ID code: '3NVI' 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' --------------------------------------------------------------------------------- 5845 C1' C E 2 beta 5840 5846 5843 5865 C1' U E 3 beta 5860 5866 5863 5885 C1' C E 4 beta 5880 5886 5883 5905 C1' U E 5 beta 5900 5906 5903 5925 C1' G E 6 beta 5920 5926 5923 5948 C1' A E 7 beta 5943 5949 5946 5970 C1' C E 8 beta 5965 5971 5968 5990 C1' C E 9 beta 5985 5991 5988 6010 C1' G E 10 beta 6005 6011 6008 6033 C1' A E 11 beta 6028 6034 6031 6055 C1' A E 12 beta 6050 6056 6053 6077 C1' A E 13 beta 6072 6078 6075 6099 C1' G E 14 beta 6094 6100 6097 6122 C1' G E 15 beta 6117 6123 6120 6145 C1' C E 16 beta 6140 6146 6143 6165 C1' G E 17 beta 6160 6166 6163 6188 C1' U E 18 beta 6183 6189 6186 6208 C1' G E 19 beta 6203 6209 6206 6231 C1' A E 20 beta 6226 6232 6229 6253 C1' U E 21 beta 6248 6254 6251 6273 C1' G E 22 beta 6268 6274 6271 6296 C1' A E 23 beta 6291 6297 6294 6318 C1' G E 24 beta 6313 6319 6316 6341 C1' C E 25 beta 6336 6342 6339 6359 C1' C F 2 beta 6354 6360 6357 6379 C1' U F 3 beta 6374 6380 6377 6399 C1' C F 4 beta 6394 6400 6397 6419 C1' U F 5 beta 6414 6420 6417 6439 C1' G F 6 beta 6434 6440 6437 6462 C1' A F 7 beta 6457 6463 6460 6484 C1' C F 8 beta 6479 6485 6482 6504 C1' C F 9 beta 6499 6505 6502 6524 C1' G F 10 beta 6519 6525 6522 6547 C1' A F 11 beta 6542 6548 6545 6569 C1' A F 12 beta 6564 6570 6567 6591 C1' A F 13 beta 6586 6592 6589 6613 C1' G F 14 beta 6608 6614 6611 6636 C1' G F 15 beta 6631 6637 6634 6659 C1' C F 16 beta 6654 6660 6657 6679 C1' G F 17 beta 6674 6680 6677 6702 C1' U F 18 beta 6697 6703 6700 6722 C1' G F 19 beta 6717 6723 6720 6745 C1' A F 20 beta 6740 6746 6743 6767 C1' U F 21 beta 6762 6768 6765 6787 C1' G F 22 beta 6782 6788 6785 6810 C1' A F 23 beta 6805 6811 6808 6832 C1' G F 24 beta 6827 6833 6830 6855 C1' C F 25 beta 6850 6856 6853 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5843 C2' C E 2 OK 5845 5841 5844 5863 C2' U E 3 OK 5865 5861 5864 5883 C2' C E 4 OK 5885 5881 5884 5903 C2' U E 5 OK 5905 5901 5904 5923 C2' G E 6 OK 5925 5921 5924 5946 C2' A E 7 OK 5948 5944 5947 5968 C2' C E 8 OK 5970 5966 5969 5988 C2' C E 9 OK 5990 5986 5989 6008 C2' G E 10 OK 6010 6006 6009 6031 C2' A E 11 OK 6033 6029 6032 6053 C2' A E 12 OK 6055 6051 6054 6075 C2' A E 13 OK 6077 6073 6076 6097 C2' G E 14 OK 6099 6095 6098 6120 C2' G E 15 OK 6122 6118 6121 6143 C2' C E 16 OK 6145 6141 6144 6163 C2' G E 17 OK 6165 6161 6164 6186 C2' U E 18 OK 6188 6184 6187 6206 C2' G E 19 OK 6208 6204 6207 6229 C2' A E 20 OK 6231 6227 6230 6251 C2' U E 21 OK 6253 6249 6252 6271 C2' G E 22 OK 6273 6269 6272 6294 C2' A E 23 OK 6296 6292 6295 6316 C2' G E 24 OK 6318 6314 6317 6339 C2' C E 25 OK 6341 6337 6340 6357 C2' C F 2 OK 6359 6355 6358 6377 C2' U F 3 OK 6379 6375 6378 6397 C2' C F 4 OK 6399 6395 6398 6417 C2' U F 5 OK 6419 6415 6418 6437 C2' G F 6 OK 6439 6435 6438 6460 C2' A F 7 OK 6462 6458 6461 6482 C2' C F 8 OK 6484 6480 6483 6502 C2' C F 9 OK 6504 6500 6503 6522 C2' G F 10 OK 6524 6520 6523 6545 C2' A F 11 OK 6547 6543 6546 6567 C2' A F 12 OK 6569 6565 6568 6589 C2' A F 13 OK 6591 6587 6590 6611 C2' G F 14 OK 6613 6609 6612 6634 C2' G F 15 OK 6636 6632 6635 6657 C2' C F 16 OK 6659 6655 6658 6677 C2' G F 17 OK 6679 6675 6678 6700 C2' U F 18 OK 6702 6698 6701 6720 C2' G F 19 OK 6722 6718 6721 6743 C2' A F 20 OK 6745 6741 6744 6765 C2' U F 21 OK 6767 6763 6766 6785 C2' G F 22 OK 6787 6783 6786 6808 C2' A F 23 OK 6810 6806 6809 6830 C2' G F 24 OK 6832 6828 6831 6853 C2' C F 25 OK 6855 6851 6854 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5841 C3' C E 2 OK 5839 5842 5843 5861 C3' U E 3 OK 5859 5862 5863 5881 C3' C E 4 OK 5879 5882 5883 5901 C3' U E 5 OK 5899 5902 5903 5921 C3' G E 6 OK 5919 5922 5923 5944 C3' A E 7 OK 5942 5945 5946 5966 C3' C E 8 OK 5964 5967 5968 5986 C3' C E 9 OK 5984 5987 5988 6006 C3' G E 10 OK 6004 6007 6008 6029 C3' A E 11 OK 6027 6030 6031 6051 C3' A E 12 OK 6049 6052 6053 6073 C3' A E 13 OK 6071 6074 6075 6095 C3' G E 14 OK 6093 6096 6097 6118 C3' G E 15 OK 6116 6119 6120 6141 C3' C E 16 OK 6139 6142 6143 6161 C3' G E 17 OK 6159 6162 6163 6184 C3' U E 18 OK 6182 6185 6186 6204 C3' G E 19 OK 6202 6205 6206 6227 C3' A E 20 OK 6225 6228 6229 6249 C3' U E 21 OK 6247 6250 6251 6269 C3' G E 22 OK 6267 6270 6271 6292 C3' A E 23 OK 6290 6293 6294 6314 C3' G E 24 OK 6312 6315 6316 6337 C3' C E 25 OK 6335 6338 6339 6355 C3' C F 2 OK 6353 6356 6357 6375 C3' U F 3 OK 6373 6376 6377 6395 C3' C F 4 OK 6393 6396 6397 6415 C3' U F 5 OK 6413 6416 6417 6435 C3' G F 6 OK 6433 6436 6437 6458 C3' A F 7 OK 6456 6459 6460 6480 C3' C F 8 OK 6478 6481 6482 6500 C3' C F 9 OK 6498 6501 6502 6520 C3' G F 10 OK 6518 6521 6522 6543 C3' A F 11 OK 6541 6544 6545 6565 C3' A F 12 OK 6563 6566 6567 6587 C3' A F 13 OK 6585 6588 6589 6609 C3' G F 14 OK 6607 6610 6611 6632 C3' G F 15 OK 6630 6633 6634 6655 C3' C F 16 OK 6653 6656 6657 6675 C3' G F 17 OK 6673 6676 6677 6698 C3' U F 18 OK 6696 6699 6700 6718 C3' G F 19 OK 6716 6719 6720 6741 C3' A F 20 OK 6739 6742 6743 6763 C3' U F 21 OK 6761 6764 6765 6783 C3' G F 22 OK 6781 6784 6785 6806 C3' A F 23 OK 6804 6807 6808 6828 C3' G F 24 OK 6826 6829 6830 6851 C3' C F 25 OK 6849 6852 6853 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5839 C4' C E 2 OK 5841 5838 5840 5859 C4' U E 3 OK 5861 5858 5860 5879 C4' C E 4 OK 5881 5878 5880 5899 C4' U E 5 OK 5901 5898 5900 5919 C4' G E 6 OK 5921 5918 5920 5942 C4' A E 7 OK 5944 5941 5943 5964 C4' C E 8 OK 5966 5963 5965 5984 C4' C E 9 OK 5986 5983 5985 6004 C4' G E 10 OK 6006 6003 6005 6027 C4' A E 11 OK 6029 6026 6028 6049 C4' A E 12 OK 6051 6048 6050 6071 C4' A E 13 OK 6073 6070 6072 6093 C4' G E 14 OK 6095 6092 6094 6116 C4' G E 15 OK 6118 6115 6117 6139 C4' C E 16 OK 6141 6138 6140 6159 C4' G E 17 OK 6161 6158 6160 6182 C4' U E 18 OK 6184 6181 6183 6202 C4' G E 19 OK 6204 6201 6203 6225 C4' A E 20 OK 6227 6224 6226 6247 C4' U E 21 OK 6249 6246 6248 6267 C4' G E 22 OK 6269 6266 6268 6290 C4' A E 23 OK 6292 6289 6291 6312 C4' G E 24 OK 6314 6311 6313 6335 C4' C E 25 OK 6337 6334 6336 6353 C4' C F 2 OK 6355 6352 6354 6373 C4' U F 3 OK 6375 6372 6374 6393 C4' C F 4 OK 6395 6392 6394 6413 C4' U F 5 OK 6415 6412 6414 6433 C4' G F 6 OK 6435 6432 6434 6456 C4' A F 7 OK 6458 6455 6457 6478 C4' C F 8 OK 6480 6477 6479 6498 C4' C F 9 OK 6500 6497 6499 6518 C4' G F 10 OK 6520 6517 6519 6541 C4' A F 11 OK 6543 6540 6542 6563 C4' A F 12 OK 6565 6562 6564 6585 C4' A F 13 OK 6587 6584 6586 6607 C4' G F 14 OK 6609 6606 6608 6630 C4' G F 15 OK 6632 6629 6631 6653 C4' C F 16 OK 6655 6652 6654 6673 C4' G F 17 OK 6675 6672 6674 6696 C4' U F 18 OK 6698 6695 6697 6716 C4' G F 19 OK 6718 6715 6717 6739 C4' A F 20 OK 6741 6738 6740 6761 C4' U F 21 OK 6763 6760 6762 6781 C4' G F 22 OK 6783 6780 6782 6804 C4' A F 23 OK 6806 6803 6805 6826 C4' G F 24 OK 6828 6825 6827 6849 C4' C F 25 OK 6851 6848 6850 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5838 C5' C E 2 5837 5839 5858 C5' U E 3 5857 5859 5878 C5' C E 4 5877 5879 5898 C5' U E 5 5897 5899 5918 C5' G E 6 5917 5919 5941 C5' A E 7 5940 5942 5963 C5' C E 8 5962 5964 5983 C5' C E 9 5982 5984 6003 C5' G E 10 6002 6004 6026 C5' A E 11 6025 6027 6048 C5' A E 12 6047 6049 6070 C5' A E 13 6069 6071 6092 C5' G E 14 6091 6093 6115 C5' G E 15 6114 6116 6138 C5' C E 16 6137 6139 6158 C5' G E 17 6157 6159 6181 C5' U E 18 6180 6182 6201 C5' G E 19 6200 6202 6224 C5' A E 20 6223 6225 6246 C5' U E 21 6245 6247 6266 C5' G E 22 6265 6267 6289 C5' A E 23 6288 6290 6311 C5' G E 24 6310 6312 6334 C5' C E 25 6333 6335 6352 C5' C F 2 6351 6353 6372 C5' U F 3 6371 6373 6392 C5' C F 4 6391 6393 6412 C5' U F 5 6411 6413 6432 C5' G F 6 6431 6433 6455 C5' A F 7 6454 6456 6477 C5' C F 8 6476 6478 6497 C5' C F 9 6496 6498 6517 C5' G F 10 6516 6518 6540 C5' A F 11 6539 6541 6562 C5' A F 12 6561 6563 6584 C5' A F 13 6583 6585 6606 C5' G F 14 6605 6607 6629 C5' G F 15 6628 6630 6652 C5' C F 16 6651 6653 6672 C5' G F 17 6671 6673 6695 C5' U F 18 6694 6696 6715 C5' G F 19 6714 6716 6738 C5' A F 20 6737 6739 6760 C5' U F 21 6759 6761 6780 C5' G F 22 6779 6781 6803 C5' A F 23 6802 6804 6825 C5' G F 24 6824 6826 6848 C5' C F 25 6847 6849 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5854 P U E 3 distorted distorted 5842 5855 5856 5857 5874 P C E 4 distorted distorted 5862 5875 5876 5877 5894 P U E 5 distorted distorted 5882 5895 5896 5897 5914 P G E 6 distorted distorted 5902 5915 5916 5917 5937 P A E 7 distorted distorted 5922 5938 5939 5940 5959 P C E 8 distorted distorted 5945 5960 5961 5962 5979 P C E 9 distorted distorted 5967 5980 5981 5982 5999 P G E 10 distorted distorted 5987 6000 6001 6002 6022 P A E 11 distorted distorted 6007 6023 6024 6025 6044 P A E 12 distorted distorted 6030 6045 6046 6047 6066 P A E 13 distorted distorted 6052 6067 6068 6069 6088 P G E 14 distorted distorted 6074 6089 6090 6091 6111 P G E 15 distorted distorted 6096 6112 6113 6114 6134 P C E 16 distorted distorted 6119 6135 6136 6137 6154 P G E 17 distorted distorted 6142 6155 6156 6157 6177 P U E 18 distorted distorted 6162 6178 6179 6180 6197 P G E 19 distorted distorted 6185 6198 6199 6200 6220 P A E 20 distorted distorted 6205 6221 6222 6223 6242 P U E 21 distorted distorted 6228 6243 6244 6245 6262 P G E 22 distorted distorted 6250 6263 6264 6265 6285 P A E 23 distorted distorted 6270 6286 6287 6288 6307 P G E 24 distorted distorted 6293 6308 6309 6310 6330 P C E 25 distorted distorted 6315 6331 6332 6333 6368 P U F 3 distorted distorted 6356 6369 6370 6371 6388 P C F 4 distorted distorted 6376 6389 6390 6391 6408 P U F 5 distorted distorted 6396 6409 6410 6411 6428 P G F 6 distorted distorted 6416 6429 6430 6431 6451 P A F 7 distorted distorted 6436 6452 6453 6454 6473 P C F 8 distorted distorted 6459 6474 6475 6476 6493 P C F 9 distorted distorted 6481 6494 6495 6496 6513 P G F 10 distorted distorted 6501 6514 6515 6516 6536 P A F 11 distorted distorted 6521 6537 6538 6539 6558 P A F 12 distorted distorted 6544 6559 6560 6561 6580 P A F 13 distorted distorted 6566 6581 6582 6583 6602 P G F 14 distorted distorted 6588 6603 6604 6605 6625 P G F 15 distorted distorted 6610 6626 6627 6628 6648 P C F 16 distorted distorted 6633 6649 6650 6651 6668 P G F 17 distorted distorted 6656 6669 6670 6671 6691 P U F 18 distorted distorted 6676 6692 6693 6694 6711 P G F 19 distorted distorted 6699 6712 6713 6714 6734 P A F 20 distorted distorted 6719 6735 6736 6737 6756 P U F 21 distorted distorted 6742 6757 6758 6759 6776 P G F 22 distorted distorted 6764 6777 6778 6779 6799 P A F 23 distorted distorted 6784 6800 6801 6802 6821 P G F 24 distorted distorted 6807 6822 6823 6824 6844 P C F 25 distorted distorted 6829 6845 6846 6847 ---------------------------------------------------------------------------------