ID code: '3LOB' 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' --------------------------------------------------------------------------------- 7153 C1' U R 3 beta 7148 7154 7151 7173 C1' U R 4 beta 7168 7174 7171 7193 C1' U R 5 beta 7188 7194 7191 7210 C1' A R 7 beta 7205 7211 7208 7232 C1' U R 8 beta 7227 7233 7230 7252 C1' C R 9 beta 7247 7253 7250 7272 C1' U R 10 beta 7267 7273 7270 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7151 C2' U R 3 OK 7153 7149 7152 7171 C2' U R 4 OK 7173 7169 7172 7191 C2' U R 5 OK 7193 7189 7192 7208 C2' A R 7 OK 7210 7206 7209 7230 C2' U R 8 OK 7232 7228 7231 7250 C2' C R 9 OK 7252 7248 7251 7270 C2' U R 10 OK 7272 7268 7271 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7149 C3' U R 3 OK 7147 7150 7151 7169 C3' U R 4 OK 7167 7170 7171 7189 C3' U R 5 OK 7187 7190 7191 7206 C3' A R 7 OK 7204 7207 7208 7228 C3' U R 8 OK 7226 7229 7230 7248 C3' C R 9 OK 7246 7249 7250 7268 C3' U R 10 OK 7266 7269 7270 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7147 C4' U R 3 OK 7149 7146 7148 7167 C4' U R 4 OK 7169 7166 7168 7187 C4' U R 5 OK 7189 7186 7188 7204 C4' A R 7 OK 7206 7203 7205 7226 C4' U R 8 OK 7228 7225 7227 7246 C4' C R 9 OK 7248 7245 7247 7266 C4' U R 10 OK 7268 7265 7267 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7146 C5' U R 3 7145 7147 7166 C5' U R 4 7165 7167 7186 C5' U R 5 7185 7187 7203 C5' A R 7 7202 7204 7225 C5' U R 8 7224 7226 7245 C5' C R 9 7244 7246 7265 C5' U R 10 7264 7266 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7162 P U R 4 distorted distorted 7150 7163 7164 7165 7182 P U R 5 distorted distorted 7170 7183 7184 7185 7221 P U R 8 distorted distorted 7207 7222 7223 7224 7241 P C R 9 distorted distorted 7229 7242 7243 7244 7261 P U R 10 distorted distorted 7249 7262 7263 7264 ---------------------------------------------------------------------------------