ID code: '5DFI' 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' --------------------------------------------------------------------------------- 4326 C1' DG P 1 beta 4322 4327 4325 4348 C1' DC P 2 beta 4344 4349 4347 4367 C1' DT P 3 beta 4363 4368 4366 4387 C1' DG P 4 beta 4383 4388 4386 4409 C1' DA P 5 beta 4405 4410 4408 4430 C1' DT P 6 beta 4426 4431 4429 4450 C1' DG P 7 beta 4446 4451 4449 4472 C1' DC P 8 beta 4468 4473 4471 4491 C1' DG P 9 beta 4487 4492 4490 4615 C1' DG P 13 beta 4611 4616 4614 4637 C1' DA P 14 beta 4633 4638 4636 4658 C1' DC P 15 beta 4654 4659 4657 4677 C1' DG P 16 beta 4673 4678 4676 4699 C1' DG P 17 beta 4695 4700 4698 4721 C1' DA P 18 beta 4717 4722 4720 4742 C1' DT P 19 beta 4738 4743 4741 4762 C1' DC P 20 beta 4758 4763 4761 4781 C1' DC P 21 beta 4777 4782 4780 4798 C1' DG V 1 beta 4794 4799 4797 4820 C1' DG V 2 beta 4816 4821 4819 4842 C1' DA V 3 beta 4838 4843 4841 4863 C1' DT V 4 beta 4859 4864 4862 4883 C1' DC V 5 beta 4879 4884 4882 4902 C1' DC V 6 beta 4898 4903 4901 4921 C1' DG V 7 beta 4917 4922 4920 4943 C1' DT V 8 beta 4939 4944 4942 4963 C1' DC V 9 beta 4959 4964 4962 4982 C1' DG V 10 beta 4978 4983 4981 5092 C1' DC V 13 beta 5088 5093 5091 5111 C1' DG V 14 beta 5107 5112 5110 5133 C1' DC V 15 beta 5129 5134 5132 5152 C1' DA V 16 beta 5148 5153 5151 5173 C1' DT V 17 beta 5169 5174 5172 5193 C1' DC V 18 beta 5189 5194 5192 5212 C1' DA V 19 beta 5208 5213 5211 5233 C1' DG V 20 beta 5229 5234 5232 5255 C1' DC V 21 beta 5251 5256 5254 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4325 C2' DG P 1 4326 4323 4347 C2' DC P 2 4348 4345 4366 C2' DT P 3 4367 4364 4386 C2' DG P 4 4387 4384 4408 C2' DA P 5 4409 4406 4429 C2' DT P 6 4430 4427 4449 C2' DG P 7 4450 4447 4471 C2' DC P 8 4472 4469 4490 C2' DG P 9 4491 4488 4614 C2' DG P 13 4615 4612 4636 C2' DA P 14 4637 4634 4657 C2' DC P 15 4658 4655 4676 C2' DG P 16 4677 4674 4698 C2' DG P 17 4699 4696 4720 C2' DA P 18 4721 4718 4741 C2' DT P 19 4742 4739 4761 C2' DC P 20 4762 4759 4780 C2' DC P 21 4781 4778 4797 C2' DG V 1 4798 4795 4819 C2' DG V 2 4820 4817 4841 C2' DA V 3 4842 4839 4862 C2' DT V 4 4863 4860 4882 C2' DC V 5 4883 4880 4901 C2' DC V 6 4902 4899 4920 C2' DG V 7 4921 4918 4942 C2' DT V 8 4943 4940 4962 C2' DC V 9 4963 4960 4981 C2' DG V 10 4982 4979 5091 C2' DC V 13 5092 5089 5110 C2' DG V 14 5111 5108 5132 C2' DC V 15 5133 5130 5151 C2' DA V 16 5152 5149 5172 C2' DT V 17 5173 5170 5192 C2' DC V 18 5193 5190 5211 C2' DA V 19 5212 5209 5232 C2' DG V 20 5233 5230 5254 C2' DC V 21 5255 5252 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4323 C3' DG P 1 OK 4321 4324 4325 4345 C3' DC P 2 OK 4343 4346 4347 4364 C3' DT P 3 OK 4362 4365 4366 4384 C3' DG P 4 OK 4382 4385 4386 4406 C3' DA P 5 OK 4404 4407 4408 4427 C3' DT P 6 OK 4425 4428 4429 4447 C3' DG P 7 OK 4445 4448 4449 4469 C3' DC P 8 OK 4467 4470 4471 4488 C3' DG P 9 OK 4486 4489 4490 4612 C3' DG P 13 OK 4610 4613 4614 4634 C3' DA P 14 OK 4632 4635 4636 4655 C3' DC P 15 OK 4653 4656 4657 4674 C3' DG P 16 OK 4672 4675 4676 4696 C3' DG P 17 OK 4694 4697 4698 4718 C3' DA P 18 OK 4716 4719 4720 4739 C3' DT P 19 OK 4737 4740 4741 4759 C3' DC P 20 OK 4757 4760 4761 4778 C3' DC P 21 OK 4776 4779 4780 4795 C3' DG V 1 OK 4793 4796 4797 4817 C3' DG V 2 OK 4815 4818 4819 4839 C3' DA V 3 OK 4837 4840 4841 4860 C3' DT V 4 OK 4858 4861 4862 4880 C3' DC V 5 OK 4878 4881 4882 4899 C3' DC V 6 OK 4897 4900 4901 4918 C3' DG V 7 OK 4916 4919 4920 4940 C3' DT V 8 OK 4938 4941 4942 4960 C3' DC V 9 OK 4958 4961 4962 4979 C3' DG V 10 OK 4977 4980 4981 5089 C3' DC V 13 OK 5087 5090 5091 5108 C3' DG V 14 OK 5106 5109 5110 5130 C3' DC V 15 OK 5128 5131 5132 5149 C3' DA V 16 OK 5147 5150 5151 5170 C3' DT V 17 OK 5168 5171 5172 5190 C3' DC V 18 OK 5188 5191 5192 5209 C3' DA V 19 OK 5207 5210 5211 5230 C3' DG V 20 OK 5228 5231 5232 5252 C3' DC V 21 OK 5250 5253 5254 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4321 C4' DG P 1 OK 4323 4320 4322 4343 C4' DC P 2 OK 4345 4342 4344 4362 C4' DT P 3 OK 4364 4361 4363 4382 C4' DG P 4 OK 4384 4381 4383 4404 C4' DA P 5 OK 4406 4403 4405 4425 C4' DT P 6 OK 4427 4424 4426 4445 C4' DG P 7 OK 4447 4444 4446 4467 C4' DC P 8 OK 4469 4466 4468 4486 C4' DG P 9 OK 4488 4485 4487 4610 C4' DG P 13 OK 4612 4609 4611 4632 C4' DA P 14 OK 4634 4631 4633 4653 C4' DC P 15 OK 4655 4652 4654 4672 C4' DG P 16 OK 4674 4671 4673 4694 C4' DG P 17 OK 4696 4693 4695 4716 C4' DA P 18 OK 4718 4715 4717 4737 C4' DT P 19 OK 4739 4736 4738 4757 C4' DC P 20 OK 4759 4756 4758 4776 C4' DC P 21 OK 4778 4775 4777 4793 C4' DG V 1 OK 4795 4792 4794 4815 C4' DG V 2 OK 4817 4814 4816 4837 C4' DA V 3 OK 4839 4836 4838 4858 C4' DT V 4 OK 4860 4857 4859 4878 C4' DC V 5 OK 4880 4877 4879 4897 C4' DC V 6 OK 4899 4896 4898 4916 C4' DG V 7 OK 4918 4915 4917 4938 C4' DT V 8 OK 4940 4937 4939 4958 C4' DC V 9 OK 4960 4957 4959 4977 C4' DG V 10 OK 4979 4976 4978 5087 C4' DC V 13 OK 5089 5086 5088 5106 C4' DG V 14 OK 5108 5105 5107 5128 C4' DC V 15 OK 5130 5127 5129 5147 C4' DA V 16 OK 5149 5146 5148 5168 C4' DT V 17 OK 5170 5167 5169 5188 C4' DC V 18 OK 5190 5187 5189 5207 C4' DA V 19 OK 5209 5206 5208 5228 C4' DG V 20 OK 5230 5227 5229 5250 C4' DC V 21 OK 5252 5249 5251 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4320 C5' DG P 1 4319 4321 4342 C5' DC P 2 4341 4343 4361 C5' DT P 3 4360 4362 4381 C5' DG P 4 4380 4382 4403 C5' DA P 5 4402 4404 4424 C5' DT P 6 4423 4425 4444 C5' DG P 7 4443 4445 4466 C5' DC P 8 4465 4467 4485 C5' DG P 9 4484 4486 4609 C5' DG P 13 4608 4610 4631 C5' DA P 14 4630 4632 4652 C5' DC P 15 4651 4653 4671 C5' DG P 16 4670 4672 4693 C5' DG P 17 4692 4694 4715 C5' DA P 18 4714 4716 4736 C5' DT P 19 4735 4737 4756 C5' DC P 20 4755 4757 4775 C5' DC P 21 4774 4776 4792 C5' DG V 1 4791 4793 4814 C5' DG V 2 4813 4815 4836 C5' DA V 3 4835 4837 4857 C5' DT V 4 4856 4858 4877 C5' DC V 5 4876 4878 4896 C5' DC V 6 4895 4897 4915 C5' DG V 7 4914 4916 4937 C5' DT V 8 4936 4938 4957 C5' DC V 9 4956 4958 4976 C5' DG V 10 4975 4977 5086 C5' DC V 13 5085 5087 5105 C5' DG V 14 5104 5106 5127 C5' DC V 15 5126 5128 5146 C5' DA V 16 5145 5147 5167 C5' DT V 17 5166 5168 5187 C5' DC V 18 5186 5188 5206 C5' DA V 19 5205 5207 5227 C5' DG V 20 5226 5228 5249 C5' DC V 21 5248 5250 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4338 P DC P 2 distorted distorted 4324 4339 4340 4341 4357 P DT P 3 distorted distorted 4346 4358 4359 4360 4377 P DG P 4 distorted distorted 4365 4378 4379 4380 4399 P DA P 5 distorted distorted 4385 4400 4401 4402 4420 P DT P 6 distorted distorted 4407 4421 4422 4423 4440 P DG P 7 distorted distorted 4428 4441 4442 4443 4462 P DC P 8 distorted distorted 4448 4463 4464 4465 4481 P DG P 9 distorted distorted 4470 4482 4483 4484 4539 P OMC P 10 4489 4540 P OMC P 10 4489 4545 P 48Z P 11 4546 P 48Z P 11 4567 P DC P 12 4568 P DC P 12 4605 P DG P 13 distorted distorted 4606 4607 4608 4627 P DA P 14 distorted distorted 4613 4628 4629 4630 4648 P DC P 15 distorted distorted 4635 4649 4650 4651 4667 P DG P 16 distorted distorted 4656 4668 4669 4670 4689 P DG P 17 distorted distorted 4675 4690 4691 4692 4711 P DA P 18 distorted distorted 4697 4712 4713 4714 4732 P DT P 19 distorted distorted 4719 4733 4734 4735 4752 P DC P 20 distorted distorted 4740 4753 4754 4755 4771 P DC P 21 distorted distorted 4760 4772 4773 4774 4810 P DG V 2 distorted distorted 4796 4811 4812 4813 4832 P DA V 3 distorted distorted 4818 4833 4834 4835 4853 P DT V 4 distorted distorted 4840 4854 4855 4856 4873 P DC V 5 distorted distorted 4861 4874 4875 4876 4892 P DC V 6 distorted distorted 4881 4893 4894 4895 4911 P DG V 7 distorted distorted 4900 4912 4913 4914 4933 P DT V 8 distorted distorted 4919 4934 4935 4936 4953 P DC V 9 distorted distorted 4941 4954 4955 4956 4972 P DG V 10 distorted distorted 4961 4973 4974 4975 4994 P DG V 11 4980 4995 P DG V 11 4980 5038 P DG V 12 5039 P DG V 12 5082 P DC V 13 distorted distorted 5083 5084 5085 5101 P DG V 14 distorted distorted 5090 5102 5103 5104 5123 P DC V 15 distorted distorted 5109 5124 5125 5126 5142 P DA V 16 distorted distorted 5131 5143 5144 5145 5163 P DT V 17 distorted distorted 5150 5164 5165 5166 5183 P DC V 18 distorted distorted 5171 5184 5185 5186 5202 P DA V 19 distorted distorted 5191 5203 5204 5205 5223 P DG V 20 distorted distorted 5210 5224 5225 5226 5245 P DC V 21 distorted distorted 5231 5246 5247 5248 ---------------------------------------------------------------------------------