ID code: '3Q2T' 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' --------------------------------------------------------------------------------- 4841 C1' U E 1 beta 4836 4842 4839 4861 C1' U E 2 beta 4856 4862 4859 4881 C1' G E 3 beta 4876 4882 4879 4904 C1' U E 4 beta 4899 4905 4902 4924 C1' A E 5 beta 4919 4925 4922 4944 C1' U F 1 beta 4939 4945 4942 4964 C1' U F 2 beta 4959 4965 4962 4984 C1' G F 3 beta 4979 4985 4982 5007 C1' U F 4 beta 5002 5008 5005 5027 C1' A F 5 beta 5022 5028 5025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4839 C2' U E 1 OK 4841 4837 4840 4859 C2' U E 2 OK 4861 4857 4860 4879 C2' G E 3 OK 4881 4877 4880 4902 C2' U E 4 OK 4904 4900 4903 4922 C2' A E 5 OK 4924 4920 4923 4942 C2' U F 1 OK 4944 4940 4943 4962 C2' U F 2 OK 4964 4960 4963 4982 C2' G F 3 OK 4984 4980 4983 5005 C2' U F 4 OK 5007 5003 5006 5025 C2' A F 5 OK 5027 5023 5026 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4837 C3' U E 1 OK 4835 4838 4839 4857 C3' U E 2 OK 4855 4858 4859 4877 C3' G E 3 OK 4875 4878 4879 4900 C3' U E 4 OK 4898 4901 4902 4920 C3' A E 5 OK 4918 4921 4922 4940 C3' U F 1 OK 4938 4941 4942 4960 C3' U F 2 OK 4958 4961 4962 4980 C3' G F 3 OK 4978 4981 4982 5003 C3' U F 4 OK 5001 5004 5005 5023 C3' A F 5 OK 5021 5024 5025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4835 C4' U E 1 OK 4837 4834 4836 4855 C4' U E 2 OK 4857 4854 4856 4875 C4' G E 3 OK 4877 4874 4876 4898 C4' U E 4 OK 4900 4897 4899 4918 C4' A E 5 OK 4920 4917 4919 4938 C4' U F 1 OK 4940 4937 4939 4958 C4' U F 2 OK 4960 4957 4959 4978 C4' G F 3 OK 4980 4977 4979 5001 C4' U F 4 OK 5003 5000 5002 5021 C4' A F 5 OK 5023 5020 5022 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4834 C5' U E 1 4833 4835 4854 C5' U E 2 4853 4855 4874 C5' G E 3 4873 4875 4897 C5' U E 4 4896 4898 4917 C5' A E 5 4916 4918 4937 C5' U F 1 4936 4938 4957 C5' U F 2 4956 4958 4977 C5' G F 3 4976 4978 5000 C5' U F 4 4999 5001 5020 C5' A F 5 5019 5021 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4850 P U E 2 distorted distorted 4838 4851 4852 4853 4870 P G E 3 distorted distorted 4858 4871 4872 4873 4893 P U E 4 distorted distorted 4878 4894 4895 4896 4913 P A E 5 distorted distorted 4901 4914 4915 4916 4953 P U F 2 distorted distorted 4941 4954 4955 4956 4973 P G F 3 distorted distorted 4961 4974 4975 4976 4996 P U F 4 distorted distorted 4981 4997 4998 4999 5016 P A F 5 distorted distorted 5004 5017 5018 5019 ---------------------------------------------------------------------------------