ID code: '4NKU' 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' --------------------------------------------------------------------------------- 5140 C1' A D 58 beta 5135 5141 5138 5162 C1' U D 59 beta 5157 5163 5160 5180 C1' A H 58 beta 5175 5181 5178 5202 C1' U H 59 beta 5197 5203 5200 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5138 C2' A D 58 OK 5140 5136 5139 5160 C2' U D 59 OK 5162 5158 5161 5178 C2' A H 58 OK 5180 5176 5179 5200 C2' U H 59 OK 5202 5198 5201 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5136 C3' A D 58 OK 5134 5137 5138 5158 C3' U D 59 OK 5156 5159 5160 5176 C3' A H 58 OK 5174 5177 5178 5198 C3' U H 59 OK 5196 5199 5200 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5134 C4' A D 58 OK 5136 5133 5135 5156 C4' U D 59 OK 5158 5155 5157 5174 C4' A H 58 OK 5176 5173 5175 5196 C4' U H 59 OK 5198 5195 5197 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5133 C5' A D 58 5132 5134 5155 C5' U D 59 5154 5156 5173 C5' A H 58 5172 5174 5195 C5' U H 59 5194 5196 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5151 P U D 59 distorted distorted 5137 5152 5153 5154 5191 P U H 59 distorted distorted 5177 5192 5193 5194 ---------------------------------------------------------------------------------