ID code: '4NGD' 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' --------------------------------------------------------------------------------- 4639 C1' G B 1 alpha beta 4634 4657 4640 4637 4673 C1' C B 2 alpha beta 4668 4688 4674 4671 4704 C1' G B 3 alpha beta 4699 4722 4705 4702 4738 C1' A B 4 alpha beta 4733 4755 4739 4736 4771 C1' A B 5 alpha beta 4766 4788 4772 4769 4804 C1' U B 6 alpha beta 4799 4819 4805 4802 4834 C1' U B 7 alpha beta 4829 4849 4835 4832 4864 C1' C B 8 alpha beta 4859 4879 4865 4862 4895 C1' G B 9 alpha beta 4890 4913 4896 4893 4929 C1' C B 10 alpha beta 4924 4944 4930 4927 4960 C1' U B 11 alpha beta 4955 4975 4961 4958 4990 C1' U B 12 alpha beta 4985 5006 4991 4988 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4637 C2' G B 1 OK OK 4639 4635 4655 4638 4671 C2' C B 2 OK OK 4673 4669 4686 4672 4702 C2' G B 3 OK OK 4704 4700 4720 4703 4736 C2' A B 4 OK OK 4738 4734 4753 4737 4769 C2' A B 5 OK OK 4771 4767 4786 4770 4802 C2' U B 6 OK OK 4804 4800 4817 4803 4832 C2' U B 7 OK OK 4834 4830 4847 4833 4862 C2' C B 8 OK OK 4864 4860 4877 4863 4893 C2' G B 9 OK OK 4895 4891 4911 4894 4927 C2' C B 10 OK OK 4929 4925 4942 4928 4958 C2' U B 11 OK OK 4960 4956 4973 4959 4988 C2' U B 12 OK OK 4990 4986 5004 4989 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4635 C3' G B 1 OK OK 4633 4654 4636 4637 4669 C3' C B 2 OK OK 4667 4685 4670 4671 4700 C3' G B 3 OK OK 4698 4719 4701 4702 4734 C3' A B 4 OK OK 4732 4752 4735 4736 4767 C3' A B 5 OK OK 4765 4785 4768 4769 4800 C3' U B 6 OK OK 4798 4816 4801 4802 4830 C3' U B 7 OK OK 4828 4846 4831 4832 4860 C3' C B 8 OK OK 4858 4876 4861 4862 4891 C3' G B 9 OK OK 4889 4910 4892 4893 4925 C3' C B 10 OK OK 4923 4941 4926 4927 4956 C3' U B 11 OK OK 4954 4972 4957 4958 4986 C3' U B 12 OK OK 4984 5002 4987 4988 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4633 C4' G B 1 OK OK 4635 4653 4632 4634 4667 C4' C B 2 OK OK 4669 4684 4666 4668 4698 C4' G B 3 OK OK 4700 4718 4697 4699 4732 C4' A B 4 OK OK 4734 4751 4731 4733 4765 C4' A B 5 OK OK 4767 4784 4764 4766 4798 C4' U B 6 OK OK 4800 4815 4797 4799 4828 C4' U B 7 OK OK 4830 4845 4827 4829 4858 C4' C B 8 OK OK 4860 4875 4857 4859 4889 C4' G B 9 OK OK 4891 4909 4888 4890 4923 C4' C B 10 OK OK 4925 4940 4922 4924 4954 C4' U B 11 OK OK 4956 4971 4953 4955 4984 C4' U B 12 OK OK 4986 5001 4983 4985 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4632 C5' G B 1 OK OK 4631 4651 4652 4633 4666 C5' C B 2 OK OK 4665 4682 4683 4667 4697 C5' G B 3 OK OK 4696 4716 4717 4698 4731 C5' A B 4 OK OK 4730 4749 4750 4732 4764 C5' A B 5 OK OK 4763 4782 4783 4765 4797 C5' U B 6 OK OK 4796 4813 4814 4798 4827 C5' U B 7 OK OK 4826 4843 4844 4828 4857 C5' C B 8 OK OK 4856 4873 4874 4858 4888 C5' G B 9 OK OK 4887 4907 4908 4889 4922 C5' C B 10 OK OK 4921 4938 4939 4923 4953 C5' U B 11 OK OK 4952 4969 4970 4954 4983 C5' U B 12 OK OK 4982 4999 5000 4984 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4628 P G B 1 OK OK 4629 4630 4631 4662 P C B 2 distorted distorted 4636 4663 4664 4665 4693 P G B 3 distorted distorted 4670 4694 4695 4696 4727 P A B 4 distorted distorted 4701 4728 4729 4730 4760 P A B 5 distorted distorted 4735 4761 4762 4763 4793 P U B 6 distorted distorted 4768 4794 4795 4796 4823 P U B 7 distorted distorted 4801 4824 4825 4826 4853 P C B 8 distorted distorted 4831 4854 4855 4856 4884 P G B 9 distorted distorted 4861 4885 4886 4887 4918 P C B 10 distorted distorted 4892 4919 4920 4921 4949 P U B 11 distorted distorted 4926 4950 4951 4952 4979 P U B 12 distorted distorted 4957 4980 4981 4982 ---------------------------------------------------------------------------------