ID code: '5CRX' 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' --------------------------------------------------------------------------------- 4730 C1' T C 3 beta 4726 4731 4729 4750 C1' A C 4 beta 4746 4751 4749 4771 C1' A C 5 beta 4767 4772 4770 4792 C1' C C 6 beta 4788 4793 4791 4811 C1' T C 7 beta 4807 4812 4810 4831 C1' T C 8 beta 4827 4832 4830 4851 C1' C C 9 beta 4847 4852 4850 4870 C1' G C 10 beta 4866 4871 4869 4892 C1' T C 11 beta 4888 4893 4891 4912 C1' A C 12 beta 4908 4913 4911 4933 C1' T C 13 beta 4929 4934 4932 4953 C1' A C 14 beta 4949 4954 4952 4974 C1' G C 15 beta 4970 4975 4973 4996 C1' C C 16 beta 4992 4997 4995 5015 C1' A C 17 beta 5011 5016 5014 5036 C1' T C 18 beta 5032 5037 5035 5056 C1' A C 19 beta 5052 5057 5055 5077 C1' T C 20 beta 5073 5078 5076 5097 C1' G C 21 beta 5093 5098 5096 5119 C1' C C 22 beta 5115 5120 5118 5138 C1' T C 23 beta 5134 5139 5137 5158 C1' A C 24 beta 5154 5159 5157 5179 C1' T C 25 beta 5175 5180 5178 5199 C1' A C 26 beta 5195 5200 5198 5220 C1' C C 27 beta 5216 5221 5219 5239 C1' G C 28 beta 5235 5240 5238 5261 C1' A C 29 beta 5257 5262 5260 5282 C1' A C 30 beta 5278 5283 5281 5303 C1' G C 31 beta 5299 5304 5302 5325 C1' T C 32 beta 5321 5326 5324 5345 C1' T C 33 beta 5341 5346 5344 5365 C1' A C 34 beta 5361 5366 5364 5408 C1' T D 3 beta 5404 5409 5407 5428 C1' A D 4 beta 5424 5429 5427 5449 C1' A D 5 beta 5445 5450 5448 5470 C1' C D 6 beta 5466 5471 5469 5489 C1' T D 7 beta 5485 5490 5488 5509 C1' T D 8 beta 5505 5510 5508 5529 C1' C D 9 beta 5525 5530 5528 5548 C1' G D 10 beta 5544 5549 5547 5570 C1' T D 11 beta 5566 5571 5569 5590 C1' A D 12 beta 5586 5591 5589 5611 C1' T D 13 beta 5607 5612 5610 5631 C1' A D 14 beta 5627 5632 5630 5652 C1' G D 15 beta 5648 5653 5651 5674 C1' C D 16 beta 5670 5675 5673 5693 C1' A D 17 beta 5689 5694 5692 5714 C1' T D 18 beta 5710 5715 5713 5734 C1' A D 19 beta 5730 5735 5733 5755 C1' T D 20 beta 5751 5756 5754 5775 C1' G D 21 beta 5771 5776 5774 5797 C1' C D 22 beta 5793 5798 5796 5816 C1' T D 23 beta 5812 5817 5815 5836 C1' A D 24 beta 5832 5837 5835 5857 C1' T D 25 beta 5853 5858 5856 5877 C1' A D 26 beta 5873 5878 5876 5898 C1' C D 27 beta 5894 5899 5897 5917 C1' G D 28 beta 5913 5918 5916 5939 C1' A D 29 beta 5935 5940 5938 5960 C1' A D 30 beta 5956 5961 5959 5981 C1' G D 31 beta 5977 5982 5980 6003 C1' T D 32 beta 5999 6004 6002 6023 C1' T D 33 beta 6019 6024 6022 6043 C1' A D 34 beta 6039 6044 6042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4729 C2' T C 3 4730 4727 4749 C2' A C 4 4750 4747 4770 C2' A C 5 4771 4768 4791 C2' C C 6 4792 4789 4810 C2' T C 7 4811 4808 4830 C2' T C 8 4831 4828 4850 C2' C C 9 4851 4848 4869 C2' G C 10 4870 4867 4891 C2' T C 11 4892 4889 4911 C2' A C 12 4912 4909 4932 C2' T C 13 4933 4930 4952 C2' A C 14 4953 4950 4973 C2' G C 15 4974 4971 4995 C2' C C 16 4996 4993 5014 C2' A C 17 5015 5012 5035 C2' T C 18 5036 5033 5055 C2' A C 19 5056 5053 5076 C2' T C 20 5077 5074 5096 C2' G C 21 5097 5094 5118 C2' C C 22 5119 5116 5137 C2' T C 23 5138 5135 5157 C2' A C 24 5158 5155 5178 C2' T C 25 5179 5176 5198 C2' A C 26 5199 5196 5219 C2' C C 27 5220 5217 5238 C2' G C 28 5239 5236 5260 C2' A C 29 5261 5258 5281 C2' A C 30 5282 5279 5302 C2' G C 31 5303 5300 5324 C2' T C 32 5325 5322 5344 C2' T C 33 5345 5342 5364 C2' A C 34 5365 5362 5407 C2' T D 3 5408 5405 5427 C2' A D 4 5428 5425 5448 C2' A D 5 5449 5446 5469 C2' C D 6 5470 5467 5488 C2' T D 7 5489 5486 5508 C2' T D 8 5509 5506 5528 C2' C D 9 5529 5526 5547 C2' G D 10 5548 5545 5569 C2' T D 11 5570 5567 5589 C2' A D 12 5590 5587 5610 C2' T D 13 5611 5608 5630 C2' A D 14 5631 5628 5651 C2' G D 15 5652 5649 5673 C2' C D 16 5674 5671 5692 C2' A D 17 5693 5690 5713 C2' T D 18 5714 5711 5733 C2' A D 19 5734 5731 5754 C2' T D 20 5755 5752 5774 C2' G D 21 5775 5772 5796 C2' C D 22 5797 5794 5815 C2' T D 23 5816 5813 5835 C2' A D 24 5836 5833 5856 C2' T D 25 5857 5854 5876 C2' A D 26 5877 5874 5897 C2' C D 27 5898 5895 5916 C2' G D 28 5917 5914 5938 C2' A D 29 5939 5936 5959 C2' A D 30 5960 5957 5980 C2' G D 31 5981 5978 6002 C2' T D 32 6003 6000 6022 C2' T D 33 6023 6020 6042 C2' A D 34 6043 6040 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4727 C3' T C 3 OK 4725 4728 4729 4747 C3' A C 4 OK 4745 4748 4749 4768 C3' A C 5 OK 4766 4769 4770 4789 C3' C C 6 OK 4787 4790 4791 4808 C3' T C 7 OK 4806 4809 4810 4828 C3' T C 8 OK 4826 4829 4830 4848 C3' C C 9 OK 4846 4849 4850 4867 C3' G C 10 OK 4865 4868 4869 4889 C3' T C 11 OK 4887 4890 4891 4909 C3' A C 12 OK 4907 4910 4911 4930 C3' T C 13 OK 4928 4931 4932 4950 C3' A C 14 OK 4948 4951 4952 4971 C3' G C 15 OK 4969 4972 4973 4993 C3' C C 16 OK 4991 4994 4995 5012 C3' A C 17 OK 5010 5013 5014 5033 C3' T C 18 OK 5031 5034 5035 5053 C3' A C 19 OK 5051 5054 5055 5074 C3' T C 20 OK 5072 5075 5076 5094 C3' G C 21 OK 5092 5095 5096 5116 C3' C C 22 OK 5114 5117 5118 5135 C3' T C 23 OK 5133 5136 5137 5155 C3' A C 24 OK 5153 5156 5157 5176 C3' T C 25 OK 5174 5177 5178 5196 C3' A C 26 OK 5194 5197 5198 5217 C3' C C 27 OK 5215 5218 5219 5236 C3' G C 28 OK 5234 5237 5238 5258 C3' A C 29 OK 5256 5259 5260 5279 C3' A C 30 OK 5277 5280 5281 5300 C3' G C 31 OK 5298 5301 5302 5322 C3' T C 32 OK 5320 5323 5324 5342 C3' T C 33 OK 5340 5343 5344 5362 C3' A C 34 OK 5360 5363 5364 5405 C3' T D 3 OK 5403 5406 5407 5425 C3' A D 4 OK 5423 5426 5427 5446 C3' A D 5 OK 5444 5447 5448 5467 C3' C D 6 OK 5465 5468 5469 5486 C3' T D 7 OK 5484 5487 5488 5506 C3' T D 8 OK 5504 5507 5508 5526 C3' C D 9 OK 5524 5527 5528 5545 C3' G D 10 OK 5543 5546 5547 5567 C3' T D 11 OK 5565 5568 5569 5587 C3' A D 12 OK 5585 5588 5589 5608 C3' T D 13 OK 5606 5609 5610 5628 C3' A D 14 OK 5626 5629 5630 5649 C3' G D 15 OK 5647 5650 5651 5671 C3' C D 16 OK 5669 5672 5673 5690 C3' A D 17 OK 5688 5691 5692 5711 C3' T D 18 OK 5709 5712 5713 5731 C3' A D 19 OK 5729 5732 5733 5752 C3' T D 20 OK 5750 5753 5754 5772 C3' G D 21 OK 5770 5773 5774 5794 C3' C D 22 OK 5792 5795 5796 5813 C3' T D 23 OK 5811 5814 5815 5833 C3' A D 24 OK 5831 5834 5835 5854 C3' T D 25 OK 5852 5855 5856 5874 C3' A D 26 OK 5872 5875 5876 5895 C3' C D 27 OK 5893 5896 5897 5914 C3' G D 28 OK 5912 5915 5916 5936 C3' A D 29 OK 5934 5937 5938 5957 C3' A D 30 OK 5955 5958 5959 5978 C3' G D 31 OK 5976 5979 5980 6000 C3' T D 32 OK 5998 6001 6002 6020 C3' T D 33 OK 6018 6021 6022 6040 C3' A D 34 OK 6038 6041 6042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4725 C4' T C 3 OK 4727 4724 4726 4745 C4' A C 4 OK 4747 4744 4746 4766 C4' A C 5 OK 4768 4765 4767 4787 C4' C C 6 OK 4789 4786 4788 4806 C4' T C 7 OK 4808 4805 4807 4826 C4' T C 8 OK 4828 4825 4827 4846 C4' C C 9 OK 4848 4845 4847 4865 C4' G C 10 OK 4867 4864 4866 4887 C4' T C 11 OK 4889 4886 4888 4907 C4' A C 12 OK 4909 4906 4908 4928 C4' T C 13 OK 4930 4927 4929 4948 C4' A C 14 OK 4950 4947 4949 4969 C4' G C 15 OK 4971 4968 4970 4991 C4' C C 16 OK 4993 4990 4992 5010 C4' A C 17 OK 5012 5009 5011 5031 C4' T C 18 OK 5033 5030 5032 5051 C4' A C 19 OK 5053 5050 5052 5072 C4' T C 20 OK 5074 5071 5073 5092 C4' G C 21 OK 5094 5091 5093 5114 C4' C C 22 OK 5116 5113 5115 5133 C4' T C 23 OK 5135 5132 5134 5153 C4' A C 24 OK 5155 5152 5154 5174 C4' T C 25 OK 5176 5173 5175 5194 C4' A C 26 OK 5196 5193 5195 5215 C4' C C 27 OK 5217 5214 5216 5234 C4' G C 28 OK 5236 5233 5235 5256 C4' A C 29 OK 5258 5255 5257 5277 C4' A C 30 OK 5279 5276 5278 5298 C4' G C 31 OK 5300 5297 5299 5320 C4' T C 32 OK 5322 5319 5321 5340 C4' T C 33 OK 5342 5339 5341 5360 C4' A C 34 OK 5362 5359 5361 5403 C4' T D 3 OK 5405 5402 5404 5423 C4' A D 4 OK 5425 5422 5424 5444 C4' A D 5 OK 5446 5443 5445 5465 C4' C D 6 OK 5467 5464 5466 5484 C4' T D 7 OK 5486 5483 5485 5504 C4' T D 8 OK 5506 5503 5505 5524 C4' C D 9 OK 5526 5523 5525 5543 C4' G D 10 OK 5545 5542 5544 5565 C4' T D 11 OK 5567 5564 5566 5585 C4' A D 12 OK 5587 5584 5586 5606 C4' T D 13 OK 5608 5605 5607 5626 C4' A D 14 OK 5628 5625 5627 5647 C4' G D 15 OK 5649 5646 5648 5669 C4' C D 16 OK 5671 5668 5670 5688 C4' A D 17 OK 5690 5687 5689 5709 C4' T D 18 OK 5711 5708 5710 5729 C4' A D 19 OK 5731 5728 5730 5750 C4' T D 20 OK 5752 5749 5751 5770 C4' G D 21 OK 5772 5769 5771 5792 C4' C D 22 OK 5794 5791 5793 5811 C4' T D 23 OK 5813 5810 5812 5831 C4' A D 24 OK 5833 5830 5832 5852 C4' T D 25 OK 5854 5851 5853 5872 C4' A D 26 OK 5874 5871 5873 5893 C4' C D 27 OK 5895 5892 5894 5912 C4' G D 28 OK 5914 5911 5913 5934 C4' A D 29 OK 5936 5933 5935 5955 C4' A D 30 OK 5957 5954 5956 5976 C4' G D 31 OK 5978 5975 5977 5998 C4' T D 32 OK 6000 5997 5999 6018 C4' T D 33 OK 6020 6017 6019 6038 C4' A D 34 OK 6040 6037 6039 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4724 C5' T C 3 4723 4725 4744 C5' A C 4 4743 4745 4765 C5' A C 5 4764 4766 4786 C5' C C 6 4785 4787 4805 C5' T C 7 4804 4806 4825 C5' T C 8 4824 4826 4845 C5' C C 9 4844 4846 4864 C5' G C 10 4863 4865 4886 C5' T C 11 4885 4887 4906 C5' A C 12 4905 4907 4927 C5' T C 13 4926 4928 4947 C5' A C 14 4946 4948 4968 C5' G C 15 4967 4969 4990 C5' C C 16 4989 4991 5009 C5' A C 17 5008 5010 5030 C5' T C 18 5029 5031 5050 C5' A C 19 5049 5051 5071 C5' T C 20 5070 5072 5091 C5' G C 21 5090 5092 5113 C5' C C 22 5112 5114 5132 C5' T C 23 5131 5133 5152 C5' A C 24 5151 5153 5173 C5' T C 25 5172 5174 5193 C5' A C 26 5192 5194 5214 C5' C C 27 5213 5215 5233 C5' G C 28 5232 5234 5255 C5' A C 29 5254 5256 5276 C5' A C 30 5275 5277 5297 C5' G C 31 5296 5298 5319 C5' T C 32 5318 5320 5339 C5' T C 33 5338 5340 5359 C5' A C 34 5358 5360 5402 C5' T D 3 5401 5403 5422 C5' A D 4 5421 5423 5443 C5' A D 5 5442 5444 5464 C5' C D 6 5463 5465 5483 C5' T D 7 5482 5484 5503 C5' T D 8 5502 5504 5523 C5' C D 9 5522 5524 5542 C5' G D 10 5541 5543 5564 C5' T D 11 5563 5565 5584 C5' A D 12 5583 5585 5605 C5' T D 13 5604 5606 5625 C5' A D 14 5624 5626 5646 C5' G D 15 5645 5647 5668 C5' C D 16 5667 5669 5687 C5' A D 17 5686 5688 5708 C5' T D 18 5707 5709 5728 C5' A D 19 5727 5729 5749 C5' T D 20 5748 5750 5769 C5' G D 21 5768 5770 5791 C5' C D 22 5790 5792 5810 C5' T D 23 5809 5811 5830 C5' A D 24 5829 5831 5851 C5' T D 25 5850 5852 5871 C5' A D 26 5870 5872 5892 C5' C D 27 5891 5893 5911 C5' G D 28 5910 5912 5933 C5' A D 29 5932 5934 5954 C5' A D 30 5953 5955 5975 C5' G D 31 5974 5976 5997 C5' T D 32 5996 5998 6017 C5' T D 33 6016 6018 6037 C5' A D 34 6036 6038 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4740 P A C 4 distorted distorted 4728 4741 4742 4743 4761 P A C 5 distorted distorted 4748 4762 4763 4764 4782 P C C 6 distorted distorted 4769 4783 4784 4785 4801 P T C 7 distorted distorted 4790 4802 4803 4804 4821 P T C 8 distorted distorted 4809 4822 4823 4824 4841 P C C 9 distorted distorted 4829 4842 4843 4844 4860 P G C 10 distorted distorted 4849 4861 4862 4863 4882 P T C 11 distorted distorted 4868 4883 4884 4885 4902 P A C 12 distorted distorted 4890 4903 4904 4905 4923 P T C 13 distorted distorted 4910 4924 4925 4926 4943 P A C 14 distorted distorted 4931 4944 4945 4946 4964 P G C 15 distorted distorted 4951 4965 4966 4967 4986 P C C 16 distorted distorted 4972 4987 4988 4989 5005 P A C 17 distorted distorted 4994 5006 5007 5008 5026 P T C 18 distorted distorted 5013 5027 5028 5029 5046 P A C 19 distorted distorted 5034 5047 5048 5049 5067 P T C 20 distorted distorted 5054 5068 5069 5070 5087 P G C 21 distorted distorted 5075 5088 5089 5090 5109 P C C 22 distorted distorted 5095 5110 5111 5112 5128 P T C 23 distorted distorted 5117 5129 5130 5131 5148 P A C 24 distorted distorted 5136 5149 5150 5151 5169 P T C 25 distorted distorted 5156 5170 5171 5172 5189 P A C 26 distorted distorted 5177 5190 5191 5192 5210 P C C 27 distorted distorted 5197 5211 5212 5213 5229 P G C 28 distorted distorted 5218 5230 5231 5232 5251 P A C 29 distorted distorted 5237 5252 5253 5254 5272 P A C 30 distorted distorted 5259 5273 5274 5275 5293 P G C 31 distorted distorted 5280 5294 5295 5296 5315 P T C 32 distorted distorted 5301 5316 5317 5318 5335 P T C 33 distorted distorted 5323 5336 5337 5338 5355 P A C 34 distorted distorted 5343 5356 5357 5358 5418 P A D 4 distorted distorted 5406 5419 5420 5421 5439 P A D 5 distorted distorted 5426 5440 5441 5442 5460 P C D 6 distorted distorted 5447 5461 5462 5463 5479 P T D 7 distorted distorted 5468 5480 5481 5482 5499 P T D 8 distorted distorted 5487 5500 5501 5502 5519 P C D 9 distorted distorted 5507 5520 5521 5522 5538 P G D 10 distorted distorted 5527 5539 5540 5541 5560 P T D 11 distorted distorted 5546 5561 5562 5563 5580 P A D 12 distorted distorted 5568 5581 5582 5583 5601 P T D 13 distorted distorted 5588 5602 5603 5604 5621 P A D 14 distorted distorted 5609 5622 5623 5624 5642 P G D 15 distorted distorted 5629 5643 5644 5645 5664 P C D 16 distorted distorted 5650 5665 5666 5667 5683 P A D 17 distorted distorted 5672 5684 5685 5686 5704 P T D 18 distorted distorted 5691 5705 5706 5707 5724 P A D 19 distorted distorted 5712 5725 5726 5727 5745 P T D 20 distorted distorted 5732 5746 5747 5748 5765 P G D 21 distorted distorted 5753 5766 5767 5768 5787 P C D 22 distorted distorted 5773 5788 5789 5790 5806 P T D 23 distorted distorted 5795 5807 5808 5809 5826 P A D 24 distorted distorted 5814 5827 5828 5829 5847 P T D 25 distorted distorted 5834 5848 5849 5850 5867 P A D 26 distorted distorted 5855 5868 5869 5870 5888 P C D 27 distorted distorted 5875 5889 5890 5891 5907 P G D 28 distorted distorted 5896 5908 5909 5910 5929 P A D 29 distorted distorted 5915 5930 5931 5932 5950 P A D 30 distorted distorted 5937 5951 5952 5953 5971 P G D 31 distorted distorted 5958 5972 5973 5974 5993 P T D 32 distorted distorted 5979 5994 5995 5996 6013 P T D 33 distorted distorted 6001 6014 6015 6016 6033 P A D 34 distorted distorted 6021 6034 6035 6036 ---------------------------------------------------------------------------------