ID code: '5JJU' 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' --------------------------------------------------------------------------------- 4815 C1' A C1003 beta 4810 4816 4813 4837 C1' A C1004 beta 4832 4838 4835 4865 C1' AMP B1003 beta 4860 4866 4863 4888 C1' AMP B1004 beta 4883 4889 4886 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4813 C2' A C1003 OK 4815 4811 4814 4835 C2' A C1004 OK 4837 4833 4836 4863 C2' AMP B1003 OK 4865 4861 4864 4886 C2' AMP B1004 OK 4888 4884 4887 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4811 C3' A C1003 OK 4809 4812 4813 4833 C3' A C1004 OK 4831 4834 4835 4861 C3' AMP B1003 OK 4859 4862 4863 4884 C3' AMP B1004 OK 4882 4885 4886 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4809 C4' A C1003 OK 4811 4808 4810 4831 C4' A C1004 OK 4833 4830 4832 4859 C4' AMP B1003 OK 4861 4858 4860 4882 C4' AMP B1004 OK 4884 4881 4883 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4808 C5' A C1003 4807 4809 4830 C5' A C1004 4829 4831 4858 C5' AMP B1003 4857 4859 4881 C5' AMP B1004 4880 4882 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4804 P A C1003 distorted distorted 4805 4806 4807 4826 P A C1004 distorted distorted 4812 4827 4828 4829 4853 P AMP B1003 distorted distorted 4854 4855 4857 4876 P AMP B1004 OK OK 4877 4878 4880 ---------------------------------------------------------------------------------