ID code: '1TSR' 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' --------------------------------------------------------------------------------- 4623 C1' T E 2 beta 4619 4624 4622 4643 C1' T E 3 beta 4639 4644 4642 4663 C1' C E 4 beta 4659 4664 4662 4682 C1' C E 5 beta 4678 4683 4681 4701 C1' T E 6 beta 4697 4702 4700 4721 C1' A E 7 beta 4717 4722 4720 4742 C1' G E 8 beta 4738 4743 4741 4764 C1' A E 9 beta 4760 4765 4763 4785 C1' C E 10 beta 4781 4786 4784 4804 C1' T E 11 beta 4800 4805 4803 4824 C1' T E 12 beta 4820 4825 4823 4844 C1' G E 13 beta 4840 4845 4843 4866 C1' C E 14 beta 4862 4867 4865 4885 C1' C E 15 beta 4881 4886 4884 4904 C1' C E 16 beta 4900 4905 4903 4923 C1' A E 17 beta 4919 4924 4922 4944 C1' A E 18 beta 4940 4945 4943 4965 C1' T E 19 beta 4961 4966 4964 4985 C1' T E 20 beta 4981 4986 4984 5005 C1' A E 21 beta 5001 5006 5004 5045 C1' T F 2 beta 5041 5046 5044 5065 C1' A F 3 beta 5061 5066 5064 5086 C1' A F 4 beta 5082 5087 5085 5107 C1' T F 5 beta 5103 5108 5106 5127 C1' T F 6 beta 5123 5128 5126 5147 C1' G F 7 beta 5143 5148 5146 5169 C1' G F 8 beta 5165 5170 5168 5191 C1' G F 9 beta 5187 5192 5190 5213 C1' C F 10 beta 5209 5214 5212 5232 C1' A F 11 beta 5228 5233 5231 5253 C1' A F 12 beta 5249 5254 5252 5274 C1' G F 13 beta 5270 5275 5273 5296 C1' T F 14 beta 5292 5297 5295 5316 C1' C F 15 beta 5312 5317 5315 5335 C1' T F 16 beta 5331 5336 5334 5355 C1' A F 17 beta 5351 5356 5354 5376 C1' G F 18 beta 5372 5377 5375 5398 C1' G F 19 beta 5394 5399 5397 5420 C1' A F 20 beta 5416 5421 5419 5441 C1' A F 21 beta 5437 5442 5440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4622 C2' T E 2 4623 4620 4642 C2' T E 3 4643 4640 4662 C2' C E 4 4663 4660 4681 C2' C E 5 4682 4679 4700 C2' T E 6 4701 4698 4720 C2' A E 7 4721 4718 4741 C2' G E 8 4742 4739 4763 C2' A E 9 4764 4761 4784 C2' C E 10 4785 4782 4803 C2' T E 11 4804 4801 4823 C2' T E 12 4824 4821 4843 C2' G E 13 4844 4841 4865 C2' C E 14 4866 4863 4884 C2' C E 15 4885 4882 4903 C2' C E 16 4904 4901 4922 C2' A E 17 4923 4920 4943 C2' A E 18 4944 4941 4964 C2' T E 19 4965 4962 4984 C2' T E 20 4985 4982 5004 C2' A E 21 5005 5002 5044 C2' T F 2 5045 5042 5064 C2' A F 3 5065 5062 5085 C2' A F 4 5086 5083 5106 C2' T F 5 5107 5104 5126 C2' T F 6 5127 5124 5146 C2' G F 7 5147 5144 5168 C2' G F 8 5169 5166 5190 C2' G F 9 5191 5188 5212 C2' C F 10 5213 5210 5231 C2' A F 11 5232 5229 5252 C2' A F 12 5253 5250 5273 C2' G F 13 5274 5271 5295 C2' T F 14 5296 5293 5315 C2' C F 15 5316 5313 5334 C2' T F 16 5335 5332 5354 C2' A F 17 5355 5352 5375 C2' G F 18 5376 5373 5397 C2' G F 19 5398 5395 5419 C2' A F 20 5420 5417 5440 C2' A F 21 5441 5438 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4620 C3' T E 2 OK 4618 4621 4622 4640 C3' T E 3 OK 4638 4641 4642 4660 C3' C E 4 OK 4658 4661 4662 4679 C3' C E 5 OK 4677 4680 4681 4698 C3' T E 6 OK 4696 4699 4700 4718 C3' A E 7 OK 4716 4719 4720 4739 C3' G E 8 OK 4737 4740 4741 4761 C3' A E 9 OK 4759 4762 4763 4782 C3' C E 10 OK 4780 4783 4784 4801 C3' T E 11 OK 4799 4802 4803 4821 C3' T E 12 OK 4819 4822 4823 4841 C3' G E 13 OK 4839 4842 4843 4863 C3' C E 14 OK 4861 4864 4865 4882 C3' C E 15 OK 4880 4883 4884 4901 C3' C E 16 OK 4899 4902 4903 4920 C3' A E 17 OK 4918 4921 4922 4941 C3' A E 18 OK 4939 4942 4943 4962 C3' T E 19 OK 4960 4963 4964 4982 C3' T E 20 OK 4980 4983 4984 5002 C3' A E 21 OK 5000 5003 5004 5042 C3' T F 2 OK 5040 5043 5044 5062 C3' A F 3 OK 5060 5063 5064 5083 C3' A F 4 OK 5081 5084 5085 5104 C3' T F 5 OK 5102 5105 5106 5124 C3' T F 6 OK 5122 5125 5126 5144 C3' G F 7 OK 5142 5145 5146 5166 C3' G F 8 OK 5164 5167 5168 5188 C3' G F 9 OK 5186 5189 5190 5210 C3' C F 10 OK 5208 5211 5212 5229 C3' A F 11 OK 5227 5230 5231 5250 C3' A F 12 OK 5248 5251 5252 5271 C3' G F 13 OK 5269 5272 5273 5293 C3' T F 14 OK 5291 5294 5295 5313 C3' C F 15 OK 5311 5314 5315 5332 C3' T F 16 OK 5330 5333 5334 5352 C3' A F 17 OK 5350 5353 5354 5373 C3' G F 18 OK 5371 5374 5375 5395 C3' G F 19 OK 5393 5396 5397 5417 C3' A F 20 OK 5415 5418 5419 5438 C3' A F 21 OK 5436 5439 5440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4618 C4' T E 2 OK 4620 4617 4619 4638 C4' T E 3 OK 4640 4637 4639 4658 C4' C E 4 OK 4660 4657 4659 4677 C4' C E 5 OK 4679 4676 4678 4696 C4' T E 6 OK 4698 4695 4697 4716 C4' A E 7 OK 4718 4715 4717 4737 C4' G E 8 OK 4739 4736 4738 4759 C4' A E 9 OK 4761 4758 4760 4780 C4' C E 10 OK 4782 4779 4781 4799 C4' T E 11 OK 4801 4798 4800 4819 C4' T E 12 OK 4821 4818 4820 4839 C4' G E 13 OK 4841 4838 4840 4861 C4' C E 14 OK 4863 4860 4862 4880 C4' C E 15 OK 4882 4879 4881 4899 C4' C E 16 OK 4901 4898 4900 4918 C4' A E 17 OK 4920 4917 4919 4939 C4' A E 18 OK 4941 4938 4940 4960 C4' T E 19 OK 4962 4959 4961 4980 C4' T E 20 OK 4982 4979 4981 5000 C4' A E 21 OK 5002 4999 5001 5040 C4' T F 2 OK 5042 5039 5041 5060 C4' A F 3 OK 5062 5059 5061 5081 C4' A F 4 OK 5083 5080 5082 5102 C4' T F 5 OK 5104 5101 5103 5122 C4' T F 6 OK 5124 5121 5123 5142 C4' G F 7 OK 5144 5141 5143 5164 C4' G F 8 OK 5166 5163 5165 5186 C4' G F 9 OK 5188 5185 5187 5208 C4' C F 10 OK 5210 5207 5209 5227 C4' A F 11 OK 5229 5226 5228 5248 C4' A F 12 OK 5250 5247 5249 5269 C4' G F 13 OK 5271 5268 5270 5291 C4' T F 14 OK 5293 5290 5292 5311 C4' C F 15 OK 5313 5310 5312 5330 C4' T F 16 OK 5332 5329 5331 5350 C4' A F 17 OK 5352 5349 5351 5371 C4' G F 18 OK 5373 5370 5372 5393 C4' G F 19 OK 5395 5392 5394 5415 C4' A F 20 OK 5417 5414 5416 5436 C4' A F 21 OK 5438 5435 5437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4617 C5' T E 2 4616 4618 4637 C5' T E 3 4636 4638 4657 C5' C E 4 4656 4658 4676 C5' C E 5 4675 4677 4695 C5' T E 6 4694 4696 4715 C5' A E 7 4714 4716 4736 C5' G E 8 4735 4737 4758 C5' A E 9 4757 4759 4779 C5' C E 10 4778 4780 4798 C5' T E 11 4797 4799 4818 C5' T E 12 4817 4819 4838 C5' G E 13 4837 4839 4860 C5' C E 14 4859 4861 4879 C5' C E 15 4878 4880 4898 C5' C E 16 4897 4899 4917 C5' A E 17 4916 4918 4938 C5' A E 18 4937 4939 4959 C5' T E 19 4958 4960 4979 C5' T E 20 4978 4980 4999 C5' A E 21 4998 5000 5039 C5' T F 2 5038 5040 5059 C5' A F 3 5058 5060 5080 C5' A F 4 5079 5081 5101 C5' T F 5 5100 5102 5121 C5' T F 6 5120 5122 5141 C5' G F 7 5140 5142 5163 C5' G F 8 5162 5164 5185 C5' G F 9 5184 5186 5207 C5' C F 10 5206 5208 5226 C5' A F 11 5225 5227 5247 C5' A F 12 5246 5248 5268 C5' G F 13 5267 5269 5290 C5' T F 14 5289 5291 5310 C5' C F 15 5309 5311 5329 C5' T F 16 5328 5330 5349 C5' A F 17 5348 5350 5370 C5' G F 18 5369 5371 5392 C5' G F 19 5391 5393 5414 C5' A F 20 5413 5415 5435 C5' A F 21 5434 5436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4633 P T E 3 OK OK 4621 4634 4635 4636 4653 P C E 4 OK OK 4641 4654 4655 4656 4672 P C E 5 distorted distorted 4661 4673 4674 4675 4691 P T E 6 OK OK 4680 4692 4693 4694 4711 P A E 7 OK OK 4699 4712 4713 4714 4732 P G E 8 OK OK 4719 4733 4734 4735 4754 P A E 9 OK OK 4740 4755 4756 4757 4775 P C E 10 OK OK 4762 4776 4777 4778 4794 P T E 11 OK OK 4783 4795 4796 4797 4814 P T E 12 OK OK 4802 4815 4816 4817 4834 P G E 13 OK OK 4822 4835 4836 4837 4856 P C E 14 OK OK 4842 4857 4858 4859 4875 P C E 15 OK OK 4864 4876 4877 4878 4894 P C E 16 OK OK 4883 4895 4896 4897 4913 P A E 17 OK OK 4902 4914 4915 4916 4934 P A E 18 OK OK 4921 4935 4936 4937 4955 P T E 19 OK OK 4942 4956 4957 4958 4975 P T E 20 OK OK 4963 4976 4977 4978 4995 P A E 21 OK OK 4983 4996 4997 4998 5055 P A F 3 OK OK 5043 5056 5057 5058 5076 P A F 4 OK OK 5063 5077 5078 5079 5097 P T F 5 OK OK 5084 5098 5099 5100 5117 P T F 6 OK OK 5105 5118 5119 5120 5137 P G F 7 OK OK 5125 5138 5139 5140 5159 P G F 8 OK OK 5145 5160 5161 5162 5181 P G F 9 OK OK 5167 5182 5183 5184 5203 P C F 10 OK OK 5189 5204 5205 5206 5222 P A F 11 OK OK 5211 5223 5224 5225 5243 P A F 12 OK OK 5230 5244 5245 5246 5264 P G F 13 OK OK 5251 5265 5266 5267 5286 P T F 14 OK OK 5272 5287 5288 5289 5306 P C F 15 OK OK 5294 5307 5308 5309 5325 P T F 16 OK OK 5314 5326 5327 5328 5345 P A F 17 OK OK 5333 5346 5347 5348 5366 P G F 18 OK OK 5353 5367 5368 5369 5388 P G F 19 OK OK 5374 5389 5390 5391 5410 P A F 20 OK OK 5396 5411 5412 5413 5431 P A F 21 OK OK 5418 5432 5433 5434 ---------------------------------------------------------------------------------