2' DC E 14 7817 7814 7835 C2' DC E 15 7836 7833 7854 C2' DC E 16 7855 7852 7873 C2' DG E 17 7874 7871 7895 C2' DC E 18 7896 7893 7914 C2' DC E 19 7915 7912 7933 C2' DC E 20 7934 7931 7950 C2' G F -7 OK OK 7952 7948 7968 7951 7985 C2' G F -6 OK OK 7987 7983 8003 7986 8019 C2' G F -5 OK OK 8021 8017 8037 8020 8052 C2' C F -4 OK OK 8054 8050 8067 8053 8083 C2' G F -3 OK OK 8085 8081 8101 8084 8117 C2' G F -2 OK OK 8119 8115 8135 8118 8151 C2' G F -1 OK OK 8153 8149 8169 8152 8185 C2' DC F 0 8186 8183 8204 C2' DC F 1 8205 8202 8223 C2' DC F 2 8224 8221 8242 C2' DG F 3 8243 8240 8264 C2' DC F 4 8265 8262 8283 C2' DC F 5 8284 8281 8302 C2' DC F 6 8303 8300 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6838 C3' G C -7 OK OK 6836 6857 6839 6840 6873 C3' G C -6 OK OK 6871 6892 6874 6875 6907 C3' G C -5 OK OK 6905 6926 6908 6909 6941 C3' C C -4 OK OK 6939 6957 6942 6943 6972 C3' G C -3 OK OK 6970 6991 6973 6974 7006 C3' G C -2 OK OK 7004 7025 7007 7008 7040 C3' G C -1 OK OK 7038 7059 7041 7042 7074 C3' DC C 0 OK 7072 7075 7076 7093 C3' DC C 1 OK 7091 7094 7095 7112 C3' DC C 2 OK 7110 7113 7114 7131 C3' DG C 3 OK 7129 7132 7133 7153 C3' DC C 4 OK 7151 7154 7155 7172 C3' DC C 5 OK 7170 7173 7174 7191 C3' DC C 6 OK 7189 7192 7193 7208 C3' G D 7 OK OK 7206 7227 7209 7210 7243 C3' G D 8 OK OK 7241 7262 7244 7245 7277 C3' G D 9 OK OK 7275 7296 7278 7279 7311 C3' C D 10 OK OK 7309 7327 7312 7313 7342 C3' G D 11 OK OK 7340 7361 7343 7344 7376 C3' G D 12 OK OK 7374 7395 7377 7378 7410 C3' G D 13 OK OK 7408 7429 7411 7412 7444 C3' DC D 14 OK 7442 7445 7446 7463 C3' DC D 15 OK 7461 7464 7465 7482 C3' DC D 16 OK 7480 7483 7484 7501 C3' DG D 17 OK 7499 7502 7503 7523 C3' DC D 18 OK 7521 7524 7525 7542 C3' DC D 19 OK 7540 7543 7544 7561 C3' DC D 20 OK 7559 7562 7563 7578 C3' G E 7 OK OK 7576 7597 7579 7580 7613 C3' G E 8 OK OK 7611 7632 7614 7615 7647 C3' G E 9 OK OK 7645 7666 7648 7649 7681 C3' C E 10 OK OK 7679 7697 7682 7683 7712 C3' G E 11 OK OK 7710 7731 7713 7714 7746 C3' G E 12 OK OK 7744 7765 7747 7748 7780 C3' G E 13 OK OK 7778 7799 7781 7782 7814 C3' DC E 14 OK 7812 7815 7816 7833 C3' DC E 15 OK 7831 7834 7835 7852 C3' DC E 16 OK 7850 7853 7854 7871 C3' DG E 17 OK 7869 7872 7873 7893 C3' DC E 18 OK 7891 7894 7895 7912 C3' DC E 19 OK 7910 7913 7914 7931 C3' DC E 20 OK 7929 7932 7933 7948 C3' G F -7 OK OK 7946 7967 7949 7950 7983 C3' G F -6 OK OK 7981 8002 7984 7985 8017 C3' G F -5 OK OK 8015 8036 8018 8019 8050 C3' C F -4 OK OK 8048 8066 8051 8052 8081 C3' G F -3 OK OK 8079 8100 8082 8083 8115 C3' G F -2 OK OK 8113 8134 8116 8117 8149 C3' G F -1 OK OK 8147 8168 8150 8151 8183 C3' DC F 0 OK 8181 8184 8185 8202 C3' DC F 1 OK 8200 8203 8204 8221 C3' DC F 2 OK 8219 8222 8223 8240 C3' DG F 3 OK 8238 8241 8242 8262 C3' DC F 4 OK 8260 8263 8264 8281 C3' DC F 5 OK 8279 8282 8283 8300 C3' DC F 6 OK 8298 8301 8302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6836 C4' G C -7 OK OK 6838 6856 6835 6837 6871 C4' G C -6 OK OK 6873 6891 6870 6872 6905 C4' G C -5 OK OK 6907 6925 6904 6906 6939 C4' C C -4 OK OK 6941 6956 6938 6940 6970 C4' G C -3 OK OK 6972 6990 6969 6971 7004 C4' G C -2 OK OK 7006 7024 7003 7005 7038 C4' G C -1 OK OK 7040 7058 7037 7039 7072 C4' DC C 0 OK 7074 7071 7073 7091 C4' DC C 1 OK 7093 7090 7092 7110 C4' DC C 2 OK 7112 7109 7111 7129 C4' DG C 3 OK 7131 7128 7130 7151 C4' DC C 4 OK 7153 7150 7152 7170 C4' DC C 5 OK 7172 7169 7171 7189 C4' DC C 6 OK 7191 7188 7190 7206 C4' G D 7 OK OK 7208 7226 7205 7207 7241 C4' G D 8 OK OK 7243 7261 7240 7242 7275 C4' G D 9 OK OK 7277 7295 7274 7276 7309 C4' C D 10 OK OK 7311 7326 7308 7310 7340 C4' G D 11 OK OK 7342 7360 7339 7341 7374 C4' G D 12 OK OK 7376 7394 7373 7375 7408 C4' G D 13 OK OK 7410 7428 7407 7409 7442 C4' DC D 14 OK 7444 7441 7443 7461 C4' DC D 15 OK 7463 7460 7462 7480 C4' DC D 16 OK 7482 7479 7481 7499 C4' DG D 17 OK 7501 7498 7500 7521 C4' DC D 18 OK 7523 7520 7522 7540 C4' DC D 19 OK 7542 7539 7541 7559 C4' DC D 20 OK 7561 7558 7560 7576 C4' G E 7 OK OK 7578 7596 7575 7577 7611 C4' G E 8 OK OK 7613 7631 7610 7612 7645 C4' G E 9 OK OK 7647 7665 7644 7646 7679 C4' C E 10 OK OK 7681 7696 7678 7680 7710 C4' G E 11 OK OK 7712 7730 7709 7711 7744 C4' G E 12 OK OK 7746 7764 7743 7745 7778 C4' G E 13 OK OK 7780 7798 7777 7779 7812 C4' DC E 14 OK 7814 7811 7813 7831 C4' DC E 15 OK 7833 7830 7832 7850 C4' DC E 16 OK 7852 7849 7851 7869 C4' DG E 17 OK 7871 7868 7870 7891 C4' DC E 18 OK 7893 7890 7892 7910 C4' DC E 19 OK 7912 7909 7911 7929 C4' DC E 20 OK 7931 7928 7930 7946 C4' G F -7 OK OK 7948 7966 7945 7947 7981 C4' G F -6 OK OK 7983 8001 7980 7982 8015 C4' G F -5 OK OK 8017 8035 8014 8016 8048 C4' C F -4 OK OK 8050 8065 8047 8049 8079 C4' G F -3 OK OK 8081 8099 8078 8080 8113 C4' G F -2 OK OK 8115 8133 8112 8114 8147 C4' G F -1 OK OK 8149 8167 8146 8148 8181 C4' DC F 0 OK 8183 8180 8182 8200 C4' DC F 1 OK 8202 8199 8201 8219 C4' DC F 2 OK 8221 8218 8220 8238 C4' DG F 3 OK 8240 8237 8239 8260 C4' DC F 4 OK 8262 8259 8261 8279 C4' DC F 5 OK 8281 8278 8280 8298 C4' DC F 6 OK 8300 8297 8299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6835 C5' G C -7 OK OK 6834 6854 6855 6836 6870 C5' G C -6 OK OK 6869 6889 6890 6871 6904 C5' G C -5 OK OK 6903 6923 6924 6905 6938 C5' C C -4 OK OK 6937 6954 6955 6939 6969 C5' G C -3 OK OK 6968 6988 6989 6970 7003 C5' G C -2 OK OK 7002 7022 7023 7004 7037 C5' G C -1 OK OK 7036 7056 7057 7038 7071 C5' DC C 0 7070 7072 7090 C5' DC C 1 7089 7091 7109 C5' DC C 2 7108 7110 7128 C5' DG C 3 7127 7129 7150 C5' DC C 4 7149 7151 7169 C5' DC C 5 7168 7170 7188 C5' DC C 6 7187 7189 7205 C5' G D 7 OK OK 7204 7224 7225 7206 7240 C5' G D 8 OK OK 7239 7259 7260 7241 7274 C5' G D 9 OK OK 7273 7293 7294 7275 7308 C5' C D 10 OK OK 7307 7324 7325 7309 7339 C5' G D 11 OK OK 7338 7358 7359 7340 7373 C5' G D 12 OK OK 7372 7392 7393 7374 7407 C5' G D 13 OK OK 7406 7426 7427 7408 7441 C5' DC D 14 7440 7442 7460 C5' DC D 15 7459 7461 7479 C5' DC D 16 7478 7480 7498 C5' DG D 17 7497 7499 7520 C5' DC D 18 7519 7521 7539 C5' DC D 19 7538 7540 7558 C5' DC D 20 7557 7559 7575 C5' G E 7 OK OK 7574 7594 7595 7576 7610 C5' G E 8 OK OK 7609 7629 7630 7611 7644 C5' G E 9 OK OK 7643 7663 7664 7645 7678 C5' C E 10 OK OK 7677 7694 7695 7679 7709 C5' G E 11 OK OK 7708 7728 7729 7710 7743 C5' G E 12 OK OK 7742 7762 7763 7744 7777 C5' G E 13 OK OK 7776 7796 7797 7778 7811 C5' DC E 14 7810 7812 7830 C5' DC E 15 7829 7831 7849 C5' DC E 16 7848 7850 7868 C5' DG E 17 7867 7869 7890 C5' DC E 18 7889 7891 7909 C5' DC E 19 7908 7910 7928 C5' DC E 20 7927 7929 7945 C5' G F -7 OK OK 7944 7964 7965 7946 7980 C5' G F -6 OK OK 7979 7999 8000 7981 8014 C5' G F -5 OK OK 8013 8033 8034 8015 8047 C5' C F -4 OK OK 8046 8063 8064 8048 8078 C5' G F -3 OK OK 8077 8097 8098 8079 8112 C5' G F -2 OK OK 8111 8131 8132 8113 8146 C5' G F -1 OK OK 8145 8165 8166 8147 8180 C5' DC F 0 8179 8181 8199 C5' DC F 1 8198 8200 8218 C5' DC F 2 8217 8219 8237 C5' DG F 3 8236 8238 8259 C5' DC F 4 8258 8260 8278 C5' DC F 5 8277 8279 8297 C5' DC F 6 8296 8298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6866 P G C -6 distorted distorted 6839 6867 6868 6869 6900 P G C -5 distorted distorted 6874 6901 6902 6903 6934 P C C -4 distorted distorted 6908 6935 6936 6937 6965 P G C -3 distorted distorted 6942 6966 6967 6968 6999 P G C -2 distorted distorted 6973 7000 7001 7002 7033 P G C -1 distorted distorted 7007 7034 7035 7036 7067 P DC C 0 distorted distorted 7041 7068 7069 7070 7086 P DC C 1 distorted distorted 7075 7087 7088 7089 7105 P DC C 2 distorted distorted 7094 7106 7107 7108 7124 P DG C 3 distorted distorted 7113 7125 7126 7127 7146 P DC C 4 distorted distorted 7132 7147 7148 7149 7165 P DC C 5 distorted distorted 7154 7166 7167 7168 7184 P DC C 6 distorted distorted 7173 7185 7186 7187 7236 P G D 8 distorted distorted 7209 7237 7238 7239 7270 P G D 9 distorted distorted 7244 7271 7272 7273 7304 P C D 10 distorted distorted 7278 7305 7306 7307 7335 P G D 11 distorted distorted 7312 7336 7337 7338 7369 P G D 12 distorted distorted 7343 7370 7371 7372 7403 P G D 13 distorted distorted 7377 7404 7405 7406 7437 P DC D 14 distorted distorted 7411 7438 7439 7440 7456 P DC D 15 distorted distorted 7445 7457 7458 7459 7475 P DC D 16 distorted distorted 7464 7476 7477 7478 7494 P DG D 17 distorted distorted 7483 7495 7496 7497 7516 P DC D 18 distorted distorted 7502 7517 7518 7519 7535 P DC D 19 distorted distorted 7524 7536 7537 7538 7554 P DC D 20 distorted distorted 7543 7555 7556 7557 7606 P G E 8 distorted distorted 7579 7607 7608 7609 7640 P G E 9 distorted distorted 7614 7641 7642 7643 7674 P C E 10 distorted distorted 7648 7675 7676 7677 7705 P G E 11 distorted distorted 7682 7706 7707 7708 7739 P G E 12 distorted distorted 7713 7740 7741 7742 7773 P G E 13 distorted distorted 7747 7774 7775 7776 7807 P DC E 14 distorted distorted 7781 7808 7809 7810 7826 P DC E 15 distorted distorted 7815 7827 7828 7829 7845 P DC E 16 distorted distorted 7834 7846 7847 7848 7864 P DG E 17 distorted distorted 7853 7865 7866 7867 7886 P DC E 18 distorted distorted 7872 7887 7888 7889 7905 P DC E 19 distorted distorted 7894 7906 7907 7908 7924 P DC E 20 distorted distorted 7913 7925 7926 7927 7976 P G F -6 distorted distorted 7949 7977 7978 7979 8010 P G F -5 distorted distorted 7984 8011 8012 8013 8044 P C F -4 8018 8045 8046 8074 P G F -3 distorted distorted 8051 8075 8076 8077 8108 P G F -2 distorted distorted 8082 8109 8110 8111 8142 P G F -1 distorted distorted 8116 8143 8144 8145 8176 P DC F 0 distorted distorted 8150 8177 8178 8179 8195 P DC F 1 distorted distorted 8184 8196 8197 8198 8214 P DC F 2 distorted distorted 8203 8215 8216 8217 8233 P DG F 3 distorted distorted 8222 8234 8235 8236 8255 P DC F 4 distorted distorted 8241 8256 8257 8258 8274 P DC F 5 distorted distorted 8263 8275 8276 8277 8293 P DC F 6 distorted distorted 8282 8294 8295 8296 ---------------------------------------------------------------------------------