ID code: '3V6K' 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' --------------------------------------------------------------------------------- 5110 C1' DG P 5 beta 5106 5111 5109 5132 C1' DA P 6 beta 5128 5133 5131 5153 C1' DA P 7 beta 5149 5154 5152 5174 C1' DG P 8 beta 5170 5175 5173 5196 C1' DG P 9 beta 5192 5197 5195 5218 C1' DA P 10 beta 5214 5219 5217 5239 C1' DT P 11 beta 5235 5240 5238 5259 C1' DT P 12 beta 5255 5260 5258 5279 C1' DC P 13 beta 5275 5280 5278 5305 C1' 2DT P 14 beta 5304 5292 5301 5315 C1' DT B 1 beta 5311 5316 5314 5335 C1' DC B 2 beta 5331 5336 5334 5354 C1' DA B 3 beta 5350 5355 5353 5375 C1' DC B 4 beta 5371 5376 5374 5397 C1' EFG B 5 beta 5398 5396 5399 5419 C1' DG B 6 beta 5415 5420 5418 5441 C1' DA B 7 beta 5437 5442 5440 5462 C1' DA B 8 beta 5458 5463 5461 5483 C1' DT B 9 beta 5479 5484 5482 5503 C1' DC B 10 beta 5499 5504 5502 5522 C1' DC B 11 beta 5518 5523 5521 5541 C1' DT B 12 beta 5537 5542 5540 5561 C1' DT B 13 beta 5557 5562 5560 5581 C1' DC B 14 beta 5577 5582 5580 5601 C1' DG K 5 beta 5597 5602 5600 5623 C1' DA K 6 beta 5619 5624 5622 5644 C1' DA K 7 beta 5640 5645 5643 5665 C1' DG K 8 beta 5661 5666 5664 5687 C1' DG K 9 beta 5683 5688 5686 5709 C1' DA K 10 beta 5705 5710 5708 5730 C1' DT K 11 beta 5726 5731 5729 5750 C1' DT K 12 beta 5746 5751 5749 5770 C1' DC K 13 beta 5766 5771 5769 5796 C1' 2DT K 14 beta 5795 5783 5792 5806 C1' DC M 2 beta 5802 5807 5805 5825 C1' DA M 3 beta 5821 5826 5824 5846 C1' DC M 4 beta 5842 5847 5845 5868 C1' EFG M 5 beta 5869 5867 5870 5890 C1' DG M 6 beta 5886 5891 5889 5912 C1' DA M 7 beta 5908 5913 5911 5933 C1' DA M 8 beta 5929 5934 5932 5954 C1' DT M 9 beta 5950 5955 5953 5974 C1' DC M 10 beta 5970 5975 5973 5993 C1' DC M 11 beta 5989 5994 5992 6012 C1' DT M 12 beta 6008 6013 6011 6032 C1' DT M 13 beta 6028 6033 6031 6052 C1' DC M 14 beta 6048 6053 6051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5109 C2' DG P 5 5110 5107 5131 C2' DA P 6 5132 5129 5152 C2' DA P 7 5153 5150 5173 C2' DG P 8 5174 5171 5195 C2' DG P 9 5196 5193 5217 C2' DA P 10 5218 5215 5238 C2' DT P 11 5239 5236 5258 C2' DT P 12 5259 5256 5278 C2' DC P 13 5279 5276 5301 C2' 2DT P 14 5305 5306 5314 C2' DT B 1 5315 5312 5334 C2' DC B 2 5335 5332 5353 C2' DA B 3 5354 5351 5374 C2' DC B 4 5375 5372 5399 C2' EFG B 5 5397 5401 5418 C2' DG B 6 5419 5416 5440 C2' DA B 7 5441 5438 5461 C2' DA B 8 5462 5459 5482 C2' DT B 9 5483 5480 5502 C2' DC B 10 5503 5500 5521 C2' DC B 11 5522 5519 5540 C2' DT B 12 5541 5538 5560 C2' DT B 13 5561 5558 5580 C2' DC B 14 5581 5578 5600 C2' DG K 5 5601 5598 5622 C2' DA K 6 5623 5620 5643 C2' DA K 7 5644 5641 5664 C2' DG K 8 5665 5662 5686 C2' DG K 9 5687 5684 5708 C2' DA K 10 5709 5706 5729 C2' DT K 11 5730 5727 5749 C2' DT K 12 5750 5747 5769 C2' DC K 13 5770 5767 5792 C2' 2DT K 14 5796 5797 5805 C2' DC M 2 5806 5803 5824 C2' DA M 3 5825 5822 5845 C2' DC M 4 5846 5843 5870 C2' EFG M 5 5868 5872 5889 C2' DG M 6 5890 5887 5911 C2' DA M 7 5912 5909 5932 C2' DA M 8 5933 5930 5953 C2' DT M 9 5954 5951 5973 C2' DC M 10 5974 5971 5992 C2' DC M 11 5993 5990 6011 C2' DT M 12 6012 6009 6031 C2' DT M 13 6032 6029 6051 C2' DC M 14 6052 6049 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5107 C3' DG P 5 OK 5105 5108 5109 5129 C3' DA P 6 OK 5127 5130 5131 5150 C3' DA P 7 OK 5148 5151 5152 5171 C3' DG P 8 OK 5169 5172 5173 5193 C3' DG P 9 OK 5191 5194 5195 5215 C3' DA P 10 OK 5213 5216 5217 5236 C3' DT P 11 OK 5234 5237 5238 5256 C3' DT P 12 OK 5254 5257 5258 5276 C3' DC P 13 OK 5274 5277 5278 5306 C3' 2DT P 14 5303 5301 5312 C3' DT B 1 OK 5310 5313 5314 5332 C3' DC B 2 OK 5330 5333 5334 5351 C3' DA B 3 OK 5349 5352 5353 5372 C3' DC B 4 OK 5370 5373 5374 5401 C3' EFG B 5 OK 5403 5402 5399 5416 C3' DG B 6 OK 5414 5417 5418 5438 C3' DA B 7 OK 5436 5439 5440 5459 C3' DA B 8 OK 5457 5460 5461 5480 C3' DT B 9 OK 5478 5481 5482 5500 C3' DC B 10 OK 5498 5501 5502 5519 C3' DC B 11 OK 5517 5520 5521 5538 C3' DT B 12 OK 5536 5539 5540 5558 C3' DT B 13 OK 5556 5559 5560 5578 C3' DC B 14 OK 5576 5579 5580 5598 C3' DG K 5 OK 5596 5599 5600 5620 C3' DA K 6 OK 5618 5621 5622 5641 C3' DA K 7 OK 5639 5642 5643 5662 C3' DG K 8 OK 5660 5663 5664 5684 C3' DG K 9 OK 5682 5685 5686 5706 C3' DA K 10 OK 5704 5707 5708 5727 C3' DT K 11 OK 5725 5728 5729 5747 C3' DT K 12 OK 5745 5748 5749 5767 C3' DC K 13 OK 5765 5768 5769 5797 C3' 2DT K 14 5794 5792 5803 C3' DC M 2 OK 5801 5804 5805 5822 C3' DA M 3 OK 5820 5823 5824 5843 C3' DC M 4 OK 5841 5844 5845 5872 C3' EFG M 5 OK 5874 5873 5870 5887 C3' DG M 6 OK 5885 5888 5889 5909 C3' DA M 7 OK 5907 5910 5911 5930 C3' DA M 8 OK 5928 5931 5932 5951 C3' DT M 9 OK 5949 5952 5953 5971 C3' DC M 10 OK 5969 5972 5973 5990 C3' DC M 11 OK 5988 5991 5992 6009 C3' DT M 12 OK 6007 6010 6011 6029 C3' DT M 13 OK 6027 6030 6031 6049 C3' DC M 14 OK 6047 6050 6051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5105 C4' DG P 5 OK 5107 5104 5106 5127 C4' DA P 6 OK 5129 5126 5128 5148 C4' DA P 7 OK 5150 5147 5149 5169 C4' DG P 8 OK 5171 5168 5170 5191 C4' DG P 9 OK 5193 5190 5192 5213 C4' DA P 10 OK 5215 5212 5214 5234 C4' DT P 11 OK 5236 5233 5235 5254 C4' DT P 12 OK 5256 5253 5255 5274 C4' DC P 13 OK 5276 5273 5275 5303 C4' 2DT P 14 OK 5306 5302 5304 5310 C4' DT B 1 OK 5312 5309 5311 5330 C4' DC B 2 OK 5332 5329 5331 5349 C4' DA B 3 OK 5351 5348 5350 5370 C4' DC B 4 OK 5372 5369 5371 5403 C4' EFG B 5 OK 5401 5404 5398 5414 C4' DG B 6 OK 5416 5413 5415 5436 C4' DA B 7 OK 5438 5435 5437 5457 C4' DA B 8 OK 5459 5456 5458 5478 C4' DT B 9 OK 5480 5477 5479 5498 C4' DC B 10 OK 5500 5497 5499 5517 C4' DC B 11 OK 5519 5516 5518 5536 C4' DT B 12 OK 5538 5535 5537 5556 C4' DT B 13 OK 5558 5555 5557 5576 C4' DC B 14 OK 5578 5575 5577 5596 C4' DG K 5 OK 5598 5595 5597 5618 C4' DA K 6 OK 5620 5617 5619 5639 C4' DA K 7 OK 5641 5638 5640 5660 C4' DG K 8 OK 5662 5659 5661 5682 C4' DG K 9 OK 5684 5681 5683 5704 C4' DA K 10 OK 5706 5703 5705 5725 C4' DT K 11 OK 5727 5724 5726 5745 C4' DT K 12 OK 5747 5744 5746 5765 C4' DC K 13 OK 5767 5764 5766 5794 C4' 2DT K 14 OK 5797 5793 5795 5801 C4' DC M 2 OK 5803 5800 5802 5820 C4' DA M 3 OK 5822 5819 5821 5841 C4' DC M 4 OK 5843 5840 5842 5874 C4' EFG M 5 OK 5872 5875 5869 5885 C4' DG M 6 OK 5887 5884 5886 5907 C4' DA M 7 OK 5909 5906 5908 5928 C4' DA M 8 OK 5930 5927 5929 5949 C4' DT M 9 OK 5951 5948 5950 5969 C4' DC M 10 OK 5971 5968 5970 5988 C4' DC M 11 OK 5990 5987 5989 6007 C4' DT M 12 OK 6009 6006 6008 6027 C4' DT M 13 OK 6029 6026 6028 6047 C4' DC M 14 OK 6049 6046 6048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5104 C5' DG P 5 5103 5105 5126 C5' DA P 6 5125 5127 5147 C5' DA P 7 5146 5148 5168 C5' DG P 8 5167 5169 5190 C5' DG P 9 5189 5191 5212 C5' DA P 10 5211 5213 5233 C5' DT P 11 5232 5234 5253 C5' DT P 12 5252 5254 5273 C5' DC P 13 5272 5274 5302 C5' 2DT P 14 5291 5303 5309 C5' DT B 1 5308 5310 5329 C5' DC B 2 5328 5330 5348 C5' DA B 3 5347 5349 5369 C5' DC B 4 5368 5370 5404 C5' EFG B 5 5405 5403 5413 C5' DG B 6 5412 5414 5435 C5' DA B 7 5434 5436 5456 C5' DA B 8 5455 5457 5477 C5' DT B 9 5476 5478 5497 C5' DC B 10 5496 5498 5516 C5' DC B 11 5515 5517 5535 C5' DT B 12 5534 5536 5555 C5' DT B 13 5554 5556 5575 C5' DC B 14 5574 5576 5595 C5' DG K 5 5594 5596 5617 C5' DA K 6 5616 5618 5638 C5' DA K 7 5637 5639 5659 C5' DG K 8 5658 5660 5681 C5' DG K 9 5680 5682 5703 C5' DA K 10 5702 5704 5724 C5' DT K 11 5723 5725 5744 C5' DT K 12 5743 5745 5764 C5' DC K 13 5763 5765 5793 C5' 2DT K 14 5782 5794 5800 C5' DC M 2 5799 5801 5819 C5' DA M 3 5818 5820 5840 C5' DC M 4 5839 5841 5875 C5' EFG M 5 5876 5874 5884 C5' DG M 6 5883 5885 5906 C5' DA M 7 5905 5907 5927 C5' DA M 8 5926 5928 5948 C5' DT M 9 5947 5949 5968 C5' DC M 10 5967 5969 5987 C5' DC M 11 5986 5988 6006 C5' DT M 12 6005 6007 6026 C5' DT M 13 6025 6027 6046 C5' DC M 14 6045 6047 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5100 P DG P 5 distorted distorted 5101 5102 5103 5122 P DA P 6 distorted distorted 5108 5123 5124 5125 5143 P DA P 7 distorted distorted 5130 5144 5145 5146 5164 P DG P 8 distorted distorted 5151 5165 5166 5167 5186 P DG P 9 distorted distorted 5172 5187 5188 5189 5208 P DA P 10 distorted distorted 5194 5209 5210 5211 5229 P DT P 11 distorted distorted 5216 5230 5231 5232 5249 P DT P 12 distorted distorted 5237 5250 5251 5252 5269 P DC P 13 distorted distorted 5257 5270 5271 5272 5288 P 2DT P 14 distorted distorted 5277 5289 5290 5291 5325 P DC B 2 distorted distorted 5313 5326 5327 5328 5344 P DA B 3 distorted distorted 5333 5345 5346 5347 5365 P DC B 4 distorted distorted 5352 5366 5367 5368 5406 P EFG B 5 distorted distorted 5373 5407 5408 5405 5409 P DG B 6 distorted distorted 5402 5410 5411 5412 5431 P DA B 7 distorted distorted 5417 5432 5433 5434 5452 P DA B 8 distorted distorted 5439 5453 5454 5455 5473 P DT B 9 distorted distorted 5460 5474 5475 5476 5493 P DC B 10 distorted distorted 5481 5494 5495 5496 5512 P DC B 11 distorted distorted 5501 5513 5514 5515 5531 P DT B 12 distorted distorted 5520 5532 5533 5534 5551 P DT B 13 distorted distorted 5539 5552 5553 5554 5571 P DC B 14 distorted distorted 5559 5572 5573 5574 5591 P DG K 5 distorted distorted 5592 5593 5594 5613 P DA K 6 distorted distorted 5599 5614 5615 5616 5634 P DA K 7 distorted distorted 5621 5635 5636 5637 5655 P DG K 8 distorted distorted 5642 5656 5657 5658 5677 P DG K 9 distorted distorted 5663 5678 5679 5680 5699 P DA K 10 distorted distorted 5685 5700 5701 5702 5720 P DT K 11 distorted distorted 5707 5721 5722 5723 5740 P DT K 12 distorted distorted 5728 5741 5742 5743 5760 P DC K 13 distorted distorted 5748 5761 5762 5763 5779 P 2DT K 14 distorted distorted 5768 5780 5781 5782 5815 P DA M 3 distorted distorted 5804 5816 5817 5818 5836 P DC M 4 distorted distorted 5823 5837 5838 5839 5877 P EFG M 5 distorted distorted 5844 5878 5879 5876 5880 P DG M 6 distorted distorted 5873 5881 5882 5883 5902 P DA M 7 distorted distorted 5888 5903 5904 5905 5923 P DA M 8 distorted distorted 5910 5924 5925 5926 5944 P DT M 9 distorted distorted 5931 5945 5946 5947 5964 P DC M 10 distorted distorted 5952 5965 5966 5967 5983 P DC M 11 distorted distorted 5972 5984 5985 5986 6002 P DT M 12 distorted distorted 5991 6003 6004 6005 6022 P DT M 13 distorted distorted 6010 6023 6024 6025 6042 P DC M 14 distorted distorted 6030 6043 6044 6045 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