ID code: '1KLN' 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' --------------------------------------------------------------------------------- 4711 C1' G B 2 beta 4707 4712 4710 4733 C1' C B 3 beta 4729 4734 4732 4752 C1' C B 4 beta 4748 4753 4751 4771 C1' T B 5 beta 4767 4772 4770 4791 C1' C B 6 beta 4787 4792 4790 4810 C1' G B 7 beta 4806 4811 4809 4832 C1' C B 8 beta 4828 4833 4831 4851 C1' G B 9 beta 4847 4852 4850 4873 C1' G B 10 beta 4869 4874 4872 4999 C1' C B 20 beta 4995 5000 4998 5018 C1' C B 21 beta 5014 5019 5017 5037 C1' G B 23 beta 5033 5038 5036 5059 C1' C B 24 beta 5055 5060 5058 5078 C1' G B 25 beta 5074 5079 5077 5100 C1' A B 26 beta 5096 5101 5099 5121 C1' G B 27 beta 5117 5122 5120 5143 C1' G B 28 beta 5139 5144 5142 5165 C1' C B 29 beta 5161 5166 5164 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4710 C2' G B 2 4711 4708 4732 C2' C B 3 4733 4730 4751 C2' C B 4 4752 4749 4770 C2' T B 5 4771 4768 4790 C2' C B 6 4791 4788 4809 C2' G B 7 4810 4807 4831 C2' C B 8 4832 4829 4850 C2' G B 9 4851 4848 4872 C2' G B 10 4873 4870 4998 C2' C B 20 4999 4996 5017 C2' C B 21 5018 5015 5036 C2' G B 23 5037 5034 5058 C2' C B 24 5059 5056 5077 C2' G B 25 5078 5075 5099 C2' A B 26 5100 5097 5120 C2' G B 27 5121 5118 5142 C2' G B 28 5143 5140 5164 C2' C B 29 5165 5162 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4708 C3' G B 2 OK 4706 4709 4710 4730 C3' C B 3 OK 4728 4731 4732 4749 C3' C B 4 OK 4747 4750 4751 4768 C3' T B 5 OK 4766 4769 4770 4788 C3' C B 6 OK 4786 4789 4790 4807 C3' G B 7 OK 4805 4808 4809 4829 C3' C B 8 OK 4827 4830 4831 4848 C3' G B 9 OK 4846 4849 4850 4870 C3' G B 10 OK 4868 4871 4872 4996 C3' C B 20 OK 4994 4997 4998 5015 C3' C B 21 OK 5013 5016 5017 5034 C3' G B 23 OK 5032 5035 5036 5056 C3' C B 24 OK 5054 5057 5058 5075 C3' G B 25 OK 5073 5076 5077 5097 C3' A B 26 OK 5095 5098 5099 5118 C3' G B 27 OK 5116 5119 5120 5140 C3' G B 28 OK 5138 5141 5142 5162 C3' C B 29 OK 5160 5163 5164 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4706 C4' G B 2 OK 4708 4705 4707 4728 C4' C B 3 OK 4730 4727 4729 4747 C4' C B 4 OK 4749 4746 4748 4766 C4' T B 5 OK 4768 4765 4767 4786 C4' C B 6 OK 4788 4785 4787 4805 C4' G B 7 OK 4807 4804 4806 4827 C4' C B 8 OK 4829 4826 4828 4846 C4' G B 9 OK 4848 4845 4847 4868 C4' G B 10 OK 4870 4867 4869 4994 C4' C B 20 OK 4996 4993 4995 5013 C4' C B 21 OK 5015 5012 5014 5032 C4' G B 23 OK 5034 5031 5033 5054 C4' C B 24 OK 5056 5053 5055 5073 C4' G B 25 OK 5075 5072 5074 5095 C4' A B 26 OK 5097 5094 5096 5116 C4' G B 27 OK 5118 5115 5117 5138 C4' G B 28 OK 5140 5137 5139 5160 C4' C B 29 OK 5162 5159 5161 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4705 C5' G B 2 4704 4706 4727 C5' C B 3 4726 4728 4746 C5' C B 4 4745 4747 4765 C5' T B 5 4764 4766 4785 C5' C B 6 4784 4786 4804 C5' G B 7 4803 4805 4826 C5' C B 8 4825 4827 4845 C5' G B 9 4844 4846 4867 C5' G B 10 4866 4868 4993 C5' C B 20 4992 4994 5012 C5' C B 21 5011 5013 5031 C5' G B 23 5030 5032 5053 C5' C B 24 5052 5054 5072 C5' G B 25 5071 5073 5094 C5' A B 26 5093 5095 5115 C5' G B 27 5114 5116 5137 C5' G B 28 5136 5138 5159 C5' C B 29 5158 5160 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4723 P C B 3 distorted distorted 4709 4724 4725 4726 4742 P C B 4 distorted distorted 4731 4743 4744 4745 4761 P T B 5 distorted distorted 4750 4762 4763 4764 4781 P C B 6 distorted distorted 4769 4782 4783 4784 4800 P G B 7 distorted distorted 4789 4801 4802 4803 4822 P C B 8 distorted distorted 4808 4823 4824 4825 4841 P G B 9 distorted distorted 4830 4842 4843 4844 4863 P G B 10 distorted distorted 4849 4864 4865 4866 5008 P C B 21 distorted distorted 4997 5009 5010 5011 5027 P G B 23 OK OK 5016 5028 5029 5030 5049 P C B 24 distorted distorted 5035 5050 5051 5052 5068 P G B 25 distorted distorted 5057 5069 5070 5071 5090 P A B 26 distorted distorted 5076 5091 5092 5093 5111 P G B 27 distorted distorted 5098 5112 5113 5114 5133 P G B 28 distorted distorted 5119 5134 5135 5136 5155 P C B 29 distorted distorted 5141 5156 5157 5158 ---------------------------------------------------------------------------------