ID code: '1RV5' 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' --------------------------------------------------------------------------------- 4682 C1' A C 2 beta 4678 4683 4681 4705 C1' A C 3 beta 4701 4706 4704 4728 C1' G C 4 beta 4724 4729 4727 4753 C1' A C 5 beta 4749 4754 4752 4776 C1' T C 6 beta 4772 4777 4775 4794 C1' A C 7 beta 4790 4795 4793 4817 C1' T C 8 beta 4813 4818 4816 4838 C1' C C 9 beta 4834 4839 4837 4859 C1' T C 10 beta 4855 4860 4858 4880 C1' T C 11 beta 4876 4881 4879 4922 C1' A D 2 beta 4918 4923 4921 4945 C1' A D 3 beta 4941 4946 4944 4968 C1' G D 4 beta 4964 4969 4967 4993 C1' A D 5 beta 4989 4994 4992 5016 C1' T D 6 beta 5012 5017 5015 5034 C1' A D 7 beta 5030 5035 5033 5057 C1' T D 8 beta 5053 5058 5056 5078 C1' C D 9 beta 5074 5079 5077 5099 C1' T D 10 beta 5095 5100 5098 5120 C1' T D 11 beta 5116 5121 5119 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4681 C2' A C 2 4682 4679 4704 C2' A C 3 4705 4702 4727 C2' G C 4 4728 4725 4752 C2' A C 5 4753 4750 4775 C2' T C 6 4776 4773 4793 C2' A C 7 4794 4791 4816 C2' T C 8 4817 4814 4837 C2' C C 9 4838 4835 4858 C2' T C 10 4859 4856 4879 C2' T C 11 4880 4877 4921 C2' A D 2 4922 4919 4944 C2' A D 3 4945 4942 4967 C2' G D 4 4968 4965 4992 C2' A D 5 4993 4990 5015 C2' T D 6 5016 5013 5033 C2' A D 7 5034 5031 5056 C2' T D 8 5057 5054 5077 C2' C D 9 5078 5075 5098 C2' T D 10 5099 5096 5119 C2' T D 11 5120 5117 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4679 C3' A C 2 OK 4677 4680 4681 4702 C3' A C 3 OK 4700 4703 4704 4725 C3' G C 4 OK 4723 4726 4727 4750 C3' A C 5 OK 4748 4751 4752 4773 C3' T C 6 OK 4771 4774 4775 4791 C3' A C 7 OK 4789 4792 4793 4814 C3' T C 8 OK 4812 4815 4816 4835 C3' C C 9 OK 4833 4836 4837 4856 C3' T C 10 OK 4854 4857 4858 4877 C3' T C 11 OK 4875 4878 4879 4919 C3' A D 2 OK 4917 4920 4921 4942 C3' A D 3 OK 4940 4943 4944 4965 C3' G D 4 OK 4963 4966 4967 4990 C3' A D 5 OK 4988 4991 4992 5013 C3' T D 6 OK 5011 5014 5015 5031 C3' A D 7 OK 5029 5032 5033 5054 C3' T D 8 OK 5052 5055 5056 5075 C3' C D 9 OK 5073 5076 5077 5096 C3' T D 10 OK 5094 5097 5098 5117 C3' T D 11 OK 5115 5118 5119 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4677 C4' A C 2 OK 4679 4676 4678 4700 C4' A C 3 OK 4702 4699 4701 4723 C4' G C 4 OK 4725 4722 4724 4748 C4' A C 5 OK 4750 4747 4749 4771 C4' T C 6 OK 4773 4770 4772 4789 C4' A C 7 OK 4791 4788 4790 4812 C4' T C 8 OK 4814 4811 4813 4833 C4' C C 9 OK 4835 4832 4834 4854 C4' T C 10 OK 4856 4853 4855 4875 C4' T C 11 OK 4877 4874 4876 4917 C4' A D 2 OK 4919 4916 4918 4940 C4' A D 3 OK 4942 4939 4941 4963 C4' G D 4 OK 4965 4962 4964 4988 C4' A D 5 OK 4990 4987 4989 5011 C4' T D 6 OK 5013 5010 5012 5029 C4' A D 7 OK 5031 5028 5030 5052 C4' T D 8 OK 5054 5051 5053 5073 C4' C D 9 OK 5075 5072 5074 5094 C4' T D 10 OK 5096 5093 5095 5115 C4' T D 11 OK 5117 5114 5116 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4676 C5' A C 2 4675 4677 4699 C5' A C 3 4698 4700 4722 C5' G C 4 4721 4723 4747 C5' A C 5 4746 4748 4770 C5' T C 6 4769 4771 4788 C5' A C 7 4787 4789 4811 C5' T C 8 4810 4812 4832 C5' C C 9 4831 4833 4853 C5' T C 10 4852 4854 4874 C5' T C 11 4873 4875 4916 C5' A D 2 4915 4917 4939 C5' A D 3 4938 4940 4962 C5' G D 4 4961 4963 4987 C5' A D 5 4986 4988 5010 C5' T D 6 5009 5011 5028 C5' A D 7 5027 5029 5051 C5' T D 8 5050 5052 5072 C5' C D 9 5071 5073 5093 C5' T D 10 5092 5094 5114 C5' T D 11 5113 5115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4695 P A C 3 OK OK 4680 4696 4697 4698 4718 P G C 4 OK OK 4703 4719 4720 4721 4743 P A C 5 OK OK 4726 4744 4745 4746 4766 P T C 6 OK OK 4751 4767 4768 4769 4807 P T C 8 OK OK 4792 4808 4809 4810 4828 P C C 9 OK OK 4815 4829 4830 4831 4849 P T C 10 OK OK 4836 4850 4851 4852 4870 P T C 11 OK OK 4857 4871 4872 4873 4935 P A D 3 OK OK 4920 4936 4937 4938 4958 P G D 4 OK OK 4943 4959 4960 4961 4983 P A D 5 OK OK 4966 4984 4985 4986 5006 P T D 6 OK OK 4991 5007 5008 5009 5047 P T D 8 OK OK 5032 5048 5049 5050 5068 P C D 9 OK OK 5055 5069 5070 5071 5089 P T D 10 OK OK 5076 5090 5091 5092 5110 P T D 11 OK OK 5097 5111 5112 5113 ---------------------------------------------------------------------------------