ID code: '3KHG' 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' --------------------------------------------------------------------------------- 5490 C1' DG D 802 beta 5486 5491 5489 5512 C1' DT D 803 beta 5508 5513 5511 5532 C1' DT D 804 beta 5528 5533 5531 5552 C1' DG D 805 beta 5548 5553 5551 5574 C1' DG D 806 beta 5570 5575 5573 5596 C1' DA D 807 beta 5592 5597 5595 5617 C1' DT D 808 beta 5613 5618 5616 5637 C1' DG D 809 beta 5633 5638 5636 5659 C1' DG D 810 beta 5655 5660 5658 5681 C1' DT D 811 beta 5677 5682 5680 5701 C1' DA D 812 beta 5697 5702 5700 5722 C1' DG D 813 beta 5718 5723 5721 5745 C1' DC E 901 beta 5741 5746 5744 5764 C1' DT E 902 beta 5760 5765 5763 5784 C1' DA E 903 beta 5780 5785 5783 5805 C1' DA E 904 beta 5801 5806 5804 5826 C1' DC E 905 beta 5822 5827 5825 5845 C1' DG E 906 beta 5841 5846 5844 5867 C1' DC E 907 beta 5863 5868 5866 5886 C1' DT E 908 beta 5882 5887 5885 5906 C1' DA E 909 beta 5902 5907 5905 5927 C1' DC E 910 beta 5923 5928 5926 5946 C1' DC E 911 beta 5942 5947 5945 5965 C1' DA E 912 beta 5961 5966 5964 5986 C1' DT E 913 beta 5982 5987 5985 6006 C1' DC E 914 beta 6002 6007 6005 6025 C1' DC E 915 beta 6021 6026 6024 6044 C1' DA E 916 beta 6040 6045 6043 6065 C1' DA E 917 beta 6061 6066 6064 6086 C1' DC E 918 beta 6082 6087 6085 6105 C1' DC E 919 beta 6101 6106 6104 6125 C1' DG H1806 beta 6121 6126 6124 6147 C1' DA H1807 beta 6143 6148 6146 6168 C1' DT H1808 beta 6164 6169 6167 6188 C1' DG H1809 beta 6184 6189 6187 6210 C1' DG H1810 beta 6206 6211 6209 6232 C1' DT H1811 beta 6228 6233 6231 6252 C1' DA H1812 beta 6248 6253 6251 6273 C1' DG H1813 beta 6269 6274 6272 6296 C1' DC J1905 beta 6292 6297 6295 6315 C1' DG J1906 beta 6311 6316 6314 6337 C1' DC J1907 beta 6333 6338 6336 6356 C1' DT J1908 beta 6352 6357 6355 6376 C1' DA J1909 beta 6372 6377 6375 6397 C1' DC J1910 beta 6393 6398 6396 6416 C1' DC J1911 beta 6412 6417 6415 6435 C1' DA J1912 beta 6431 6436 6434 6456 C1' DT J1913 beta 6452 6457 6455 6476 C1' DC J1914 beta 6472 6477 6475 6505 C1' DGT A 414 beta 6501 6506 6504 6554 C1' DGT B1414 beta 6550 6555 6553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5489 C2' DG D 802 5490 5487 5511 C2' DT D 803 5512 5509 5531 C2' DT D 804 5532 5529 5551 C2' DG D 805 5552 5549 5573 C2' DG D 806 5574 5571 5595 C2' DA D 807 5596 5593 5616 C2' DT D 808 5617 5614 5636 C2' DG D 809 5637 5634 5658 C2' DG D 810 5659 5656 5680 C2' DT D 811 5681 5678 5700 C2' DA D 812 5701 5698 5721 C2' DG D 813 5722 5719 5744 C2' DC E 901 5745 5742 5763 C2' DT E 902 5764 5761 5783 C2' DA E 903 5784 5781 5804 C2' DA E 904 5805 5802 5825 C2' DC E 905 5826 5823 5844 C2' DG E 906 5845 5842 5866 C2' DC E 907 5867 5864 5885 C2' DT E 908 5886 5883 5905 C2' DA E 909 5906 5903 5926 C2' DC E 910 5927 5924 5945 C2' DC E 911 5946 5943 5964 C2' DA E 912 5965 5962 5985 C2' DT E 913 5986 5983 6005 C2' DC E 914 6006 6003 6024 C2' DC E 915 6025 6022 6043 C2' DA E 916 6044 6041 6064 C2' DA E 917 6065 6062 6085 C2' DC E 918 6086 6083 6104 C2' DC E 919 6105 6102 6124 C2' DG H1806 6125 6122 6146 C2' DA H1807 6147 6144 6167 C2' DT H1808 6168 6165 6187 C2' DG H1809 6188 6185 6209 C2' DG H1810 6210 6207 6231 C2' DT H1811 6232 6229 6251 C2' DA H1812 6252 6249 6272 C2' DG H1813 6273 6270 6295 C2' DC J1905 6296 6293 6314 C2' DG J1906 6315 6312 6336 C2' DC J1907 6337 6334 6355 C2' DT J1908 6356 6353 6375 C2' DA J1909 6376 6373 6396 C2' DC J1910 6397 6394 6415 C2' DC J1911 6416 6413 6434 C2' DA J1912 6435 6432 6455 C2' DT J1913 6456 6453 6475 C2' DC J1914 6476 6473 6504 C2' DGT A 414 6505 6502 6553 C2' DGT B1414 6554 6551 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5487 C3' DG D 802 OK 5485 5488 5489 5509 C3' DT D 803 OK 5507 5510 5511 5529 C3' DT D 804 OK 5527 5530 5531 5549 C3' DG D 805 OK 5547 5550 5551 5571 C3' DG D 806 OK 5569 5572 5573 5593 C3' DA D 807 OK 5591 5594 5595 5614 C3' DT D 808 OK 5612 5615 5616 5634 C3' DG D 809 OK 5632 5635 5636 5656 C3' DG D 810 OK 5654 5657 5658 5678 C3' DT D 811 OK 5676 5679 5680 5698 C3' DA D 812 OK 5696 5699 5700 5719 C3' DG D 813 OK 5717 5720 5721 5742 C3' DC E 901 OK 5740 5743 5744 5761 C3' DT E 902 OK 5759 5762 5763 5781 C3' DA E 903 OK 5779 5782 5783 5802 C3' DA E 904 OK 5800 5803 5804 5823 C3' DC E 905 OK 5821 5824 5825 5842 C3' DG E 906 OK 5840 5843 5844 5864 C3' DC E 907 OK 5862 5865 5866 5883 C3' DT E 908 OK 5881 5884 5885 5903 C3' DA E 909 OK 5901 5904 5905 5924 C3' DC E 910 OK 5922 5925 5926 5943 C3' DC E 911 OK 5941 5944 5945 5962 C3' DA E 912 OK 5960 5963 5964 5983 C3' DT E 913 OK 5981 5984 5985 6003 C3' DC E 914 OK 6001 6004 6005 6022 C3' DC E 915 OK 6020 6023 6024 6041 C3' DA E 916 OK 6039 6042 6043 6062 C3' DA E 917 OK 6060 6063 6064 6083 C3' DC E 918 OK 6081 6084 6085 6102 C3' DC E 919 OK 6100 6103 6104 6122 C3' DG H1806 OK 6120 6123 6124 6144 C3' DA H1807 OK 6142 6145 6146 6165 C3' DT H1808 OK 6163 6166 6167 6185 C3' DG H1809 OK 6183 6186 6187 6207 C3' DG H1810 OK 6205 6208 6209 6229 C3' DT H1811 OK 6227 6230 6231 6249 C3' DA H1812 OK 6247 6250 6251 6270 C3' DG H1813 OK 6268 6271 6272 6293 C3' DC J1905 OK 6291 6294 6295 6312 C3' DG J1906 OK 6310 6313 6314 6334 C3' DC J1907 OK 6332 6335 6336 6353 C3' DT J1908 OK 6351 6354 6355 6373 C3' DA J1909 OK 6371 6374 6375 6394 C3' DC J1910 OK 6392 6395 6396 6413 C3' DC J1911 OK 6411 6414 6415 6432 C3' DA J1912 OK 6430 6433 6434 6453 C3' DT J1913 OK 6451 6454 6455 6473 C3' DC J1914 OK 6471 6474 6475 6502 C3' DGT A 414 OK 6500 6503 6504 6551 C3' DGT B1414 OK 6549 6552 6553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5485 C4' DG D 802 OK 5487 5484 5486 5507 C4' DT D 803 OK 5509 5506 5508 5527 C4' DT D 804 OK 5529 5526 5528 5547 C4' DG D 805 OK 5549 5546 5548 5569 C4' DG D 806 OK 5571 5568 5570 5591 C4' DA D 807 OK 5593 5590 5592 5612 C4' DT D 808 OK 5614 5611 5613 5632 C4' DG D 809 OK 5634 5631 5633 5654 C4' DG D 810 OK 5656 5653 5655 5676 C4' DT D 811 OK 5678 5675 5677 5696 C4' DA D 812 OK 5698 5695 5697 5717 C4' DG D 813 OK 5719 5716 5718 5740 C4' DC E 901 OK 5742 5739 5741 5759 C4' DT E 902 OK 5761 5758 5760 5779 C4' DA E 903 OK 5781 5778 5780 5800 C4' DA E 904 OK 5802 5799 5801 5821 C4' DC E 905 OK 5823 5820 5822 5840 C4' DG E 906 OK 5842 5839 5841 5862 C4' DC E 907 OK 5864 5861 5863 5881 C4' DT E 908 OK 5883 5880 5882 5901 C4' DA E 909 OK 5903 5900 5902 5922 C4' DC E 910 OK 5924 5921 5923 5941 C4' DC E 911 OK 5943 5940 5942 5960 C4' DA E 912 OK 5962 5959 5961 5981 C4' DT E 913 OK 5983 5980 5982 6001 C4' DC E 914 OK 6003 6000 6002 6020 C4' DC E 915 OK 6022 6019 6021 6039 C4' DA E 916 OK 6041 6038 6040 6060 C4' DA E 917 OK 6062 6059 6061 6081 C4' DC E 918 OK 6083 6080 6082 6100 C4' DC E 919 OK 6102 6099 6101 6120 C4' DG H1806 OK 6122 6119 6121 6142 C4' DA H1807 OK 6144 6141 6143 6163 C4' DT H1808 OK 6165 6162 6164 6183 C4' DG H1809 OK 6185 6182 6184 6205 C4' DG H1810 OK 6207 6204 6206 6227 C4' DT H1811 OK 6229 6226 6228 6247 C4' DA H1812 OK 6249 6246 6248 6268 C4' DG H1813 OK 6270 6267 6269 6291 C4' DC J1905 OK 6293 6290 6292 6310 C4' DG J1906 OK 6312 6309 6311 6332 C4' DC J1907 OK 6334 6331 6333 6351 C4' DT J1908 OK 6353 6350 6352 6371 C4' DA J1909 OK 6373 6370 6372 6392 C4' DC J1910 OK 6394 6391 6393 6411 C4' DC J1911 OK 6413 6410 6412 6430 C4' DA J1912 OK 6432 6429 6431 6451 C4' DT J1913 OK 6453 6450 6452 6471 C4' DC J1914 OK 6473 6470 6472 6500 C4' DGT A 414 OK 6502 6499 6501 6549 C4' DGT B1414 OK 6551 6548 6550 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5484 C5' DG D 802 5483 5485 5506 C5' DT D 803 5505 5507 5526 C5' DT D 804 5525 5527 5546 C5' DG D 805 5545 5547 5568 C5' DG D 806 5567 5569 5590 C5' DA D 807 5589 5591 5611 C5' DT D 808 5610 5612 5631 C5' DG D 809 5630 5632 5653 C5' DG D 810 5652 5654 5675 C5' DT D 811 5674 5676 5695 C5' DA D 812 5694 5696 5716 C5' DG D 813 5715 5717 5739 C5' DC E 901 5738 5740 5758 C5' DT E 902 5757 5759 5778 C5' DA E 903 5777 5779 5799 C5' DA E 904 5798 5800 5820 C5' DC E 905 5819 5821 5839 C5' DG E 906 5838 5840 5861 C5' DC E 907 5860 5862 5880 C5' DT E 908 5879 5881 5900 C5' DA E 909 5899 5901 5921 C5' DC E 910 5920 5922 5940 C5' DC E 911 5939 5941 5959 C5' DA E 912 5958 5960 5980 C5' DT E 913 5979 5981 6000 C5' DC E 914 5999 6001 6019 C5' DC E 915 6018 6020 6038 C5' DA E 916 6037 6039 6059 C5' DA E 917 6058 6060 6080 C5' DC E 918 6079 6081 6099 C5' DC E 919 6098 6100 6119 C5' DG H1806 6118 6120 6141 C5' DA H1807 6140 6142 6162 C5' DT H1808 6161 6163 6182 C5' DG H1809 6181 6183 6204 C5' DG H1810 6203 6205 6226 C5' DT H1811 6225 6227 6246 C5' DA H1812 6245 6247 6267 C5' DG H1813 6266 6268 6290 C5' DC J1905 6289 6291 6309 C5' DG J1906 6308 6310 6331 C5' DC J1907 6330 6332 6350 C5' DT J1908 6349 6351 6370 C5' DA J1909 6369 6371 6391 C5' DC J1910 6390 6392 6410 C5' DC J1911 6409 6411 6429 C5' DA J1912 6428 6430 6450 C5' DT J1913 6449 6451 6470 C5' DC J1914 6469 6471 6499 C5' DGT A 414 6498 6500 6548 C5' DGT B1414 6547 6549 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5502 P DT D 803 distorted distorted 5488 5503 5504 5505 5522 P DT D 804 distorted distorted 5510 5523 5524 5525 5542 P DG D 805 distorted distorted 5530 5543 5544 5545 5564 P DG D 806 distorted distorted 5550 5565 5566 5567 5586 P DA D 807 distorted distorted 5572 5587 5588 5589 5607 P DT D 808 distorted distorted 5594 5608 5609 5610 5627 P DG D 809 distorted distorted 5615 5628 5629 5630 5649 P DG D 810 distorted distorted 5635 5650 5651 5652 5671 P DT D 811 distorted distorted 5657 5672 5673 5674 5691 P DA D 812 distorted distorted 5679 5692 5693 5694 5712 P DG D 813 distorted distorted 5699 5713 5714 5715 5734 P 2DA D 814 distorted distorted 5720 5735 5736 5754 P DT E 902 distorted distorted 5743 5755 5756 5757 5774 P DA E 903 distorted distorted 5762 5775 5776 5777 5795 P DA E 904 distorted distorted 5782 5796 5797 5798 5816 P DC E 905 distorted distorted 5803 5817 5818 5819 5835 P DG E 906 distorted distorted 5824 5836 5837 5838 5857 P DC E 907 distorted distorted 5843 5858 5859 5860 5876 P DT E 908 distorted distorted 5865 5877 5878 5879 5896 P DA E 909 distorted distorted 5884 5897 5898 5899 5917 P DC E 910 distorted distorted 5904 5918 5919 5920 5936 P DC E 911 distorted distorted 5925 5937 5938 5939 5955 P DA E 912 distorted distorted 5944 5956 5957 5958 5976 P DT E 913 distorted distorted 5963 5977 5978 5979 5996 P DC E 914 distorted distorted 5984 5997 5998 5999 6015 P DC E 915 distorted distorted 6004 6016 6017 6018 6034 P DA E 916 distorted distorted 6023 6035 6036 6037 6055 P DA E 917 distorted distorted 6042 6056 6057 6058 6076 P DC E 918 distorted distorted 6063 6077 6078 6079 6095 P DC E 919 distorted distorted 6084 6096 6097 6098 6115 P DG H1806 distorted distorted 6116 6117 6118 6137 P DA H1807 distorted distorted 6123 6138 6139 6140 6158 P DT H1808 distorted distorted 6145 6159 6160 6161 6178 P DG H1809 distorted distorted 6166 6179 6180 6181 6200 P DG H1810 distorted distorted 6186 6201 6202 6203 6222 P DT H1811 distorted distorted 6208 6223 6224 6225 6242 P DA H1812 distorted distorted 6230 6243 6244 6245 6263 P DG H1813 distorted distorted 6250 6264 6265 6266 6286 P DC J1905 distorted distorted 6287 6288 6289 6305 P DG J1906 distorted distorted 6294 6306 6307 6308 6327 P DC J1907 distorted distorted 6313 6328 6329 6330 6346 P DT J1908 distorted distorted 6335 6347 6348 6349 6366 P DA J1909 distorted distorted 6354 6367 6368 6369 6387 P DC J1910 distorted distorted 6374 6388 6389 6390 6406 P DC J1911 distorted distorted 6395 6407 6408 6409 6425 P DA J1912 distorted distorted 6414 6426 6427 6428 6446 P DT J1913 distorted distorted 6433 6447 6448 6449 6466 P DC J1914 distorted distorted 6454 6467 6468 6469 ---------------------------------------------------------------------------------