ID code: '3RC8' 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' --------------------------------------------------------------------------------- 4881 C1' C E 4 beta 4876 4882 4879 4901 C1' C E 5 beta 4896 4902 4899 4921 C1' G E 6 beta 4916 4922 4919 4944 C1' C E 7 beta 4939 4945 4942 4964 C1' C E 8 beta 4959 4965 4962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4879 C2' C E 4 OK 4881 4877 4880 4899 C2' C E 5 OK 4901 4897 4900 4919 C2' G E 6 OK 4921 4917 4920 4942 C2' C E 7 OK 4944 4940 4943 4962 C2' C E 8 OK 4964 4960 4963 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4877 C3' C E 4 OK 4875 4878 4879 4897 C3' C E 5 OK 4895 4898 4899 4917 C3' G E 6 OK 4915 4918 4919 4940 C3' C E 7 OK 4938 4941 4942 4960 C3' C E 8 OK 4958 4961 4962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4875 C4' C E 4 OK 4877 4874 4876 4895 C4' C E 5 OK 4897 4894 4896 4915 C4' G E 6 OK 4917 4914 4916 4938 C4' C E 7 OK 4940 4937 4939 4958 C4' C E 8 OK 4960 4957 4959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4874 C5' C E 4 4873 4875 4894 C5' C E 5 4893 4895 4914 C5' G E 6 4913 4915 4937 C5' C E 7 4936 4938 4957 C5' C E 8 4956 4958 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4870 P C E 4 OK OK 4871 4872 4873 4890 P C E 5 distorted distorted 4878 4891 4892 4893 4910 P G E 6 distorted distorted 4898 4911 4912 4913 4933 P C E 7 distorted distorted 4918 4934 4935 4936 4953 P C E 8 distorted distorted 4941 4954 4955 4956 4973 P C E 9 distorted distorted 4961 4974 4975 4976 ---------------------------------------------------------------------------------