ID code: '1VKX' 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' --------------------------------------------------------------------------------- 4660 C1' G C 2 beta 4656 4661 4659 4682 C1' G C 3 beta 4678 4683 4681 4704 C1' G C 4 beta 4700 4705 4703 4726 C1' G C 5 beta 4722 4727 4725 4748 C1' A C 6 beta 4744 4749 4747 4769 C1' C C 7 beta 4765 4770 4768 4788 C1' T C 8 beta 4784 4789 4787 4808 C1' T C 9 beta 4804 4809 4807 4828 C1' T C 10 beta 4824 4829 4827 4848 C1' C C 11 beta 4844 4849 4847 4867 C1' C C 12 beta 4863 4868 4866 4905 C1' G D 14 beta 4901 4906 4904 4927 C1' G D 15 beta 4923 4928 4926 4949 C1' A D 16 beta 4945 4950 4948 4970 C1' A D 17 beta 4966 4971 4969 4991 C1' A D 18 beta 4987 4992 4990 5012 C1' G D 19 beta 5008 5013 5011 5034 C1' T D 20 beta 5030 5035 5033 5054 C1' C D 21 beta 5050 5055 5053 5073 C1' C D 22 beta 5069 5074 5072 5092 C1' C D 23 beta 5088 5093 5091 5111 C1' C D 24 beta 5107 5112 5110 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4659 C2' G C 2 4660 4657 4681 C2' G C 3 4682 4679 4703 C2' G C 4 4704 4701 4725 C2' G C 5 4726 4723 4747 C2' A C 6 4748 4745 4768 C2' C C 7 4769 4766 4787 C2' T C 8 4788 4785 4807 C2' T C 9 4808 4805 4827 C2' T C 10 4828 4825 4847 C2' C C 11 4848 4845 4866 C2' C C 12 4867 4864 4904 C2' G D 14 4905 4902 4926 C2' G D 15 4927 4924 4948 C2' A D 16 4949 4946 4969 C2' A D 17 4970 4967 4990 C2' A D 18 4991 4988 5011 C2' G D 19 5012 5009 5033 C2' T D 20 5034 5031 5053 C2' C D 21 5054 5051 5072 C2' C D 22 5073 5070 5091 C2' C D 23 5092 5089 5110 C2' C D 24 5111 5108 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4657 C3' G C 2 OK 4655 4658 4659 4679 C3' G C 3 OK 4677 4680 4681 4701 C3' G C 4 OK 4699 4702 4703 4723 C3' G C 5 OK 4721 4724 4725 4745 C3' A C 6 OK 4743 4746 4747 4766 C3' C C 7 OK 4764 4767 4768 4785 C3' T C 8 OK 4783 4786 4787 4805 C3' T C 9 OK 4803 4806 4807 4825 C3' T C 10 OK 4823 4826 4827 4845 C3' C C 11 OK 4843 4846 4847 4864 C3' C C 12 OK 4862 4865 4866 4902 C3' G D 14 OK 4900 4903 4904 4924 C3' G D 15 OK 4922 4925 4926 4946 C3' A D 16 OK 4944 4947 4948 4967 C3' A D 17 OK 4965 4968 4969 4988 C3' A D 18 OK 4986 4989 4990 5009 C3' G D 19 OK 5007 5010 5011 5031 C3' T D 20 OK 5029 5032 5033 5051 C3' C D 21 OK 5049 5052 5053 5070 C3' C D 22 OK 5068 5071 5072 5089 C3' C D 23 OK 5087 5090 5091 5108 C3' C D 24 OK 5106 5109 5110 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4655 C4' G C 2 OK 4657 4654 4656 4677 C4' G C 3 OK 4679 4676 4678 4699 C4' G C 4 OK 4701 4698 4700 4721 C4' G C 5 OK 4723 4720 4722 4743 C4' A C 6 OK 4745 4742 4744 4764 C4' C C 7 OK 4766 4763 4765 4783 C4' T C 8 OK 4785 4782 4784 4803 C4' T C 9 OK 4805 4802 4804 4823 C4' T C 10 OK 4825 4822 4824 4843 C4' C C 11 OK 4845 4842 4844 4862 C4' C C 12 OK 4864 4861 4863 4900 C4' G D 14 OK 4902 4899 4901 4922 C4' G D 15 OK 4924 4921 4923 4944 C4' A D 16 OK 4946 4943 4945 4965 C4' A D 17 OK 4967 4964 4966 4986 C4' A D 18 OK 4988 4985 4987 5007 C4' G D 19 OK 5009 5006 5008 5029 C4' T D 20 OK 5031 5028 5030 5049 C4' C D 21 OK 5051 5048 5050 5068 C4' C D 22 OK 5070 5067 5069 5087 C4' C D 23 OK 5089 5086 5088 5106 C4' C D 24 OK 5108 5105 5107 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4654 C5' G C 2 4653 4655 4676 C5' G C 3 4675 4677 4698 C5' G C 4 4697 4699 4720 C5' G C 5 4719 4721 4742 C5' A C 6 4741 4743 4763 C5' C C 7 4762 4764 4782 C5' T C 8 4781 4783 4802 C5' T C 9 4801 4803 4822 C5' T C 10 4821 4823 4842 C5' C C 11 4841 4843 4861 C5' C C 12 4860 4862 4899 C5' G D 14 4898 4900 4921 C5' G D 15 4920 4922 4943 C5' A D 16 4942 4944 4964 C5' A D 17 4963 4965 4985 C5' A D 18 4984 4986 5006 C5' G D 19 5005 5007 5028 C5' T D 20 5027 5029 5048 C5' C D 21 5047 5049 5067 C5' C D 22 5066 5068 5086 C5' C D 23 5085 5087 5105 C5' C D 24 5104 5106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4672 P G C 3 OK OK 4658 4673 4674 4675 4694 P G C 4 OK OK 4680 4695 4696 4697 4716 P G C 5 OK OK 4702 4717 4718 4719 4738 P A C 6 OK OK 4724 4739 4740 4741 4759 P C C 7 OK OK 4746 4760 4761 4762 4778 P T C 8 OK OK 4767 4779 4780 4781 4798 P T C 9 OK OK 4786 4799 4800 4801 4818 P T C 10 OK OK 4806 4819 4820 4821 4838 P C C 11 OK OK 4826 4839 4840 4841 4857 P C C 12 OK OK 4846 4858 4859 4860 4917 P G D 15 OK OK 4903 4918 4919 4920 4939 P A D 16 OK OK 4925 4940 4941 4942 4960 P A D 17 OK OK 4947 4961 4962 4963 4981 P A D 18 OK OK 4968 4982 4983 4984 5002 P G D 19 OK OK 4989 5003 5004 5005 5024 P T D 20 OK OK 5010 5025 5026 5027 5044 P C D 21 OK OK 5032 5045 5046 5047 5063 P C D 22 OK OK 5052 5064 5065 5066 5082 P C D 23 OK OK 5071 5083 5084 5085 5101 P C D 24 OK OK 5090 5102 5103 5104 ---------------------------------------------------------------------------------