ID code: '4BHH' 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' --------------------------------------------------------------------------------- 5500 C1' U R 1 beta 5495 5501 5498 5520 C1' U R 2 beta 5515 5521 5518 5540 C1' U R 3 beta 5535 5541 5538 5560 C1' U R 4 beta 5555 5561 5558 5580 C1' U R 5 beta 5575 5581 5578 5600 C1' U R 6 beta 5595 5601 5598 5620 C1' U R 7 beta 5615 5621 5618 5640 C1' U R 8 beta 5635 5641 5638 5660 C1' U R 9 beta 5655 5661 5658 5680 C1' U R 10 beta 5675 5681 5678 5700 C1' U R 11 beta 5695 5701 5698 5720 C1' U R 12 beta 5715 5721 5718 5740 C1' U R 13 beta 5735 5741 5738 5760 C1' U R 14 beta 5755 5761 5758 5780 C1' U R 15 beta 5775 5781 5778 5800 C1' U R 16 beta 5795 5801 5798 5820 C1' U R 17 beta 5815 5821 5818 5840 C1' U R 18 beta 5835 5841 5838 5860 C1' U R 19 beta 5855 5861 5858 5880 C1' U R 20 beta 5875 5881 5878 5900 C1' U R 21 beta 5895 5901 5898 5920 C1' U R 22 beta 5915 5921 5918 5940 C1' U R 23 beta 5935 5941 5938 5960 C1' U R 24 beta 5955 5961 5958 5980 C1' U R 25 beta 5975 5981 5978 6000 C1' U R 26 beta 5995 6001 5998 6020 C1' U R 27 beta 6015 6021 6018 6040 C1' U R 28 beta 6035 6041 6038 6060 C1' U R 29 beta 6055 6061 6058 6080 C1' U R 30 beta 6075 6081 6078 6100 C1' U R 31 beta 6095 6101 6098 6120 C1' U R 32 beta 6115 6121 6118 6140 C1' U R 33 beta 6135 6141 6138 6160 C1' U R 34 beta 6155 6161 6158 6180 C1' U R 35 beta 6175 6181 6178 6200 C1' U R 36 beta 6195 6201 6198 6220 C1' U R 37 beta 6215 6221 6218 6240 C1' U R 38 beta 6235 6241 6238 6260 C1' U R 39 beta 6255 6261 6258 6280 C1' U R 40 beta 6275 6281 6278 6300 C1' U R 41 beta 6295 6301 6298 6320 C1' U R 42 beta 6315 6321 6318 6340 C1' U R 43 beta 6335 6341 6338 6360 C1' U R 44 beta 6355 6361 6358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5498 C2' U R 1 OK 5500 5496 5499 5518 C2' U R 2 OK 5520 5516 5519 5538 C2' U R 3 OK 5540 5536 5539 5558 C2' U R 4 OK 5560 5556 5559 5578 C2' U R 5 OK 5580 5576 5579 5598 C2' U R 6 OK 5600 5596 5599 5618 C2' U R 7 OK 5620 5616 5619 5638 C2' U R 8 OK 5640 5636 5639 5658 C2' U R 9 OK 5660 5656 5659 5678 C2' U R 10 OK 5680 5676 5679 5698 C2' U R 11 OK 5700 5696 5699 5718 C2' U R 12 OK 5720 5716 5719 5738 C2' U R 13 OK 5740 5736 5739 5758 C2' U R 14 OK 5760 5756 5759 5778 C2' U R 15 OK 5780 5776 5779 5798 C2' U R 16 OK 5800 5796 5799 5818 C2' U R 17 OK 5820 5816 5819 5838 C2' U R 18 OK 5840 5836 5839 5858 C2' U R 19 OK 5860 5856 5859 5878 C2' U R 20 OK 5880 5876 5879 5898 C2' U R 21 OK 5900 5896 5899 5918 C2' U R 22 OK 5920 5916 5919 5938 C2' U R 23 OK 5940 5936 5939 5958 C2' U R 24 OK 5960 5956 5959 5978 C2' U R 25 OK 5980 5976 5979 5998 C2' U R 26 OK 6000 5996 5999 6018 C2' U R 27 OK 6020 6016 6019 6038 C2' U R 28 OK 6040 6036 6039 6058 C2' U R 29 OK 6060 6056 6059 6078 C2' U R 30 OK 6080 6076 6079 6098 C2' U R 31 OK 6100 6096 6099 6118 C2' U R 32 OK 6120 6116 6119 6138 C2' U R 33 OK 6140 6136 6139 6158 C2' U R 34 OK 6160 6156 6159 6178 C2' U R 35 OK 6180 6176 6179 6198 C2' U R 36 OK 6200 6196 6199 6218 C2' U R 37 OK 6220 6216 6219 6238 C2' U R 38 OK 6240 6236 6239 6258 C2' U R 39 OK 6260 6256 6259 6278 C2' U R 40 OK 6280 6276 6279 6298 C2' U R 41 OK 6300 6296 6299 6318 C2' U R 42 OK 6320 6316 6319 6338 C2' U R 43 OK 6340 6336 6339 6358 C2' U R 44 OK 6360 6356 6359 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5496 C3' U R 1 OK 5494 5497 5498 5516 C3' U R 2 OK 5514 5517 5518 5536 C3' U R 3 OK 5534 5537 5538 5556 C3' U R 4 OK 5554 5557 5558 5576 C3' U R 5 OK 5574 5577 5578 5596 C3' U R 6 OK 5594 5597 5598 5616 C3' U R 7 OK 5614 5617 5618 5636 C3' U R 8 OK 5634 5637 5638 5656 C3' U R 9 OK 5654 5657 5658 5676 C3' U R 10 OK 5674 5677 5678 5696 C3' U R 11 OK 5694 5697 5698 5716 C3' U R 12 OK 5714 5717 5718 5736 C3' U R 13 OK 5734 5737 5738 5756 C3' U R 14 OK 5754 5757 5758 5776 C3' U R 15 OK 5774 5777 5778 5796 C3' U R 16 OK 5794 5797 5798 5816 C3' U R 17 OK 5814 5817 5818 5836 C3' U R 18 OK 5834 5837 5838 5856 C3' U R 19 OK 5854 5857 5858 5876 C3' U R 20 OK 5874 5877 5878 5896 C3' U R 21 OK 5894 5897 5898 5916 C3' U R 22 OK 5914 5917 5918 5936 C3' U R 23 OK 5934 5937 5938 5956 C3' U R 24 OK 5954 5957 5958 5976 C3' U R 25 OK 5974 5977 5978 5996 C3' U R 26 OK 5994 5997 5998 6016 C3' U R 27 OK 6014 6017 6018 6036 C3' U R 28 OK 6034 6037 6038 6056 C3' U R 29 OK 6054 6057 6058 6076 C3' U R 30 OK 6074 6077 6078 6096 C3' U R 31 OK 6094 6097 6098 6116 C3' U R 32 OK 6114 6117 6118 6136 C3' U R 33 OK 6134 6137 6138 6156 C3' U R 34 OK 6154 6157 6158 6176 C3' U R 35 OK 6174 6177 6178 6196 C3' U R 36 OK 6194 6197 6198 6216 C3' U R 37 OK 6214 6217 6218 6236 C3' U R 38 OK 6234 6237 6238 6256 C3' U R 39 OK 6254 6257 6258 6276 C3' U R 40 OK 6274 6277 6278 6296 C3' U R 41 OK 6294 6297 6298 6316 C3' U R 42 OK 6314 6317 6318 6336 C3' U R 43 OK 6334 6337 6338 6356 C3' U R 44 OK 6354 6357 6358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5494 C4' U R 1 OK 5496 5493 5495 5514 C4' U R 2 OK 5516 5513 5515 5534 C4' U R 3 OK 5536 5533 5535 5554 C4' U R 4 OK 5556 5553 5555 5574 C4' U R 5 OK 5576 5573 5575 5594 C4' U R 6 OK 5596 5593 5595 5614 C4' U R 7 OK 5616 5613 5615 5634 C4' U R 8 OK 5636 5633 5635 5654 C4' U R 9 OK 5656 5653 5655 5674 C4' U R 10 OK 5676 5673 5675 5694 C4' U R 11 OK 5696 5693 5695 5714 C4' U R 12 OK 5716 5713 5715 5734 C4' U R 13 OK 5736 5733 5735 5754 C4' U R 14 OK 5756 5753 5755 5774 C4' U R 15 OK 5776 5773 5775 5794 C4' U R 16 OK 5796 5793 5795 5814 C4' U R 17 OK 5816 5813 5815 5834 C4' U R 18 OK 5836 5833 5835 5854 C4' U R 19 OK 5856 5853 5855 5874 C4' U R 20 OK 5876 5873 5875 5894 C4' U R 21 OK 5896 5893 5895 5914 C4' U R 22 OK 5916 5913 5915 5934 C4' U R 23 OK 5936 5933 5935 5954 C4' U R 24 OK 5956 5953 5955 5974 C4' U R 25 OK 5976 5973 5975 5994 C4' U R 26 OK 5996 5993 5995 6014 C4' U R 27 OK 6016 6013 6015 6034 C4' U R 28 OK 6036 6033 6035 6054 C4' U R 29 OK 6056 6053 6055 6074 C4' U R 30 OK 6076 6073 6075 6094 C4' U R 31 OK 6096 6093 6095 6114 C4' U R 32 OK 6116 6113 6115 6134 C4' U R 33 OK 6136 6133 6135 6154 C4' U R 34 OK 6156 6153 6155 6174 C4' U R 35 OK 6176 6173 6175 6194 C4' U R 36 OK 6196 6193 6195 6214 C4' U R 37 OK 6216 6213 6215 6234 C4' U R 38 OK 6236 6233 6235 6254 C4' U R 39 OK 6256 6253 6255 6274 C4' U R 40 OK 6276 6273 6275 6294 C4' U R 41 OK 6296 6293 6295 6314 C4' U R 42 OK 6316 6313 6315 6334 C4' U R 43 OK 6336 6333 6335 6354 C4' U R 44 OK 6356 6353 6355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5493 C5' U R 1 5492 5494 5513 C5' U R 2 5512 5514 5533 C5' U R 3 5532 5534 5553 C5' U R 4 5552 5554 5573 C5' U R 5 5572 5574 5593 C5' U R 6 5592 5594 5613 C5' U R 7 5612 5614 5633 C5' U R 8 5632 5634 5653 C5' U R 9 5652 5654 5673 C5' U R 10 5672 5674 5693 C5' U R 11 5692 5694 5713 C5' U R 12 5712 5714 5733 C5' U R 13 5732 5734 5753 C5' U R 14 5752 5754 5773 C5' U R 15 5772 5774 5793 C5' U R 16 5792 5794 5813 C5' U R 17 5812 5814 5833 C5' U R 18 5832 5834 5853 C5' U R 19 5852 5854 5873 C5' U R 20 5872 5874 5893 C5' U R 21 5892 5894 5913 C5' U R 22 5912 5914 5933 C5' U R 23 5932 5934 5953 C5' U R 24 5952 5954 5973 C5' U R 25 5972 5974 5993 C5' U R 26 5992 5994 6013 C5' U R 27 6012 6014 6033 C5' U R 28 6032 6034 6053 C5' U R 29 6052 6054 6073 C5' U R 30 6072 6074 6093 C5' U R 31 6092 6094 6113 C5' U R 32 6112 6114 6133 C5' U R 33 6132 6134 6153 C5' U R 34 6152 6154 6173 C5' U R 35 6172 6174 6193 C5' U R 36 6192 6194 6213 C5' U R 37 6212 6214 6233 C5' U R 38 6232 6234 6253 C5' U R 39 6252 6254 6273 C5' U R 40 6272 6274 6293 C5' U R 41 6292 6294 6313 C5' U R 42 6312 6314 6333 C5' U R 43 6332 6334 6353 C5' U R 44 6352 6354 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5509 P U R 2 distorted distorted 5497 5510 5511 5512 5529 P U R 3 OK OK 5517 5530 5531 5532 5549 P U R 4 distorted distorted 5537 5550 5551 5552 5569 P U R 5 distorted distorted 5557 5570 5571 5572 5589 P U R 6 distorted distorted 5577 5590 5591 5592 5609 P U R 7 distorted distorted 5597 5610 5611 5612 5629 P U R 8 distorted distorted 5617 5630 5631 5632 5649 P U R 9 distorted distorted 5637 5650 5651 5652 5669 P U R 10 distorted distorted 5657 5670 5671 5672 5689 P U R 11 distorted distorted 5677 5690 5691 5692 5709 P U R 12 OK OK 5697 5710 5711 5712 5729 P U R 13 distorted distorted 5717 5730 5731 5732 5749 P U R 14 OK OK 5737 5750 5751 5752 5769 P U R 15 distorted distorted 5757 5770 5771 5772 5789 P U R 16 distorted distorted 5777 5790 5791 5792 5809 P U R 17 distorted distorted 5797 5810 5811 5812 5829 P U R 18 distorted distorted 5817 5830 5831 5832 5849 P U R 19 distorted distorted 5837 5850 5851 5852 5869 P U R 20 distorted distorted 5857 5870 5871 5872 5889 P U R 21 distorted distorted 5877 5890 5891 5892 5909 P U R 22 distorted distorted 5897 5910 5911 5912 5929 P U R 23 distorted distorted 5917 5930 5931 5932 5949 P U R 24 distorted distorted 5937 5950 5951 5952 5969 P U R 25 OK OK 5957 5970 5971 5972 5989 P U R 26 distorted distorted 5977 5990 5991 5992 6009 P U R 27 distorted distorted 5997 6010 6011 6012 6029 P U R 28 distorted distorted 6017 6030 6031 6032 6049 P U R 29 distorted distorted 6037 6050 6051 6052 6069 P U R 30 distorted distorted 6057 6070 6071 6072 6089 P U R 31 distorted distorted 6077 6090 6091 6092 6109 P U R 32 distorted distorted 6097 6110 6111 6112 6129 P U R 33 distorted distorted 6117 6130 6131 6132 6149 P U R 34 OK OK 6137 6150 6151 6152 6169 P U R 35 distorted distorted 6157 6170 6171 6172 6189 P U R 36 OK OK 6177 6190 6191 6192 6209 P U R 37 distorted distorted 6197 6210 6211 6212 6229 P U R 38 distorted distorted 6217 6230 6231 6232 6249 P U R 39 distorted distorted 6237 6250 6251 6252 6269 P U R 40 distorted distorted 6257 6270 6271 6272 6289 P U R 41 distorted distorted 6277 6290 6291 6292 6309 P U R 42 distorted distorted 6297 6310 6311 6312 6329 P U R 43 distorted distorted 6317 6330 6331 6332 6349 P U R 44 distorted distorted 6337 6350 6351 6352 ---------------------------------------------------------------------------------