ID code: '4QCL' 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' --------------------------------------------------------------------------------- 6957 C1' G B 1 beta 6952 6958 6955 6980 C1' C B 2 beta 6975 6981 6978 7000 C1' C B 3 beta 6995 7001 6998 7020 C1' U B 4 beta 7015 7021 7018 7040 C1' G B 5 beta 7035 7041 7038 7063 C1' G B 6 beta 7058 7064 7061 7086 C1' A B 7 beta 7081 7087 7084 7108 C1' G B 8 beta 7103 7109 7106 7131 C1' C B 9 beta 7126 7132 7129 7151 C1' G B 10 beta 7146 7152 7149 7172 C1' DC B 11 beta 7169 7173 7171 7189 C1' DA C 109 beta 7185 7190 7188 7210 C1' DG C 110 beta 7206 7211 7209 7232 C1' DG C 111 beta 7228 7233 7231 7254 C1' DC C 112 beta 7250 7255 7253 7273 C1' DG C 113 beta 7269 7274 7272 7295 C1' DC C 114 beta 7291 7296 7294 7314 C1' DT C 115 beta 7310 7315 7313 7334 C1' DC C 116 beta 7330 7335 7333 7353 C1' DC C 117 beta 7349 7354 7352 7372 C1' DA C 118 beta 7368 7373 7371 7393 C1' DG C 119 beta 7389 7394 7392 7415 C1' DG C 120 beta 7411 7416 7414 7437 C1' DC C 121 beta 7433 7438 7436 7455 C1' DCP A1301 beta 7459 7447 7456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6955 C2' G B 1 OK 6957 6953 6956 6978 C2' C B 2 OK 6980 6976 6979 6998 C2' C B 3 OK 7000 6996 6999 7018 C2' U B 4 OK 7020 7016 7019 7038 C2' G B 5 OK 7040 7036 7039 7061 C2' G B 6 OK 7063 7059 7062 7084 C2' A B 7 OK 7086 7082 7085 7106 C2' G B 8 OK 7108 7104 7107 7129 C2' C B 9 OK 7131 7127 7130 7149 C2' G B 10 OK 7151 7147 7150 7171 C2' DC B 11 7172 7170 7188 C2' DA C 109 7189 7186 7209 C2' DG C 110 7210 7207 7231 C2' DG C 111 7232 7229 7253 C2' DC C 112 7254 7251 7272 C2' DG C 113 7273 7270 7294 C2' DC C 114 7295 7292 7313 C2' DT C 115 7314 7311 7333 C2' DC C 116 7334 7331 7352 C2' DC C 117 7353 7350 7371 C2' DA C 118 7372 7369 7392 C2' DG C 119 7393 7390 7414 C2' DG C 120 7415 7412 7436 C2' DC C 121 7437 7434 7456 C2' DCP A1301 7455 7457 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6953 C3' G B 1 OK 6951 6954 6955 6976 C3' C B 2 OK 6974 6977 6978 6996 C3' C B 3 OK 6994 6997 6998 7016 C3' U B 4 OK 7014 7017 7018 7036 C3' G B 5 OK 7034 7037 7038 7059 C3' G B 6 OK 7057 7060 7061 7082 C3' A B 7 OK 7080 7083 7084 7104 C3' G B 8 OK 7102 7105 7106 7127 C3' C B 9 OK 7125 7128 7129 7147 C3' G B 10 OK 7145 7148 7149 7170 C3' DC B 11 7168 7171 7186 C3' DA C 109 OK 7184 7187 7188 7207 C3' DG C 110 OK 7205 7208 7209 7229 C3' DG C 111 OK 7227 7230 7231 7251 C3' DC C 112 OK 7249 7252 7253 7270 C3' DG C 113 OK 7268 7271 7272 7292 C3' DC C 114 OK 7290 7293 7294 7311 C3' DT C 115 OK 7309 7312 7313 7331 C3' DC C 116 OK 7329 7332 7333 7350 C3' DC C 117 OK 7348 7351 7352 7369 C3' DA C 118 OK 7367 7370 7371 7390 C3' DG C 119 OK 7388 7391 7392 7412 C3' DG C 120 OK 7410 7413 7414 7434 C3' DC C 121 OK 7432 7435 7436 7457 C3' DCP A1301 OK 7458 7460 7456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6951 C4' G B 1 OK 6953 6950 6952 6974 C4' C B 2 OK 6976 6973 6975 6994 C4' C B 3 OK 6996 6993 6995 7014 C4' U B 4 OK 7016 7013 7015 7034 C4' G B 5 OK 7036 7033 7035 7057 C4' G B 6 OK 7059 7056 7058 7080 C4' A B 7 OK 7082 7079 7081 7102 C4' G B 8 OK 7104 7101 7103 7125 C4' C B 9 OK 7127 7124 7126 7145 C4' G B 10 OK 7147 7144 7146 7168 C4' DC B 11 OK 7170 7167 7169 7184 C4' DA C 109 OK 7186 7183 7185 7205 C4' DG C 110 OK 7207 7204 7206 7227 C4' DG C 111 OK 7229 7226 7228 7249 C4' DC C 112 OK 7251 7248 7250 7268 C4' DG C 113 OK 7270 7267 7269 7290 C4' DC C 114 OK 7292 7289 7291 7309 C4' DT C 115 OK 7311 7308 7310 7329 C4' DC C 116 OK 7331 7328 7330 7348 C4' DC C 117 OK 7350 7347 7349 7367 C4' DA C 118 OK 7369 7366 7368 7388 C4' DG C 119 OK 7390 7387 7389 7410 C4' DG C 120 OK 7412 7409 7411 7432 C4' DC C 121 OK 7434 7431 7433 7458 C4' DCP A1301 OK 7457 7461 7459 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6950 C5' G B 1 6949 6951 6973 C5' C B 2 6972 6974 6993 C5' C B 3 6992 6994 7013 C5' U B 4 7012 7014 7033 C5' G B 5 7032 7034 7056 C5' G B 6 7055 7057 7079 C5' A B 7 7078 7080 7101 C5' G B 8 7100 7102 7124 C5' C B 9 7123 7125 7144 C5' G B 10 7143 7145 7167 C5' DC B 11 7166 7168 7183 C5' DA C 109 7182 7184 7204 C5' DG C 110 7203 7205 7226 C5' DG C 111 7225 7227 7248 C5' DC C 112 7247 7249 7267 C5' DG C 113 7266 7268 7289 C5' DC C 114 7288 7290 7308 C5' DT C 115 7307 7309 7328 C5' DC C 116 7327 7329 7347 C5' DC C 117 7346 7348 7366 C5' DA C 118 7365 7367 7387 C5' DG C 119 7386 7388 7409 C5' DG C 120 7408 7410 7431 C5' DC C 121 7430 7432 7461 C5' DCP A1301 7462 7458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6969 P C B 2 distorted distorted 6954 6970 6971 6972 6989 P C B 3 distorted distorted 6977 6990 6991 6992 7009 P U B 4 distorted distorted 6997 7010 7011 7012 7029 P G B 5 distorted distorted 7017 7030 7031 7032 7052 P G B 6 distorted distorted 7037 7053 7054 7055 7075 P A B 7 distorted distorted 7060 7076 7077 7078 7097 P G B 8 distorted distorted 7083 7098 7099 7100 7120 P C B 9 distorted distorted 7105 7121 7122 7123 7140 P G B 10 distorted distorted 7128 7141 7142 7143 7163 P DC B 11 distorted distorted 7148 7164 7165 7166 7200 P DG C 110 distorted distorted 7187 7201 7202 7203 7222 P DG C 111 distorted distorted 7208 7223 7224 7225 7244 P DC C 112 distorted distorted 7230 7245 7246 7247 7263 P DG C 113 distorted distorted 7252 7264 7265 7266 7285 P DC C 114 distorted distorted 7271 7286 7287 7288 7304 P DT C 115 distorted distorted 7293 7305 7306 7307 7324 P DC C 116 distorted distorted 7312 7325 7326 7327 7343 P DC C 117 distorted distorted 7332 7344 7345 7346 7362 P DA C 118 distorted distorted 7351 7363 7364 7365 7383 P DG C 119 distorted distorted 7370 7384 7385 7386 7405 P DG C 120 distorted distorted 7391 7406 7407 7408 7427 P DC C 121 distorted distorted 7413 7428 7429 7430 ---------------------------------------------------------------------------------