ID code: '2W2H' 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' --------------------------------------------------------------------------------- 4666 C1' G R 3 beta 4661 4667 4664 4689 C1' C R 4 beta 4684 4690 4687 4709 C1' U R 5 beta 4704 4710 4707 4729 C1' C R 6 beta 4724 4730 4727 4749 C1' A R 7 beta 4744 4750 4747 4771 C1' G R 8 beta 4766 4772 4769 4794 C1' A R 9 beta 4789 4795 4792 4816 C1' U R 10 beta 4811 4817 4814 4836 C1' U R 11 beta 4831 4837 4834 4856 C1' C R 12 beta 4851 4857 4854 4876 C1' U R 13 beta 4871 4877 4874 4896 C1' G R 14 beta 4891 4897 4894 4919 C1' C R 15 beta 4914 4920 4917 4939 C1' G R 16 beta 4934 4940 4937 4962 C1' G R 17 beta 4957 4963 4960 4985 C1' U R 18 beta 4980 4986 4983 5005 C1' C R 19 beta 5000 5006 5003 5025 C1' U R 20 beta 5020 5026 5023 5045 C1' G R 21 beta 5040 5046 5043 5068 C1' A R 22 beta 5063 5069 5066 5090 C1' G R 23 beta 5085 5091 5088 5113 C1' C R 24 beta 5108 5114 5111 5135 C1' G S 3 beta 5130 5136 5133 5158 C1' C S 4 beta 5153 5159 5156 5178 C1' U S 5 beta 5173 5179 5176 5198 C1' C S 6 beta 5193 5199 5196 5218 C1' A S 7 beta 5213 5219 5216 5240 C1' G S 8 beta 5235 5241 5238 5263 C1' A S 9 beta 5258 5264 5261 5285 C1' U S 10 beta 5280 5286 5283 5305 C1' U S 11 beta 5300 5306 5303 5325 C1' C S 12 beta 5320 5326 5323 5345 C1' U S 13 beta 5340 5346 5343 5365 C1' G S 14 beta 5360 5366 5363 5388 C1' C S 15 beta 5383 5389 5386 5408 C1' G S 16 beta 5403 5409 5406 5431 C1' G S 17 beta 5426 5432 5429 5454 C1' U S 18 beta 5449 5455 5452 5474 C1' C S 19 beta 5469 5475 5472 5494 C1' U S 20 beta 5489 5495 5492 5514 C1' G S 21 beta 5509 5515 5512 5537 C1' A S 22 beta 5532 5538 5535 5559 C1' G S 23 beta 5554 5560 5557 5582 C1' C S 24 beta 5577 5583 5580 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4664 C2' G R 3 OK 4666 4662 4665 4687 C2' C R 4 OK 4689 4685 4688 4707 C2' U R 5 OK 4709 4705 4708 4727 C2' C R 6 OK 4729 4725 4728 4747 C2' A R 7 OK 4749 4745 4748 4769 C2' G R 8 OK 4771 4767 4770 4792 C2' A R 9 OK 4794 4790 4793 4814 C2' U R 10 OK 4816 4812 4815 4834 C2' U R 11 OK 4836 4832 4835 4854 C2' C R 12 OK 4856 4852 4855 4874 C2' U R 13 OK 4876 4872 4875 4894 C2' G R 14 OK 4896 4892 4895 4917 C2' C R 15 OK 4919 4915 4918 4937 C2' G R 16 OK 4939 4935 4938 4960 C2' G R 17 OK 4962 4958 4961 4983 C2' U R 18 OK 4985 4981 4984 5003 C2' C R 19 OK 5005 5001 5004 5023 C2' U R 20 OK 5025 5021 5024 5043 C2' G R 21 OK 5045 5041 5044 5066 C2' A R 22 OK 5068 5064 5067 5088 C2' G R 23 OK 5090 5086 5089 5111 C2' C R 24 OK 5113 5109 5112 5133 C2' G S 3 OK 5135 5131 5134 5156 C2' C S 4 OK 5158 5154 5157 5176 C2' U S 5 OK 5178 5174 5177 5196 C2' C S 6 OK 5198 5194 5197 5216 C2' A S 7 OK 5218 5214 5217 5238 C2' G S 8 OK 5240 5236 5239 5261 C2' A S 9 OK 5263 5259 5262 5283 C2' U S 10 OK 5285 5281 5284 5303 C2' U S 11 OK 5305 5301 5304 5323 C2' C S 12 OK 5325 5321 5324 5343 C2' U S 13 OK 5345 5341 5344 5363 C2' G S 14 OK 5365 5361 5364 5386 C2' C S 15 OK 5388 5384 5387 5406 C2' G S 16 OK 5408 5404 5407 5429 C2' G S 17 OK 5431 5427 5430 5452 C2' U S 18 OK 5454 5450 5453 5472 C2' C S 19 OK 5474 5470 5473 5492 C2' U S 20 OK 5494 5490 5493 5512 C2' G S 21 OK 5514 5510 5513 5535 C2' A S 22 OK 5537 5533 5536 5557 C2' G S 23 OK 5559 5555 5558 5580 C2' C S 24 OK 5582 5578 5581 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4662 C3' G R 3 OK 4660 4663 4664 4685 C3' C R 4 OK 4683 4686 4687 4705 C3' U R 5 OK 4703 4706 4707 4725 C3' C R 6 OK 4723 4726 4727 4745 C3' A R 7 OK 4743 4746 4747 4767 C3' G R 8 OK 4765 4768 4769 4790 C3' A R 9 OK 4788 4791 4792 4812 C3' U R 10 OK 4810 4813 4814 4832 C3' U R 11 OK 4830 4833 4834 4852 C3' C R 12 OK 4850 4853 4854 4872 C3' U R 13 OK 4870 4873 4874 4892 C3' G R 14 OK 4890 4893 4894 4915 C3' C R 15 OK 4913 4916 4917 4935 C3' G R 16 OK 4933 4936 4937 4958 C3' G R 17 OK 4956 4959 4960 4981 C3' U R 18 OK 4979 4982 4983 5001 C3' C R 19 OK 4999 5002 5003 5021 C3' U R 20 OK 5019 5022 5023 5041 C3' G R 21 OK 5039 5042 5043 5064 C3' A R 22 OK 5062 5065 5066 5086 C3' G R 23 OK 5084 5087 5088 5109 C3' C R 24 OK 5107 5110 5111 5131 C3' G S 3 OK 5129 5132 5133 5154 C3' C S 4 OK 5152 5155 5156 5174 C3' U S 5 OK 5172 5175 5176 5194 C3' C S 6 OK 5192 5195 5196 5214 C3' A S 7 OK 5212 5215 5216 5236 C3' G S 8 OK 5234 5237 5238 5259 C3' A S 9 OK 5257 5260 5261 5281 C3' U S 10 OK 5279 5282 5283 5301 C3' U S 11 OK 5299 5302 5303 5321 C3' C S 12 OK 5319 5322 5323 5341 C3' U S 13 OK 5339 5342 5343 5361 C3' G S 14 OK 5359 5362 5363 5384 C3' C S 15 OK 5382 5385 5386 5404 C3' G S 16 OK 5402 5405 5406 5427 C3' G S 17 OK 5425 5428 5429 5450 C3' U S 18 OK 5448 5451 5452 5470 C3' C S 19 OK 5468 5471 5472 5490 C3' U S 20 OK 5488 5491 5492 5510 C3' G S 21 OK 5508 5511 5512 5533 C3' A S 22 OK 5531 5534 5535 5555 C3' G S 23 OK 5553 5556 5557 5578 C3' C S 24 OK 5576 5579 5580 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4660 C4' G R 3 OK 4662 4659 4661 4683 C4' C R 4 OK 4685 4682 4684 4703 C4' U R 5 OK 4705 4702 4704 4723 C4' C R 6 OK 4725 4722 4724 4743 C4' A R 7 OK 4745 4742 4744 4765 C4' G R 8 OK 4767 4764 4766 4788 C4' A R 9 OK 4790 4787 4789 4810 C4' U R 10 OK 4812 4809 4811 4830 C4' U R 11 OK 4832 4829 4831 4850 C4' C R 12 OK 4852 4849 4851 4870 C4' U R 13 OK 4872 4869 4871 4890 C4' G R 14 OK 4892 4889 4891 4913 C4' C R 15 OK 4915 4912 4914 4933 C4' G R 16 OK 4935 4932 4934 4956 C4' G R 17 OK 4958 4955 4957 4979 C4' U R 18 OK 4981 4978 4980 4999 C4' C R 19 OK 5001 4998 5000 5019 C4' U R 20 OK 5021 5018 5020 5039 C4' G R 21 OK 5041 5038 5040 5062 C4' A R 22 OK 5064 5061 5063 5084 C4' G R 23 OK 5086 5083 5085 5107 C4' C R 24 OK 5109 5106 5108 5129 C4' G S 3 OK 5131 5128 5130 5152 C4' C S 4 OK 5154 5151 5153 5172 C4' U S 5 OK 5174 5171 5173 5192 C4' C S 6 OK 5194 5191 5193 5212 C4' A S 7 OK 5214 5211 5213 5234 C4' G S 8 OK 5236 5233 5235 5257 C4' A S 9 OK 5259 5256 5258 5279 C4' U S 10 OK 5281 5278 5280 5299 C4' U S 11 OK 5301 5298 5300 5319 C4' C S 12 OK 5321 5318 5320 5339 C4' U S 13 OK 5341 5338 5340 5359 C4' G S 14 OK 5361 5358 5360 5382 C4' C S 15 OK 5384 5381 5383 5402 C4' G S 16 OK 5404 5401 5403 5425 C4' G S 17 OK 5427 5424 5426 5448 C4' U S 18 OK 5450 5447 5449 5468 C4' C S 19 OK 5470 5467 5469 5488 C4' U S 20 OK 5490 5487 5489 5508 C4' G S 21 OK 5510 5507 5509 5531 C4' A S 22 OK 5533 5530 5532 5553 C4' G S 23 OK 5555 5552 5554 5576 C4' C S 24 OK 5578 5575 5577 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4659 C5' G R 3 4658 4660 4682 C5' C R 4 4681 4683 4702 C5' U R 5 4701 4703 4722 C5' C R 6 4721 4723 4742 C5' A R 7 4741 4743 4764 C5' G R 8 4763 4765 4787 C5' A R 9 4786 4788 4809 C5' U R 10 4808 4810 4829 C5' U R 11 4828 4830 4849 C5' C R 12 4848 4850 4869 C5' U R 13 4868 4870 4889 C5' G R 14 4888 4890 4912 C5' C R 15 4911 4913 4932 C5' G R 16 4931 4933 4955 C5' G R 17 4954 4956 4978 C5' U R 18 4977 4979 4998 C5' C R 19 4997 4999 5018 C5' U R 20 5017 5019 5038 C5' G R 21 5037 5039 5061 C5' A R 22 5060 5062 5083 C5' G R 23 5082 5084 5106 C5' C R 24 5105 5107 5128 C5' G S 3 5127 5129 5151 C5' C S 4 5150 5152 5171 C5' U S 5 5170 5172 5191 C5' C S 6 5190 5192 5211 C5' A S 7 5210 5212 5233 C5' G S 8 5232 5234 5256 C5' A S 9 5255 5257 5278 C5' U S 10 5277 5279 5298 C5' U S 11 5297 5299 5318 C5' C S 12 5317 5319 5338 C5' U S 13 5337 5339 5358 C5' G S 14 5357 5359 5381 C5' C S 15 5380 5382 5401 C5' G S 16 5400 5402 5424 C5' G S 17 5423 5425 5447 C5' U S 18 5446 5448 5467 C5' C S 19 5466 5468 5487 C5' U S 20 5486 5488 5507 C5' G S 21 5506 5508 5530 C5' A S 22 5529 5531 5552 C5' G S 23 5551 5553 5575 C5' C S 24 5574 5576 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4655 P G R 3 distorted distorted 4656 4657 4658 4678 P C R 4 distorted distorted 4663 4679 4680 4681 4698 P U R 5 distorted distorted 4686 4699 4700 4701 4718 P C R 6 distorted distorted 4706 4719 4720 4721 4738 P A R 7 distorted distorted 4726 4739 4740 4741 4760 P G R 8 distorted distorted 4746 4761 4762 4763 4783 P A R 9 distorted distorted 4768 4784 4785 4786 4805 P U R 10 distorted distorted 4791 4806 4807 4808 4825 P U R 11 distorted distorted 4813 4826 4827 4828 4845 P C R 12 distorted distorted 4833 4846 4847 4848 4865 P U R 13 distorted distorted 4853 4866 4867 4868 4885 P G R 14 distorted distorted 4873 4886 4887 4888 4908 P C R 15 distorted distorted 4893 4909 4910 4911 4928 P G R 16 OK OK 4916 4929 4930 4931 4951 P G R 17 distorted distorted 4936 4952 4953 4954 4974 P U R 18 distorted distorted 4959 4975 4976 4977 4994 P C R 19 distorted distorted 4982 4995 4996 4997 5014 P U R 20 distorted distorted 5002 5015 5016 5017 5034 P G R 21 distorted distorted 5022 5035 5036 5037 5057 P A R 22 OK OK 5042 5058 5059 5060 5079 P G R 23 distorted distorted 5065 5080 5081 5082 5102 P C R 24 distorted distorted 5087 5103 5104 5105 5124 P G S 3 distorted distorted 5125 5126 5127 5147 P C S 4 distorted distorted 5132 5148 5149 5150 5167 P U S 5 distorted distorted 5155 5168 5169 5170 5187 P C S 6 distorted distorted 5175 5188 5189 5190 5207 P A S 7 distorted distorted 5195 5208 5209 5210 5229 P G S 8 distorted distorted 5215 5230 5231 5232 5252 P A S 9 distorted distorted 5237 5253 5254 5255 5274 P U S 10 distorted distorted 5260 5275 5276 5277 5294 P U S 11 distorted distorted 5282 5295 5296 5297 5314 P C S 12 distorted distorted 5302 5315 5316 5317 5334 P U S 13 distorted distorted 5322 5335 5336 5337 5354 P G S 14 distorted distorted 5342 5355 5356 5357 5377 P C S 15 distorted distorted 5362 5378 5379 5380 5397 P G S 16 OK OK 5385 5398 5399 5400 5420 P G S 17 distorted distorted 5405 5421 5422 5423 5443 P U S 18 distorted distorted 5428 5444 5445 5446 5463 P C S 19 distorted distorted 5451 5464 5465 5466 5483 P U S 20 distorted distorted 5471 5484 5485 5486 5503 P G S 21 distorted distorted 5491 5504 5505 5506 5526 P A S 22 OK OK 5511 5527 5528 5529 5548 P G S 23 distorted distorted 5534 5549 5550 5551 5571 P C S 24 distorted distorted 5556 5572 5573 5574 ---------------------------------------------------------------------------------