ID code: '2PUC' 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' --------------------------------------------------------------------------------- 5322 C1' A B 700 beta 5318 5323 5321 5343 C1' C B 701 beta 5339 5344 5342 5362 C1' G B 702 beta 5358 5363 5361 5384 C1' C B 703 beta 5380 5385 5383 5403 C1' A B 704 beta 5399 5404 5402 5424 C1' A B 705 beta 5420 5425 5423 5445 C1' A B 706 beta 5441 5446 5444 5466 C1' C B 707 beta 5462 5467 5465 5485 C1' G B 708 beta 5481 5486 5484 5507 C1' T B 709 beta 5503 5508 5506 5527 C1' T B 710 beta 5523 5528 5526 5547 C1' T B 711 beta 5543 5548 5546 5567 C1' G B 712 beta 5563 5568 5566 5589 C1' C B 713 beta 5585 5590 5588 5608 C1' G B 714 beta 5604 5609 5607 5630 C1' T B 715 beta 5626 5631 5629 5668 C1' A E 700 beta 5664 5669 5667 5689 C1' C E 701 beta 5685 5690 5688 5708 C1' G E 702 beta 5704 5709 5707 5730 C1' C E 703 beta 5726 5731 5729 5749 C1' A E 704 beta 5745 5750 5748 5770 C1' A E 705 beta 5766 5771 5769 5791 C1' A E 706 beta 5787 5792 5790 5812 C1' C E 707 beta 5808 5813 5811 5831 C1' G E 708 beta 5827 5832 5830 5853 C1' T E 709 beta 5849 5854 5852 5873 C1' T E 710 beta 5869 5874 5872 5893 C1' T E 711 beta 5889 5894 5892 5913 C1' G E 712 beta 5909 5914 5912 5935 C1' C E 713 beta 5931 5936 5934 5954 C1' G E 714 beta 5950 5955 5953 5976 C1' T E 715 beta 5972 5977 5975 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5321 C2' A B 700 5322 5319 5342 C2' C B 701 5343 5340 5361 C2' G B 702 5362 5359 5383 C2' C B 703 5384 5381 5402 C2' A B 704 5403 5400 5423 C2' A B 705 5424 5421 5444 C2' A B 706 5445 5442 5465 C2' C B 707 5466 5463 5484 C2' G B 708 5485 5482 5506 C2' T B 709 5507 5504 5526 C2' T B 710 5527 5524 5546 C2' T B 711 5547 5544 5566 C2' G B 712 5567 5564 5588 C2' C B 713 5589 5586 5607 C2' G B 714 5608 5605 5629 C2' T B 715 5630 5627 5667 C2' A E 700 5668 5665 5688 C2' C E 701 5689 5686 5707 C2' G E 702 5708 5705 5729 C2' C E 703 5730 5727 5748 C2' A E 704 5749 5746 5769 C2' A E 705 5770 5767 5790 C2' A E 706 5791 5788 5811 C2' C E 707 5812 5809 5830 C2' G E 708 5831 5828 5852 C2' T E 709 5853 5850 5872 C2' T E 710 5873 5870 5892 C2' T E 711 5893 5890 5912 C2' G E 712 5913 5910 5934 C2' C E 713 5935 5932 5953 C2' G E 714 5954 5951 5975 C2' T E 715 5976 5973 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5319 C3' A B 700 OK 5317 5320 5321 5340 C3' C B 701 OK 5338 5341 5342 5359 C3' G B 702 OK 5357 5360 5361 5381 C3' C B 703 OK 5379 5382 5383 5400 C3' A B 704 OK 5398 5401 5402 5421 C3' A B 705 OK 5419 5422 5423 5442 C3' A B 706 OK 5440 5443 5444 5463 C3' C B 707 OK 5461 5464 5465 5482 C3' G B 708 OK 5480 5483 5484 5504 C3' T B 709 OK 5502 5505 5506 5524 C3' T B 710 OK 5522 5525 5526 5544 C3' T B 711 OK 5542 5545 5546 5564 C3' G B 712 OK 5562 5565 5566 5586 C3' C B 713 OK 5584 5587 5588 5605 C3' G B 714 OK 5603 5606 5607 5627 C3' T B 715 OK 5625 5628 5629 5665 C3' A E 700 OK 5663 5666 5667 5686 C3' C E 701 OK 5684 5687 5688 5705 C3' G E 702 OK 5703 5706 5707 5727 C3' C E 703 OK 5725 5728 5729 5746 C3' A E 704 OK 5744 5747 5748 5767 C3' A E 705 OK 5765 5768 5769 5788 C3' A E 706 OK 5786 5789 5790 5809 C3' C E 707 OK 5807 5810 5811 5828 C3' G E 708 OK 5826 5829 5830 5850 C3' T E 709 OK 5848 5851 5852 5870 C3' T E 710 OK 5868 5871 5872 5890 C3' T E 711 OK 5888 5891 5892 5910 C3' G E 712 OK 5908 5911 5912 5932 C3' C E 713 OK 5930 5933 5934 5951 C3' G E 714 OK 5949 5952 5953 5973 C3' T E 715 OK 5971 5974 5975 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5317 C4' A B 700 OK 5319 5316 5318 5338 C4' C B 701 OK 5340 5337 5339 5357 C4' G B 702 OK 5359 5356 5358 5379 C4' C B 703 OK 5381 5378 5380 5398 C4' A B 704 OK 5400 5397 5399 5419 C4' A B 705 OK 5421 5418 5420 5440 C4' A B 706 OK 5442 5439 5441 5461 C4' C B 707 OK 5463 5460 5462 5480 C4' G B 708 OK 5482 5479 5481 5502 C4' T B 709 OK 5504 5501 5503 5522 C4' T B 710 OK 5524 5521 5523 5542 C4' T B 711 OK 5544 5541 5543 5562 C4' G B 712 OK 5564 5561 5563 5584 C4' C B 713 OK 5586 5583 5585 5603 C4' G B 714 OK 5605 5602 5604 5625 C4' T B 715 OK 5627 5624 5626 5663 C4' A E 700 OK 5665 5662 5664 5684 C4' C E 701 OK 5686 5683 5685 5703 C4' G E 702 OK 5705 5702 5704 5725 C4' C E 703 OK 5727 5724 5726 5744 C4' A E 704 OK 5746 5743 5745 5765 C4' A E 705 OK 5767 5764 5766 5786 C4' A E 706 OK 5788 5785 5787 5807 C4' C E 707 OK 5809 5806 5808 5826 C4' G E 708 OK 5828 5825 5827 5848 C4' T E 709 OK 5850 5847 5849 5868 C4' T E 710 OK 5870 5867 5869 5888 C4' T E 711 OK 5890 5887 5889 5908 C4' G E 712 OK 5910 5907 5909 5930 C4' C E 713 OK 5932 5929 5931 5949 C4' G E 714 OK 5951 5948 5950 5971 C4' T E 715 OK 5973 5970 5972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5316 C5' A B 700 5315 5317 5337 C5' C B 701 5336 5338 5356 C5' G B 702 5355 5357 5378 C5' C B 703 5377 5379 5397 C5' A B 704 5396 5398 5418 C5' A B 705 5417 5419 5439 C5' A B 706 5438 5440 5460 C5' C B 707 5459 5461 5479 C5' G B 708 5478 5480 5501 C5' T B 709 5500 5502 5521 C5' T B 710 5520 5522 5541 C5' T B 711 5540 5542 5561 C5' G B 712 5560 5562 5583 C5' C B 713 5582 5584 5602 C5' G B 714 5601 5603 5624 C5' T B 715 5623 5625 5662 C5' A E 700 5661 5663 5683 C5' C E 701 5682 5684 5702 C5' G E 702 5701 5703 5724 C5' C E 703 5723 5725 5743 C5' A E 704 5742 5744 5764 C5' A E 705 5763 5765 5785 C5' A E 706 5784 5786 5806 C5' C E 707 5805 5807 5825 C5' G E 708 5824 5826 5847 C5' T E 709 5846 5848 5867 C5' T E 710 5866 5868 5887 C5' T E 711 5886 5888 5907 C5' G E 712 5906 5908 5929 C5' C E 713 5928 5930 5948 C5' G E 714 5947 5949 5970 C5' T E 715 5969 5971 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5333 P C B 701 distorted distorted 5320 5334 5335 5336 5352 P G B 702 distorted distorted 5341 5353 5354 5355 5374 P C B 703 distorted distorted 5360 5375 5376 5377 5393 P A B 704 distorted distorted 5382 5394 5395 5396 5414 P A B 705 distorted distorted 5401 5415 5416 5417 5435 P A B 706 distorted distorted 5422 5436 5437 5438 5456 P C B 707 distorted distorted 5443 5457 5458 5459 5475 P G B 708 distorted distorted 5464 5476 5477 5478 5497 P T B 709 distorted distorted 5483 5498 5499 5500 5517 P T B 710 distorted distorted 5505 5518 5519 5520 5537 P T B 711 distorted distorted 5525 5538 5539 5540 5557 P G B 712 distorted distorted 5545 5558 5559 5560 5579 P C B 713 distorted distorted 5565 5580 5581 5582 5598 P G B 714 distorted distorted 5587 5599 5600 5601 5620 P T B 715 distorted distorted 5606 5621 5622 5623 5679 P C E 701 distorted distorted 5666 5680 5681 5682 5698 P G E 702 distorted distorted 5687 5699 5700 5701 5720 P C E 703 distorted distorted 5706 5721 5722 5723 5739 P A E 704 distorted distorted 5728 5740 5741 5742 5760 P A E 705 distorted distorted 5747 5761 5762 5763 5781 P A E 706 distorted distorted 5768 5782 5783 5784 5802 P C E 707 distorted distorted 5789 5803 5804 5805 5821 P G E 708 distorted distorted 5810 5822 5823 5824 5843 P T E 709 distorted distorted 5829 5844 5845 5846 5863 P T E 710 distorted distorted 5851 5864 5865 5866 5883 P T E 711 distorted distorted 5871 5884 5885 5886 5903 P G E 712 distorted distorted 5891 5904 5905 5906 5925 P C E 713 distorted distorted 5911 5926 5927 5928 5944 P G E 714 distorted distorted 5933 5945 5946 5947 5966 P T E 715 distorted distorted 5952 5967 5968 5969 ---------------------------------------------------------------------------------