ID code: '3ER9' 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' --------------------------------------------------------------------------------- 6023 C1' U D 600 beta 6018 6024 6021 6043 C1' U D 601 beta 6038 6044 6041 6090 C1' 3AT B 800 beta 6086 6091 6088 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6021 C2' U D 600 OK 6023 6019 6022 6041 C2' U D 601 OK 6043 6039 6042 6088 C2' 3AT B 800 OK 6090 6087 6089 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6019 C3' U D 600 OK 6017 6020 6021 6039 C3' U D 601 OK 6037 6040 6041 6087 C3' 3AT B 800 6085 6088 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6017 C4' U D 600 OK 6019 6016 6018 6037 C4' U D 601 OK 6039 6036 6038 6085 C4' 3AT B 800 OK 6087 6084 6086 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6016 C5' U D 600 6015 6017 6036 C5' U D 601 6035 6037 6084 C5' 3AT B 800 6083 6085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6012 P U D 600 OK OK 6013 6014 6015 6032 P U D 601 distorted distorted 6020 6033 6034 6035 ---------------------------------------------------------------------------------