ID code: '1MJQ' 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' --------------------------------------------------------------------------------- 6796 C1' T E 0 beta 6792 6797 6795 6816 C1' A E 1 beta 6812 6817 6815 6837 C1' G E 2 beta 6833 6838 6836 6859 C1' A E 3 beta 6855 6860 6858 6880 C1' T E 4 beta 6876 6881 6879 6900 C1' A E 5 beta 6896 6901 6899 6921 C1' T E 6 beta 6917 6922 6920 6941 C1' C E 7 beta 6937 6942 6940 6960 C1' T E 8 beta 6956 6961 6959 6980 C1' A E 9 beta 6976 6981 6979 7001 C1' G E 10 beta 6997 7002 7000 7023 C1' A E 11 beta 7019 7024 7022 7044 C1' T E 12 beta 7040 7045 7043 7064 C1' A E 13 beta 7060 7065 7063 7085 C1' T E 14 beta 7081 7086 7084 7105 C1' C E 15 beta 7101 7106 7104 7124 C1' T E 16 beta 7120 7125 7123 7144 C1' A E 17 beta 7140 7145 7143 7183 C1' T F 0 beta 7179 7184 7182 7203 C1' A F 1 beta 7199 7204 7202 7224 C1' G F 2 beta 7220 7225 7223 7246 C1' A F 3 beta 7242 7247 7245 7267 C1' T F 4 beta 7263 7268 7266 7287 C1' A F 5 beta 7283 7288 7286 7308 C1' T F 6 beta 7304 7309 7307 7328 C1' C F 7 beta 7324 7329 7327 7347 C1' T F 8 beta 7343 7348 7346 7367 C1' A F 9 beta 7363 7368 7366 7388 C1' G F 10 beta 7384 7389 7387 7410 C1' A F 11 beta 7406 7411 7409 7431 C1' T F 12 beta 7427 7432 7430 7451 C1' A F 13 beta 7447 7452 7450 7472 C1' T F 14 beta 7468 7473 7471 7492 C1' C F 15 beta 7488 7493 7491 7511 C1' T F 16 beta 7507 7512 7510 7531 C1' A F 17 beta 7527 7532 7530 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6795 C2' T E 0 6796 6793 6815 C2' A E 1 6816 6813 6836 C2' G E 2 6837 6834 6858 C2' A E 3 6859 6856 6879 C2' T E 4 6880 6877 6899 C2' A E 5 6900 6897 6920 C2' T E 6 6921 6918 6940 C2' C E 7 6941 6938 6959 C2' T E 8 6960 6957 6979 C2' A E 9 6980 6977 7000 C2' G E 10 7001 6998 7022 C2' A E 11 7023 7020 7043 C2' T E 12 7044 7041 7063 C2' A E 13 7064 7061 7084 C2' T E 14 7085 7082 7104 C2' C E 15 7105 7102 7123 C2' T E 16 7124 7121 7143 C2' A E 17 7144 7141 7182 C2' T F 0 7183 7180 7202 C2' A F 1 7203 7200 7223 C2' G F 2 7224 7221 7245 C2' A F 3 7246 7243 7266 C2' T F 4 7267 7264 7286 C2' A F 5 7287 7284 7307 C2' T F 6 7308 7305 7327 C2' C F 7 7328 7325 7346 C2' T F 8 7347 7344 7366 C2' A F 9 7367 7364 7387 C2' G F 10 7388 7385 7409 C2' A F 11 7410 7407 7430 C2' T F 12 7431 7428 7450 C2' A F 13 7451 7448 7471 C2' T F 14 7472 7469 7491 C2' C F 15 7492 7489 7510 C2' T F 16 7511 7508 7530 C2' A F 17 7531 7528 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6793 C3' T E 0 OK 6791 6794 6795 6813 C3' A E 1 OK 6811 6814 6815 6834 C3' G E 2 OK 6832 6835 6836 6856 C3' A E 3 OK 6854 6857 6858 6877 C3' T E 4 OK 6875 6878 6879 6897 C3' A E 5 OK 6895 6898 6899 6918 C3' T E 6 OK 6916 6919 6920 6938 C3' C E 7 OK 6936 6939 6940 6957 C3' T E 8 OK 6955 6958 6959 6977 C3' A E 9 OK 6975 6978 6979 6998 C3' G E 10 OK 6996 6999 7000 7020 C3' A E 11 OK 7018 7021 7022 7041 C3' T E 12 OK 7039 7042 7043 7061 C3' A E 13 OK 7059 7062 7063 7082 C3' T E 14 OK 7080 7083 7084 7102 C3' C E 15 OK 7100 7103 7104 7121 C3' T E 16 OK 7119 7122 7123 7141 C3' A E 17 OK 7139 7142 7143 7180 C3' T F 0 OK 7178 7181 7182 7200 C3' A F 1 OK 7198 7201 7202 7221 C3' G F 2 OK 7219 7222 7223 7243 C3' A F 3 OK 7241 7244 7245 7264 C3' T F 4 OK 7262 7265 7266 7284 C3' A F 5 OK 7282 7285 7286 7305 C3' T F 6 OK 7303 7306 7307 7325 C3' C F 7 OK 7323 7326 7327 7344 C3' T F 8 OK 7342 7345 7346 7364 C3' A F 9 OK 7362 7365 7366 7385 C3' G F 10 OK 7383 7386 7387 7407 C3' A F 11 OK 7405 7408 7409 7428 C3' T F 12 OK 7426 7429 7430 7448 C3' A F 13 OK 7446 7449 7450 7469 C3' T F 14 OK 7467 7470 7471 7489 C3' C F 15 OK 7487 7490 7491 7508 C3' T F 16 OK 7506 7509 7510 7528 C3' A F 17 OK 7526 7529 7530 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6791 C4' T E 0 OK 6793 6790 6792 6811 C4' A E 1 OK 6813 6810 6812 6832 C4' G E 2 OK 6834 6831 6833 6854 C4' A E 3 OK 6856 6853 6855 6875 C4' T E 4 OK 6877 6874 6876 6895 C4' A E 5 OK 6897 6894 6896 6916 C4' T E 6 OK 6918 6915 6917 6936 C4' C E 7 OK 6938 6935 6937 6955 C4' T E 8 OK 6957 6954 6956 6975 C4' A E 9 OK 6977 6974 6976 6996 C4' G E 10 OK 6998 6995 6997 7018 C4' A E 11 OK 7020 7017 7019 7039 C4' T E 12 OK 7041 7038 7040 7059 C4' A E 13 OK 7061 7058 7060 7080 C4' T E 14 OK 7082 7079 7081 7100 C4' C E 15 OK 7102 7099 7101 7119 C4' T E 16 OK 7121 7118 7120 7139 C4' A E 17 OK 7141 7138 7140 7178 C4' T F 0 OK 7180 7177 7179 7198 C4' A F 1 OK 7200 7197 7199 7219 C4' G F 2 OK 7221 7218 7220 7241 C4' A F 3 OK 7243 7240 7242 7262 C4' T F 4 OK 7264 7261 7263 7282 C4' A F 5 OK 7284 7281 7283 7303 C4' T F 6 OK 7305 7302 7304 7323 C4' C F 7 OK 7325 7322 7324 7342 C4' T F 8 OK 7344 7341 7343 7362 C4' A F 9 OK 7364 7361 7363 7383 C4' G F 10 OK 7385 7382 7384 7405 C4' A F 11 OK 7407 7404 7406 7426 C4' T F 12 OK 7428 7425 7427 7446 C4' A F 13 OK 7448 7445 7447 7467 C4' T F 14 OK 7469 7466 7468 7487 C4' C F 15 OK 7489 7486 7488 7506 C4' T F 16 OK 7508 7505 7507 7526 C4' A F 17 OK 7528 7525 7527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6790 C5' T E 0 6789 6791 6810 C5' A E 1 6809 6811 6831 C5' G E 2 6830 6832 6853 C5' A E 3 6852 6854 6874 C5' T E 4 6873 6875 6894 C5' A E 5 6893 6895 6915 C5' T E 6 6914 6916 6935 C5' C E 7 6934 6936 6954 C5' T E 8 6953 6955 6974 C5' A E 9 6973 6975 6995 C5' G E 10 6994 6996 7017 C5' A E 11 7016 7018 7038 C5' T E 12 7037 7039 7058 C5' A E 13 7057 7059 7079 C5' T E 14 7078 7080 7099 C5' C E 15 7098 7100 7118 C5' T E 16 7117 7119 7138 C5' A E 17 7137 7139 7177 C5' T F 0 7176 7178 7197 C5' A F 1 7196 7198 7218 C5' G F 2 7217 7219 7240 C5' A F 3 7239 7241 7261 C5' T F 4 7260 7262 7281 C5' A F 5 7280 7282 7302 C5' T F 6 7301 7303 7322 C5' C F 7 7321 7323 7341 C5' T F 8 7340 7342 7361 C5' A F 9 7360 7362 7382 C5' G F 10 7381 7383 7404 C5' A F 11 7403 7405 7425 C5' T F 12 7424 7426 7445 C5' A F 13 7444 7446 7466 C5' T F 14 7465 7467 7486 C5' C F 15 7485 7487 7505 C5' T F 16 7504 7506 7525 C5' A F 17 7524 7526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6806 P A E 1 distorted distorted 6794 6807 6808 6809 6827 P G E 2 distorted distorted 6814 6828 6829 6830 6849 P A E 3 distorted distorted 6835 6850 6851 6852 6870 P T E 4 distorted distorted 6857 6871 6872 6873 6890 P A E 5 distorted distorted 6878 6891 6892 6893 6911 P T E 6 distorted distorted 6898 6912 6913 6914 6931 P C E 7 distorted distorted 6919 6932 6933 6934 6950 P T E 8 distorted distorted 6939 6951 6952 6953 6970 P A E 9 distorted distorted 6958 6971 6972 6973 6991 P G E 10 distorted distorted 6978 6992 6993 6994 7013 P A E 11 distorted distorted 6999 7014 7015 7016 7034 P T E 12 distorted distorted 7021 7035 7036 7037 7054 P A E 13 distorted distorted 7042 7055 7056 7057 7075 P T E 14 distorted distorted 7062 7076 7077 7078 7095 P C E 15 distorted distorted 7083 7096 7097 7098 7114 P T E 16 distorted distorted 7103 7115 7116 7117 7134 P A E 17 distorted distorted 7122 7135 7136 7137 7193 P A F 1 distorted distorted 7181 7194 7195 7196 7214 P G F 2 distorted distorted 7201 7215 7216 7217 7236 P A F 3 distorted distorted 7222 7237 7238 7239 7257 P T F 4 distorted distorted 7244 7258 7259 7260 7277 P A F 5 distorted distorted 7265 7278 7279 7280 7298 P T F 6 distorted distorted 7285 7299 7300 7301 7318 P C F 7 distorted distorted 7306 7319 7320 7321 7337 P T F 8 distorted distorted 7326 7338 7339 7340 7357 P A F 9 distorted distorted 7345 7358 7359 7360 7378 P G F 10 distorted distorted 7365 7379 7380 7381 7400 P A F 11 distorted distorted 7386 7401 7402 7403 7421 P T F 12 distorted distorted 7408 7422 7423 7424 7441 P A F 13 distorted distorted 7429 7442 7443 7444 7462 P T F 14 distorted distorted 7449 7463 7464 7465 7482 P C F 15 distorted distorted 7470 7483 7484 7485 7501 P T F 16 distorted distorted 7490 7502 7503 7504 7521 P A F 17 distorted distorted 7509 7522 7523 7524 ---------------------------------------------------------------------------------