ID code: '3V6J' 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' --------------------------------------------------------------------------------- 5526 C1' DG P 2 beta 5522 5527 5525 5548 C1' DG P 3 beta 5544 5549 5547 5570 C1' DG P 4 beta 5566 5571 5569 5592 C1' DG P 5 beta 5588 5593 5591 5614 C1' DA P 6 beta 5610 5615 5613 5635 C1' DA P 7 beta 5631 5636 5634 5656 C1' DG P 8 beta 5652 5657 5655 5678 C1' DG P 9 beta 5674 5679 5677 5700 C1' DA P 10 beta 5696 5701 5699 5721 C1' DT P 11 beta 5717 5722 5720 5741 C1' DT P 12 beta 5737 5742 5740 5759 C1' DOC P 13 beta 5763 5751 5760 5777 C1' DT B 1 beta 5773 5778 5776 5797 C1' DC B 2 beta 5793 5798 5796 5816 C1' DA B 3 beta 5812 5817 5815 5837 C1' DT B 4 beta 5833 5838 5836 5860 C1' EFG B 5 beta 5861 5859 5862 5882 C1' DG B 6 beta 5878 5883 5881 5904 C1' DA B 7 beta 5900 5905 5903 5925 C1' DA B 8 beta 5921 5926 5924 5946 C1' DT B 9 beta 5942 5947 5945 5966 C1' DC B 10 beta 5962 5967 5965 5985 C1' DC B 11 beta 5981 5986 5984 6004 C1' DT B 12 beta 6000 6005 6003 6024 C1' DT B 13 beta 6020 6025 6023 6044 C1' DC B 14 beta 6040 6045 6043 6063 C1' DC B 15 beta 6059 6064 6062 6082 C1' DC B 16 beta 6078 6083 6081 6101 C1' DC B 17 beta 6097 6102 6100 6121 C1' DG K 3 beta 6117 6122 6120 6143 C1' DG K 4 beta 6139 6144 6142 6165 C1' DG K 5 beta 6161 6166 6164 6187 C1' DA K 6 beta 6183 6188 6186 6208 C1' DA K 7 beta 6204 6209 6207 6229 C1' DG K 8 beta 6225 6230 6228 6251 C1' DG K 9 beta 6247 6252 6250 6273 C1' DA K 10 beta 6269 6274 6272 6294 C1' DT K 11 beta 6290 6295 6293 6314 C1' DT K 12 beta 6310 6315 6313 6332 C1' DOC K 13 beta 6336 6324 6333 6353 C1' DT M 4 beta 6349 6354 6352 6376 C1' EFG M 5 beta 6377 6375 6378 6398 C1' DG M 6 beta 6394 6399 6397 6420 C1' DA M 7 beta 6416 6421 6419 6441 C1' DA M 8 beta 6437 6442 6440 6462 C1' DT M 9 beta 6458 6463 6461 6482 C1' DC M 10 beta 6478 6483 6481 6501 C1' DC M 11 beta 6497 6502 6500 6520 C1' DT M 12 beta 6516 6521 6519 6540 C1' DT M 13 beta 6536 6541 6539 6560 C1' DC M 14 beta 6556 6561 6559 6579 C1' DC M 15 beta 6575 6580 6578 6598 C1' DC M 16 beta 6594 6599 6597 6616 C1' DCP A 401 beta 6620 6608 6617 6646 C1' DCP J 401 beta 6650 6638 6647 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5525 C2' DG P 2 5526 5523 5547 C2' DG P 3 5548 5545 5569 C2' DG P 4 5570 5567 5591 C2' DG P 5 5592 5589 5613 C2' DA P 6 5614 5611 5634 C2' DA P 7 5635 5632 5655 C2' DG P 8 5656 5653 5677 C2' DG P 9 5678 5675 5699 C2' DA P 10 5700 5697 5720 C2' DT P 11 5721 5718 5740 C2' DT P 12 5741 5738 5760 C2' DOC P 13 5759 5761 5776 C2' DT B 1 5777 5774 5796 C2' DC B 2 5797 5794 5815 C2' DA B 3 5816 5813 5836 C2' DT B 4 5837 5834 5862 C2' EFG B 5 5860 5864 5881 C2' DG B 6 5882 5879 5903 C2' DA B 7 5904 5901 5924 C2' DA B 8 5925 5922 5945 C2' DT B 9 5946 5943 5965 C2' DC B 10 5966 5963 5984 C2' DC B 11 5985 5982 6003 C2' DT B 12 6004 6001 6023 C2' DT B 13 6024 6021 6043 C2' DC B 14 6044 6041 6062 C2' DC B 15 6063 6060 6081 C2' DC B 16 6082 6079 6100 C2' DC B 17 6101 6098 6120 C2' DG K 3 6121 6118 6142 C2' DG K 4 6143 6140 6164 C2' DG K 5 6165 6162 6186 C2' DA K 6 6187 6184 6207 C2' DA K 7 6208 6205 6228 C2' DG K 8 6229 6226 6250 C2' DG K 9 6251 6248 6272 C2' DA K 10 6273 6270 6293 C2' DT K 11 6294 6291 6313 C2' DT K 12 6314 6311 6333 C2' DOC K 13 6332 6334 6352 C2' DT M 4 6353 6350 6378 C2' EFG M 5 6376 6380 6397 C2' DG M 6 6398 6395 6419 C2' DA M 7 6420 6417 6440 C2' DA M 8 6441 6438 6461 C2' DT M 9 6462 6459 6481 C2' DC M 10 6482 6479 6500 C2' DC M 11 6501 6498 6519 C2' DT M 12 6520 6517 6539 C2' DT M 13 6540 6537 6559 C2' DC M 14 6560 6557 6578 C2' DC M 15 6579 6576 6597 C2' DC M 16 6598 6595 6617 C2' DCP A 401 6616 6618 6647 C2' DCP J 401 6646 6648 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5523 C3' DG P 2 OK 5521 5524 5525 5545 C3' DG P 3 OK 5543 5546 5547 5567 C3' DG P 4 OK 5565 5568 5569 5589 C3' DG P 5 OK 5587 5590 5591 5611 C3' DA P 6 OK 5609 5612 5613 5632 C3' DA P 7 OK 5630 5633 5634 5653 C3' DG P 8 OK 5651 5654 5655 5675 C3' DG P 9 OK 5673 5676 5677 5697 C3' DA P 10 OK 5695 5698 5699 5718 C3' DT P 11 OK 5716 5719 5720 5738 C3' DT P 12 OK 5736 5739 5740 5761 C3' DOC P 13 5762 5760 5774 C3' DT B 1 OK 5772 5775 5776 5794 C3' DC B 2 OK 5792 5795 5796 5813 C3' DA B 3 OK 5811 5814 5815 5834 C3' DT B 4 OK 5832 5835 5836 5864 C3' EFG B 5 OK 5866 5865 5862 5879 C3' DG B 6 OK 5877 5880 5881 5901 C3' DA B 7 OK 5899 5902 5903 5922 C3' DA B 8 OK 5920 5923 5924 5943 C3' DT B 9 OK 5941 5944 5945 5963 C3' DC B 10 OK 5961 5964 5965 5982 C3' DC B 11 OK 5980 5983 5984 6001 C3' DT B 12 OK 5999 6002 6003 6021 C3' DT B 13 OK 6019 6022 6023 6041 C3' DC B 14 OK 6039 6042 6043 6060 C3' DC B 15 OK 6058 6061 6062 6079 C3' DC B 16 OK 6077 6080 6081 6098 C3' DC B 17 OK 6096 6099 6100 6118 C3' DG K 3 OK 6116 6119 6120 6140 C3' DG K 4 OK 6138 6141 6142 6162 C3' DG K 5 OK 6160 6163 6164 6184 C3' DA K 6 OK 6182 6185 6186 6205 C3' DA K 7 OK 6203 6206 6207 6226 C3' DG K 8 OK 6224 6227 6228 6248 C3' DG K 9 OK 6246 6249 6250 6270 C3' DA K 10 OK 6268 6271 6272 6291 C3' DT K 11 OK 6289 6292 6293 6311 C3' DT K 12 OK 6309 6312 6313 6334 C3' DOC K 13 6335 6333 6350 C3' DT M 4 OK 6348 6351 6352 6380 C3' EFG M 5 OK 6382 6381 6378 6395 C3' DG M 6 OK 6393 6396 6397 6417 C3' DA M 7 OK 6415 6418 6419 6438 C3' DA M 8 OK 6436 6439 6440 6459 C3' DT M 9 OK 6457 6460 6461 6479 C3' DC M 10 OK 6477 6480 6481 6498 C3' DC M 11 OK 6496 6499 6500 6517 C3' DT M 12 OK 6515 6518 6519 6537 C3' DT M 13 OK 6535 6538 6539 6557 C3' DC M 14 OK 6555 6558 6559 6576 C3' DC M 15 OK 6574 6577 6578 6595 C3' DC M 16 OK 6593 6596 6597 6618 C3' DCP A 401 OK 6619 6621 6617 6648 C3' DCP J 401 OK 6649 6651 6647 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5521 C4' DG P 2 OK 5523 5520 5522 5543 C4' DG P 3 OK 5545 5542 5544 5565 C4' DG P 4 OK 5567 5564 5566 5587 C4' DG P 5 OK 5589 5586 5588 5609 C4' DA P 6 OK 5611 5608 5610 5630 C4' DA P 7 OK 5632 5629 5631 5651 C4' DG P 8 OK 5653 5650 5652 5673 C4' DG P 9 OK 5675 5672 5674 5695 C4' DA P 10 OK 5697 5694 5696 5716 C4' DT P 11 OK 5718 5715 5717 5736 C4' DT P 12 OK 5738 5735 5737 5762 C4' DOC P 13 OK 5761 5764 5763 5772 C4' DT B 1 OK 5774 5771 5773 5792 C4' DC B 2 OK 5794 5791 5793 5811 C4' DA B 3 OK 5813 5810 5812 5832 C4' DT B 4 OK 5834 5831 5833 5866 C4' EFG B 5 OK 5864 5867 5861 5877 C4' DG B 6 OK 5879 5876 5878 5899 C4' DA B 7 OK 5901 5898 5900 5920 C4' DA B 8 OK 5922 5919 5921 5941 C4' DT B 9 OK 5943 5940 5942 5961 C4' DC B 10 OK 5963 5960 5962 5980 C4' DC B 11 OK 5982 5979 5981 5999 C4' DT B 12 OK 6001 5998 6000 6019 C4' DT B 13 OK 6021 6018 6020 6039 C4' DC B 14 OK 6041 6038 6040 6058 C4' DC B 15 OK 6060 6057 6059 6077 C4' DC B 16 OK 6079 6076 6078 6096 C4' DC B 17 OK 6098 6095 6097 6116 C4' DG K 3 OK 6118 6115 6117 6138 C4' DG K 4 OK 6140 6137 6139 6160 C4' DG K 5 OK 6162 6159 6161 6182 C4' DA K 6 OK 6184 6181 6183 6203 C4' DA K 7 OK 6205 6202 6204 6224 C4' DG K 8 OK 6226 6223 6225 6246 C4' DG K 9 OK 6248 6245 6247 6268 C4' DA K 10 OK 6270 6267 6269 6289 C4' DT K 11 OK 6291 6288 6290 6309 C4' DT K 12 OK 6311 6308 6310 6335 C4' DOC K 13 OK 6334 6337 6336 6348 C4' DT M 4 OK 6350 6347 6349 6382 C4' EFG M 5 OK 6380 6383 6377 6393 C4' DG M 6 OK 6395 6392 6394 6415 C4' DA M 7 OK 6417 6414 6416 6436 C4' DA M 8 OK 6438 6435 6437 6457 C4' DT M 9 OK 6459 6456 6458 6477 C4' DC M 10 OK 6479 6476 6478 6496 C4' DC M 11 OK 6498 6495 6497 6515 C4' DT M 12 OK 6517 6514 6516 6535 C4' DT M 13 OK 6537 6534 6536 6555 C4' DC M 14 OK 6557 6554 6556 6574 C4' DC M 15 OK 6576 6573 6575 6593 C4' DC M 16 OK 6595 6592 6594 6619 C4' DCP A 401 OK 6618 6622 6620 6649 C4' DCP J 401 OK 6648 6652 6650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5520 C5' DG P 2 5519 5521 5542 C5' DG P 3 5541 5543 5564 C5' DG P 4 5563 5565 5586 C5' DG P 5 5585 5587 5608 C5' DA P 6 5607 5609 5629 C5' DA P 7 5628 5630 5650 C5' DG P 8 5649 5651 5672 C5' DG P 9 5671 5673 5694 C5' DA P 10 5693 5695 5715 C5' DT P 11 5714 5716 5735 C5' DT P 12 5734 5736 5764 C5' DOC P 13 5765 5762 5771 C5' DT B 1 5770 5772 5791 C5' DC B 2 5790 5792 5810 C5' DA B 3 5809 5811 5831 C5' DT B 4 5830 5832 5867 C5' EFG B 5 5868 5866 5876 C5' DG B 6 5875 5877 5898 C5' DA B 7 5897 5899 5919 C5' DA B 8 5918 5920 5940 C5' DT B 9 5939 5941 5960 C5' DC B 10 5959 5961 5979 C5' DC B 11 5978 5980 5998 C5' DT B 12 5997 5999 6018 C5' DT B 13 6017 6019 6038 C5' DC B 14 6037 6039 6057 C5' DC B 15 6056 6058 6076 C5' DC B 16 6075 6077 6095 C5' DC B 17 6094 6096 6115 C5' DG K 3 6114 6116 6137 C5' DG K 4 6136 6138 6159 C5' DG K 5 6158 6160 6181 C5' DA K 6 6180 6182 6202 C5' DA K 7 6201 6203 6223 C5' DG K 8 6222 6224 6245 C5' DG K 9 6244 6246 6267 C5' DA K 10 6266 6268 6288 C5' DT K 11 6287 6289 6308 C5' DT K 12 6307 6309 6337 C5' DOC K 13 6338 6335 6347 C5' DT M 4 6346 6348 6383 C5' EFG M 5 6384 6382 6392 C5' DG M 6 6391 6393 6414 C5' DA M 7 6413 6415 6435 C5' DA M 8 6434 6436 6456 C5' DT M 9 6455 6457 6476 C5' DC M 10 6475 6477 6495 C5' DC M 11 6494 6496 6514 C5' DT M 12 6513 6515 6534 C5' DT M 13 6533 6535 6554 C5' DC M 14 6553 6555 6573 C5' DC M 15 6572 6574 6592 C5' DC M 16 6591 6593 6622 C5' DCP A 401 6623 6619 6652 C5' DCP J 401 6653 6649 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5538 P DG P 3 distorted distorted 5524 5539 5540 5541 5560 P DG P 4 distorted distorted 5546 5561 5562 5563 5582 P DG P 5 distorted distorted 5568 5583 5584 5585 5604 P DA P 6 distorted distorted 5590 5605 5606 5607 5625 P DA P 7 distorted distorted 5612 5626 5627 5628 5646 P DG P 8 distorted distorted 5633 5647 5648 5649 5668 P DG P 9 distorted distorted 5654 5669 5670 5671 5690 P DA P 10 distorted distorted 5676 5691 5692 5693 5711 P DT P 11 distorted distorted 5698 5712 5713 5714 5731 P DT P 12 distorted distorted 5719 5732 5733 5734 5766 P DOC P 13 OK OK 5739 5767 5768 5765 5787 P DC B 2 distorted distorted 5775 5788 5789 5790 5806 P DA B 3 distorted distorted 5795 5807 5808 5809 5827 P DT B 4 distorted distorted 5814 5828 5829 5830 5869 P EFG B 5 distorted distorted 5835 5870 5871 5868 5872 P DG B 6 distorted distorted 5865 5873 5874 5875 5894 P DA B 7 distorted distorted 5880 5895 5896 5897 5915 P DA B 8 distorted distorted 5902 5916 5917 5918 5936 P DT B 9 distorted distorted 5923 5937 5938 5939 5956 P DC B 10 distorted distorted 5944 5957 5958 5959 5975 P DC B 11 distorted distorted 5964 5976 5977 5978 5994 P DT B 12 distorted distorted 5983 5995 5996 5997 6014 P DT B 13 distorted distorted 6002 6015 6016 6017 6034 P DC B 14 distorted distorted 6022 6035 6036 6037 6053 P DC B 15 distorted distorted 6042 6054 6055 6056 6072 P DC B 16 distorted distorted 6061 6073 6074 6075 6091 P DC B 17 distorted distorted 6080 6092 6093 6094 6111 P DG K 3 distorted distorted 6112 6113 6114 6133 P DG K 4 distorted distorted 6119 6134 6135 6136 6155 P DG K 5 distorted distorted 6141 6156 6157 6158 6177 P DA K 6 distorted distorted 6163 6178 6179 6180 6198 P DA K 7 distorted distorted 6185 6199 6200 6201 6219 P DG K 8 distorted distorted 6206 6220 6221 6222 6241 P DG K 9 distorted distorted 6227 6242 6243 6244 6263 P DA K 10 distorted distorted 6249 6264 6265 6266 6284 P DT K 11 distorted distorted 6271 6285 6286 6287 6304 P DT K 12 distorted distorted 6292 6305 6306 6307 6339 P DOC K 13 OK OK 6312 6340 6341 6338 6343 P DT M 4 distorted distorted 6344 6345 6346 6385 P EFG M 5 distorted distorted 6351 6386 6387 6384 6388 P DG M 6 distorted distorted 6381 6389 6390 6391 6410 P DA M 7 distorted distorted 6396 6411 6412 6413 6431 P DA M 8 distorted distorted 6418 6432 6433 6434 6452 P DT M 9 distorted distorted 6439 6453 6454 6455 6472 P DC M 10 distorted distorted 6460 6473 6474 6475 6491 P DC M 11 distorted distorted 6480 6492 6493 6494 6510 P DT M 12 distorted distorted 6499 6511 6512 6513 6530 P DT M 13 distorted distorted 6518 6531 6532 6533 6550 P DC M 14 distorted distorted 6538 6551 6552 6553 6569 P DC M 15 distorted distorted 6558 6570 6571 6572 6588 P DC M 16 distorted distorted 6577 6589 6590 6591 ---------------------------------------------------------------------------------