ID code: '1TUP' 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' --------------------------------------------------------------------------------- 4620 C1' T E1002 beta 4616 4621 4619 4640 C1' T E1003 beta 4636 4641 4639 4660 C1' C E1004 beta 4656 4661 4659 4679 C1' C E1005 beta 4675 4680 4678 4698 C1' T E1006 beta 4694 4699 4697 4718 C1' A E1007 beta 4714 4719 4717 4739 C1' G E1008 beta 4735 4740 4738 4761 C1' A E1009 beta 4757 4762 4760 4782 C1' C E1010 beta 4778 4783 4781 4801 C1' T E1011 beta 4797 4802 4800 4821 C1' T E1012 beta 4817 4822 4820 4841 C1' G E1013 beta 4837 4842 4840 4863 C1' C E1014 beta 4859 4864 4862 4882 C1' C E1015 beta 4878 4883 4881 4901 C1' C E1016 beta 4897 4902 4900 4920 C1' A E1017 beta 4916 4921 4919 4941 C1' A E1018 beta 4937 4942 4940 4962 C1' T E1019 beta 4958 4963 4961 4982 C1' T E1020 beta 4978 4983 4981 5002 C1' A E1021 beta 4998 5003 5001 5042 C1' T F1102 beta 5038 5043 5041 5062 C1' A F1103 beta 5058 5063 5061 5083 C1' A F1104 beta 5079 5084 5082 5104 C1' T F1105 beta 5100 5105 5103 5124 C1' T F1106 beta 5120 5125 5123 5144 C1' G F1107 beta 5140 5145 5143 5166 C1' G F1108 beta 5162 5167 5165 5188 C1' G F1109 beta 5184 5189 5187 5210 C1' C F1110 beta 5206 5211 5209 5229 C1' A F1111 beta 5225 5230 5228 5250 C1' A F1112 beta 5246 5251 5249 5271 C1' G F1113 beta 5267 5272 5270 5293 C1' T F1114 beta 5289 5294 5292 5313 C1' C F1115 beta 5309 5314 5312 5332 C1' T F1116 beta 5328 5333 5331 5352 C1' A F1117 beta 5348 5353 5351 5373 C1' G F1118 beta 5369 5374 5372 5395 C1' G F1119 beta 5391 5396 5394 5417 C1' A F1120 beta 5413 5418 5416 5438 C1' A F1121 beta 5434 5439 5437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4619 C2' T E1002 4620 4617 4639 C2' T E1003 4640 4637 4659 C2' C E1004 4660 4657 4678 C2' C E1005 4679 4676 4697 C2' T E1006 4698 4695 4717 C2' A E1007 4718 4715 4738 C2' G E1008 4739 4736 4760 C2' A E1009 4761 4758 4781 C2' C E1010 4782 4779 4800 C2' T E1011 4801 4798 4820 C2' T E1012 4821 4818 4840 C2' G E1013 4841 4838 4862 C2' C E1014 4863 4860 4881 C2' C E1015 4882 4879 4900 C2' C E1016 4901 4898 4919 C2' A E1017 4920 4917 4940 C2' A E1018 4941 4938 4961 C2' T E1019 4962 4959 4981 C2' T E1020 4982 4979 5001 C2' A E1021 5002 4999 5041 C2' T F1102 5042 5039 5061 C2' A F1103 5062 5059 5082 C2' A F1104 5083 5080 5103 C2' T F1105 5104 5101 5123 C2' T F1106 5124 5121 5143 C2' G F1107 5144 5141 5165 C2' G F1108 5166 5163 5187 C2' G F1109 5188 5185 5209 C2' C F1110 5210 5207 5228 C2' A F1111 5229 5226 5249 C2' A F1112 5250 5247 5270 C2' G F1113 5271 5268 5292 C2' T F1114 5293 5290 5312 C2' C F1115 5313 5310 5331 C2' T F1116 5332 5329 5351 C2' A F1117 5352 5349 5372 C2' G F1118 5373 5370 5394 C2' G F1119 5395 5392 5416 C2' A F1120 5417 5414 5437 C2' A F1121 5438 5435 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4617 C3' T E1002 OK 4615 4618 4619 4637 C3' T E1003 OK 4635 4638 4639 4657 C3' C E1004 OK 4655 4658 4659 4676 C3' C E1005 OK 4674 4677 4678 4695 C3' T E1006 OK 4693 4696 4697 4715 C3' A E1007 OK 4713 4716 4717 4736 C3' G E1008 OK 4734 4737 4738 4758 C3' A E1009 OK 4756 4759 4760 4779 C3' C E1010 OK 4777 4780 4781 4798 C3' T E1011 OK 4796 4799 4800 4818 C3' T E1012 OK 4816 4819 4820 4838 C3' G E1013 OK 4836 4839 4840 4860 C3' C E1014 OK 4858 4861 4862 4879 C3' C E1015 OK 4877 4880 4881 4898 C3' C E1016 OK 4896 4899 4900 4917 C3' A E1017 OK 4915 4918 4919 4938 C3' A E1018 OK 4936 4939 4940 4959 C3' T E1019 OK 4957 4960 4961 4979 C3' T E1020 OK 4977 4980 4981 4999 C3' A E1021 OK 4997 5000 5001 5039 C3' T F1102 OK 5037 5040 5041 5059 C3' A F1103 OK 5057 5060 5061 5080 C3' A F1104 OK 5078 5081 5082 5101 C3' T F1105 OK 5099 5102 5103 5121 C3' T F1106 OK 5119 5122 5123 5141 C3' G F1107 OK 5139 5142 5143 5163 C3' G F1108 OK 5161 5164 5165 5185 C3' G F1109 OK 5183 5186 5187 5207 C3' C F1110 OK 5205 5208 5209 5226 C3' A F1111 OK 5224 5227 5228 5247 C3' A F1112 OK 5245 5248 5249 5268 C3' G F1113 OK 5266 5269 5270 5290 C3' T F1114 OK 5288 5291 5292 5310 C3' C F1115 OK 5308 5311 5312 5329 C3' T F1116 OK 5327 5330 5331 5349 C3' A F1117 OK 5347 5350 5351 5370 C3' G F1118 OK 5368 5371 5372 5392 C3' G F1119 OK 5390 5393 5394 5414 C3' A F1120 OK 5412 5415 5416 5435 C3' A F1121 OK 5433 5436 5437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4615 C4' T E1002 OK 4617 4614 4616 4635 C4' T E1003 OK 4637 4634 4636 4655 C4' C E1004 OK 4657 4654 4656 4674 C4' C E1005 OK 4676 4673 4675 4693 C4' T E1006 OK 4695 4692 4694 4713 C4' A E1007 OK 4715 4712 4714 4734 C4' G E1008 OK 4736 4733 4735 4756 C4' A E1009 OK 4758 4755 4757 4777 C4' C E1010 OK 4779 4776 4778 4796 C4' T E1011 OK 4798 4795 4797 4816 C4' T E1012 OK 4818 4815 4817 4836 C4' G E1013 OK 4838 4835 4837 4858 C4' C E1014 OK 4860 4857 4859 4877 C4' C E1015 OK 4879 4876 4878 4896 C4' C E1016 OK 4898 4895 4897 4915 C4' A E1017 OK 4917 4914 4916 4936 C4' A E1018 OK 4938 4935 4937 4957 C4' T E1019 OK 4959 4956 4958 4977 C4' T E1020 OK 4979 4976 4978 4997 C4' A E1021 OK 4999 4996 4998 5037 C4' T F1102 OK 5039 5036 5038 5057 C4' A F1103 OK 5059 5056 5058 5078 C4' A F1104 OK 5080 5077 5079 5099 C4' T F1105 OK 5101 5098 5100 5119 C4' T F1106 OK 5121 5118 5120 5139 C4' G F1107 OK 5141 5138 5140 5161 C4' G F1108 OK 5163 5160 5162 5183 C4' G F1109 OK 5185 5182 5184 5205 C4' C F1110 OK 5207 5204 5206 5224 C4' A F1111 OK 5226 5223 5225 5245 C4' A F1112 OK 5247 5244 5246 5266 C4' G F1113 OK 5268 5265 5267 5288 C4' T F1114 OK 5290 5287 5289 5308 C4' C F1115 OK 5310 5307 5309 5327 C4' T F1116 OK 5329 5326 5328 5347 C4' A F1117 OK 5349 5346 5348 5368 C4' G F1118 OK 5370 5367 5369 5390 C4' G F1119 OK 5392 5389 5391 5412 C4' A F1120 OK 5414 5411 5413 5433 C4' A F1121 OK 5435 5432 5434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4614 C5' T E1002 4613 4615 4634 C5' T E1003 4633 4635 4654 C5' C E1004 4653 4655 4673 C5' C E1005 4672 4674 4692 C5' T E1006 4691 4693 4712 C5' A E1007 4711 4713 4733 C5' G E1008 4732 4734 4755 C5' A E1009 4754 4756 4776 C5' C E1010 4775 4777 4795 C5' T E1011 4794 4796 4815 C5' T E1012 4814 4816 4835 C5' G E1013 4834 4836 4857 C5' C E1014 4856 4858 4876 C5' C E1015 4875 4877 4895 C5' C E1016 4894 4896 4914 C5' A E1017 4913 4915 4935 C5' A E1018 4934 4936 4956 C5' T E1019 4955 4957 4976 C5' T E1020 4975 4977 4996 C5' A E1021 4995 4997 5036 C5' T F1102 5035 5037 5056 C5' A F1103 5055 5057 5077 C5' A F1104 5076 5078 5098 C5' T F1105 5097 5099 5118 C5' T F1106 5117 5119 5138 C5' G F1107 5137 5139 5160 C5' G F1108 5159 5161 5182 C5' G F1109 5181 5183 5204 C5' C F1110 5203 5205 5223 C5' A F1111 5222 5224 5244 C5' A F1112 5243 5245 5265 C5' G F1113 5264 5266 5287 C5' T F1114 5286 5288 5307 C5' C F1115 5306 5308 5326 C5' T F1116 5325 5327 5346 C5' A F1117 5345 5347 5367 C5' G F1118 5366 5368 5389 C5' G F1119 5388 5390 5411 C5' A F1120 5410 5412 5432 C5' A F1121 5431 5433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4630 P T E1003 OK OK 4618 4631 4632 4633 4650 P C E1004 OK OK 4638 4651 4652 4653 4669 P C E1005 distorted distorted 4658 4670 4671 4672 4688 P T E1006 OK OK 4677 4689 4690 4691 4708 P A E1007 OK OK 4696 4709 4710 4711 4729 P G E1008 OK OK 4716 4730 4731 4732 4751 P A E1009 OK OK 4737 4752 4753 4754 4772 P C E1010 OK OK 4759 4773 4774 4775 4791 P T E1011 OK OK 4780 4792 4793 4794 4811 P T E1012 OK OK 4799 4812 4813 4814 4831 P G E1013 OK OK 4819 4832 4833 4834 4853 P C E1014 OK OK 4839 4854 4855 4856 4872 P C E1015 OK OK 4861 4873 4874 4875 4891 P C E1016 OK OK 4880 4892 4893 4894 4910 P A E1017 OK OK 4899 4911 4912 4913 4931 P A E1018 OK OK 4918 4932 4933 4934 4952 P T E1019 OK OK 4939 4953 4954 4955 4972 P T E1020 OK OK 4960 4973 4974 4975 4992 P A E1021 OK OK 4980 4993 4994 4995 5052 P A F1103 OK OK 5040 5053 5054 5055 5073 P A F1104 OK OK 5060 5074 5075 5076 5094 P T F1105 OK OK 5081 5095 5096 5097 5114 P T F1106 OK OK 5102 5115 5116 5117 5134 P G F1107 OK OK 5122 5135 5136 5137 5156 P G F1108 OK OK 5142 5157 5158 5159 5178 P G F1109 OK OK 5164 5179 5180 5181 5200 P C F1110 OK OK 5186 5201 5202 5203 5219 P A F1111 OK OK 5208 5220 5221 5222 5240 P A F1112 OK OK 5227 5241 5242 5243 5261 P G F1113 OK OK 5248 5262 5263 5264 5283 P T F1114 OK OK 5269 5284 5285 5286 5303 P C F1115 OK OK 5291 5304 5305 5306 5322 P T F1116 OK OK 5311 5323 5324 5325 5342 P A F1117 OK OK 5330 5343 5344 5345 5363 P G F1118 OK OK 5350 5364 5365 5366 5385 P G F1119 OK OK 5371 5386 5387 5388 5407 P A F1120 OK OK 5393 5408 5409 5410 5428 P A F1121 OK OK 5415 5429 5430 5431 ---------------------------------------------------------------------------------