ID code: '4QIL' 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' --------------------------------------------------------------------------------- 4711 C1' U D 2 beta 4706 4712 4709 4731 C1' C D 3 beta 4726 4732 4729 4751 C1' C D 4 beta 4746 4752 4749 4771 C1' C D 5 beta 4766 4772 4769 4791 C1' U D 6 beta 4786 4792 4789 4811 C1' U D 7 beta 4806 4812 4809 4831 C1' C D 8 beta 4826 4832 4829 4851 C1' U D 9 beta 4846 4852 4849 4871 C1' G D 10 beta 4866 4872 4869 4894 C1' U D 11 beta 4889 4895 4892 4914 C1' G D 12 beta 4909 4915 4912 4937 C1' A D 13 beta 4932 4938 4935 4959 C1' A D 14 beta 4954 4960 4957 4981 C1' G D 15 beta 4976 4982 4979 5004 C1' G D 16 beta 4999 5005 5002 5027 C1' G D 17 beta 5022 5028 5025 5051 C1' U C 2 beta 5046 5052 5049 5071 C1' C C 3 beta 5066 5072 5069 5091 C1' C C 4 beta 5086 5092 5089 5111 C1' C C 5 beta 5106 5112 5109 5131 C1' U C 6 beta 5126 5132 5129 5151 C1' U C 7 beta 5146 5152 5149 5171 C1' C C 8 beta 5166 5172 5169 5191 C1' U C 9 beta 5186 5192 5189 5211 C1' G C 10 beta 5206 5212 5209 5234 C1' U C 11 beta 5229 5235 5232 5254 C1' G C 12 beta 5249 5255 5252 5277 C1' A C 13 beta 5272 5278 5275 5299 C1' A C 14 beta 5294 5300 5297 5321 C1' G C 15 beta 5316 5322 5319 5344 C1' G C 16 beta 5339 5345 5342 5367 C1' G C 17 beta 5362 5368 5365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4709 C2' U D 2 OK 4711 4707 4710 4729 C2' C D 3 OK 4731 4727 4730 4749 C2' C D 4 OK 4751 4747 4750 4769 C2' C D 5 OK 4771 4767 4770 4789 C2' U D 6 OK 4791 4787 4790 4809 C2' U D 7 OK 4811 4807 4810 4829 C2' C D 8 OK 4831 4827 4830 4849 C2' U D 9 OK 4851 4847 4850 4869 C2' G D 10 OK 4871 4867 4870 4892 C2' U D 11 OK 4894 4890 4893 4912 C2' G D 12 OK 4914 4910 4913 4935 C2' A D 13 OK 4937 4933 4936 4957 C2' A D 14 OK 4959 4955 4958 4979 C2' G D 15 OK 4981 4977 4980 5002 C2' G D 16 OK 5004 5000 5003 5025 C2' G D 17 OK 5027 5023 5026 5049 C2' U C 2 OK 5051 5047 5050 5069 C2' C C 3 OK 5071 5067 5070 5089 C2' C C 4 OK 5091 5087 5090 5109 C2' C C 5 OK 5111 5107 5110 5129 C2' U C 6 OK 5131 5127 5130 5149 C2' U C 7 OK 5151 5147 5150 5169 C2' C C 8 OK 5171 5167 5170 5189 C2' U C 9 OK 5191 5187 5190 5209 C2' G C 10 OK 5211 5207 5210 5232 C2' U C 11 OK 5234 5230 5233 5252 C2' G C 12 OK 5254 5250 5253 5275 C2' A C 13 OK 5277 5273 5276 5297 C2' A C 14 OK 5299 5295 5298 5319 C2' G C 15 OK 5321 5317 5320 5342 C2' G C 16 OK 5344 5340 5343 5365 C2' G C 17 OK 5367 5363 5366 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4707 C3' U D 2 OK 4705 4708 4709 4727 C3' C D 3 OK 4725 4728 4729 4747 C3' C D 4 OK 4745 4748 4749 4767 C3' C D 5 OK 4765 4768 4769 4787 C3' U D 6 OK 4785 4788 4789 4807 C3' U D 7 OK 4805 4808 4809 4827 C3' C D 8 OK 4825 4828 4829 4847 C3' U D 9 OK 4845 4848 4849 4867 C3' G D 10 OK 4865 4868 4869 4890 C3' U D 11 OK 4888 4891 4892 4910 C3' G D 12 OK 4908 4911 4912 4933 C3' A D 13 OK 4931 4934 4935 4955 C3' A D 14 OK 4953 4956 4957 4977 C3' G D 15 OK 4975 4978 4979 5000 C3' G D 16 OK 4998 5001 5002 5023 C3' G D 17 OK 5021 5024 5025 5047 C3' U C 2 OK 5045 5048 5049 5067 C3' C C 3 OK 5065 5068 5069 5087 C3' C C 4 OK 5085 5088 5089 5107 C3' C C 5 OK 5105 5108 5109 5127 C3' U C 6 OK 5125 5128 5129 5147 C3' U C 7 OK 5145 5148 5149 5167 C3' C C 8 OK 5165 5168 5169 5187 C3' U C 9 OK 5185 5188 5189 5207 C3' G C 10 OK 5205 5208 5209 5230 C3' U C 11 OK 5228 5231 5232 5250 C3' G C 12 OK 5248 5251 5252 5273 C3' A C 13 OK 5271 5274 5275 5295 C3' A C 14 OK 5293 5296 5297 5317 C3' G C 15 OK 5315 5318 5319 5340 C3' G C 16 OK 5338 5341 5342 5363 C3' G C 17 OK 5361 5364 5365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4705 C4' U D 2 OK 4707 4704 4706 4725 C4' C D 3 OK 4727 4724 4726 4745 C4' C D 4 OK 4747 4744 4746 4765 C4' C D 5 OK 4767 4764 4766 4785 C4' U D 6 OK 4787 4784 4786 4805 C4' U D 7 OK 4807 4804 4806 4825 C4' C D 8 OK 4827 4824 4826 4845 C4' U D 9 OK 4847 4844 4846 4865 C4' G D 10 OK 4867 4864 4866 4888 C4' U D 11 OK 4890 4887 4889 4908 C4' G D 12 OK 4910 4907 4909 4931 C4' A D 13 OK 4933 4930 4932 4953 C4' A D 14 OK 4955 4952 4954 4975 C4' G D 15 OK 4977 4974 4976 4998 C4' G D 16 OK 5000 4997 4999 5021 C4' G D 17 OK 5023 5020 5022 5045 C4' U C 2 OK 5047 5044 5046 5065 C4' C C 3 OK 5067 5064 5066 5085 C4' C C 4 OK 5087 5084 5086 5105 C4' C C 5 OK 5107 5104 5106 5125 C4' U C 6 OK 5127 5124 5126 5145 C4' U C 7 OK 5147 5144 5146 5165 C4' C C 8 OK 5167 5164 5166 5185 C4' U C 9 OK 5187 5184 5186 5205 C4' G C 10 OK 5207 5204 5206 5228 C4' U C 11 OK 5230 5227 5229 5248 C4' G C 12 OK 5250 5247 5249 5271 C4' A C 13 OK 5273 5270 5272 5293 C4' A C 14 OK 5295 5292 5294 5315 C4' G C 15 OK 5317 5314 5316 5338 C4' G C 16 OK 5340 5337 5339 5361 C4' G C 17 OK 5363 5360 5362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4704 C5' U D 2 4703 4705 4724 C5' C D 3 4723 4725 4744 C5' C D 4 4743 4745 4764 C5' C D 5 4763 4765 4784 C5' U D 6 4783 4785 4804 C5' U D 7 4803 4805 4824 C5' C D 8 4823 4825 4844 C5' U D 9 4843 4845 4864 C5' G D 10 4863 4865 4887 C5' U D 11 4886 4888 4907 C5' G D 12 4906 4908 4930 C5' A D 13 4929 4931 4952 C5' A D 14 4951 4953 4974 C5' G D 15 4973 4975 4997 C5' G D 16 4996 4998 5020 C5' G D 17 5019 5021 5044 C5' U C 2 5043 5045 5064 C5' C C 3 5063 5065 5084 C5' C C 4 5083 5085 5104 C5' C C 5 5103 5105 5124 C5' U C 6 5123 5125 5144 C5' U C 7 5143 5145 5164 C5' C C 8 5163 5165 5184 C5' U C 9 5183 5185 5204 C5' G C 10 5203 5205 5227 C5' U C 11 5226 5228 5247 C5' G C 12 5246 5248 5270 C5' A C 13 5269 5271 5292 C5' A C 14 5291 5293 5314 C5' G C 15 5313 5315 5337 C5' G C 16 5336 5338 5360 C5' G C 17 5359 5361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4700 P U D 2 distorted distorted 4701 4702 4703 4720 P C D 3 distorted distorted 4708 4721 4722 4723 4740 P C D 4 distorted distorted 4728 4741 4742 4743 4760 P C D 5 distorted distorted 4748 4761 4762 4763 4780 P U D 6 distorted distorted 4768 4781 4782 4783 4800 P U D 7 distorted distorted 4788 4801 4802 4803 4820 P C D 8 distorted distorted 4808 4821 4822 4823 4840 P U D 9 distorted distorted 4828 4841 4842 4843 4860 P G D 10 distorted distorted 4848 4861 4862 4863 4883 P U D 11 distorted distorted 4868 4884 4885 4886 4903 P G D 12 distorted distorted 4891 4904 4905 4906 4926 P A D 13 distorted distorted 4911 4927 4928 4929 4948 P A D 14 distorted distorted 4934 4949 4950 4951 4970 P G D 15 distorted distorted 4956 4971 4972 4973 4993 P G D 16 distorted distorted 4978 4994 4995 4996 5016 P G D 17 distorted distorted 5001 5017 5018 5019 5040 P U C 2 distorted distorted 5041 5042 5043 5060 P C C 3 distorted distorted 5048 5061 5062 5063 5080 P C C 4 distorted distorted 5068 5081 5082 5083 5100 P C C 5 distorted distorted 5088 5101 5102 5103 5120 P U C 6 distorted distorted 5108 5121 5122 5123 5140 P U C 7 distorted distorted 5128 5141 5142 5143 5160 P C C 8 distorted distorted 5148 5161 5162 5163 5180 P U C 9 distorted distorted 5168 5181 5182 5183 5200 P G C 10 distorted distorted 5188 5201 5202 5203 5223 P U C 11 distorted distorted 5208 5224 5225 5226 5243 P G C 12 distorted distorted 5231 5244 5245 5246 5266 P A C 13 distorted distorted 5251 5267 5268 5269 5288 P A C 14 distorted distorted 5274 5289 5290 5291 5310 P G C 15 distorted distorted 5296 5311 5312 5313 5333 P G C 16 distorted distorted 5318 5334 5335 5336 5356 P G C 17 distorted distorted 5341 5357 5358 5359 ---------------------------------------------------------------------------------