ID code: '1BDI' 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' --------------------------------------------------------------------------------- 5334 C1' A B 700 beta 5330 5335 5333 5355 C1' C B 701 beta 5351 5356 5354 5374 C1' G B 702 beta 5370 5375 5373 5396 C1' C B 703 beta 5392 5397 5395 5415 C1' A B 704 beta 5411 5416 5414 5436 C1' A B 705 beta 5432 5437 5435 5457 C1' A B 706 beta 5453 5458 5456 5478 C1' C B 707 beta 5474 5479 5477 5497 C1' G B 708 beta 5493 5498 5496 5519 C1' T B 709 beta 5515 5520 5518 5539 C1' T B 710 beta 5535 5540 5538 5559 C1' T B 711 beta 5555 5560 5558 5579 C1' G B 712 beta 5575 5580 5578 5601 C1' C B 713 beta 5597 5602 5600 5620 C1' G B 714 beta 5616 5621 5619 5642 C1' T B 715 beta 5638 5643 5641 5680 C1' A D 700 beta 5676 5681 5679 5701 C1' C D 701 beta 5697 5702 5700 5720 C1' G D 702 beta 5716 5721 5719 5742 C1' C D 703 beta 5738 5743 5741 5761 C1' A D 704 beta 5757 5762 5760 5782 C1' A D 705 beta 5778 5783 5781 5803 C1' A D 706 beta 5799 5804 5802 5824 C1' C D 707 beta 5820 5825 5823 5843 C1' G D 708 beta 5839 5844 5842 5865 C1' T D 709 beta 5861 5866 5864 5885 C1' T D 710 beta 5881 5886 5884 5905 C1' T D 711 beta 5901 5906 5904 5925 C1' G D 712 beta 5921 5926 5924 5947 C1' C D 713 beta 5943 5948 5946 5966 C1' G D 714 beta 5962 5967 5965 5988 C1' T D 715 beta 5984 5989 5987 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5333 C2' A B 700 5334 5331 5354 C2' C B 701 5355 5352 5373 C2' G B 702 5374 5371 5395 C2' C B 703 5396 5393 5414 C2' A B 704 5415 5412 5435 C2' A B 705 5436 5433 5456 C2' A B 706 5457 5454 5477 C2' C B 707 5478 5475 5496 C2' G B 708 5497 5494 5518 C2' T B 709 5519 5516 5538 C2' T B 710 5539 5536 5558 C2' T B 711 5559 5556 5578 C2' G B 712 5579 5576 5600 C2' C B 713 5601 5598 5619 C2' G B 714 5620 5617 5641 C2' T B 715 5642 5639 5679 C2' A D 700 5680 5677 5700 C2' C D 701 5701 5698 5719 C2' G D 702 5720 5717 5741 C2' C D 703 5742 5739 5760 C2' A D 704 5761 5758 5781 C2' A D 705 5782 5779 5802 C2' A D 706 5803 5800 5823 C2' C D 707 5824 5821 5842 C2' G D 708 5843 5840 5864 C2' T D 709 5865 5862 5884 C2' T D 710 5885 5882 5904 C2' T D 711 5905 5902 5924 C2' G D 712 5925 5922 5946 C2' C D 713 5947 5944 5965 C2' G D 714 5966 5963 5987 C2' T D 715 5988 5985 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5331 C3' A B 700 OK 5329 5332 5333 5352 C3' C B 701 OK 5350 5353 5354 5371 C3' G B 702 OK 5369 5372 5373 5393 C3' C B 703 OK 5391 5394 5395 5412 C3' A B 704 OK 5410 5413 5414 5433 C3' A B 705 OK 5431 5434 5435 5454 C3' A B 706 OK 5452 5455 5456 5475 C3' C B 707 OK 5473 5476 5477 5494 C3' G B 708 OK 5492 5495 5496 5516 C3' T B 709 OK 5514 5517 5518 5536 C3' T B 710 OK 5534 5537 5538 5556 C3' T B 711 OK 5554 5557 5558 5576 C3' G B 712 OK 5574 5577 5578 5598 C3' C B 713 OK 5596 5599 5600 5617 C3' G B 714 OK 5615 5618 5619 5639 C3' T B 715 OK 5637 5640 5641 5677 C3' A D 700 OK 5675 5678 5679 5698 C3' C D 701 OK 5696 5699 5700 5717 C3' G D 702 OK 5715 5718 5719 5739 C3' C D 703 OK 5737 5740 5741 5758 C3' A D 704 OK 5756 5759 5760 5779 C3' A D 705 OK 5777 5780 5781 5800 C3' A D 706 OK 5798 5801 5802 5821 C3' C D 707 OK 5819 5822 5823 5840 C3' G D 708 OK 5838 5841 5842 5862 C3' T D 709 OK 5860 5863 5864 5882 C3' T D 710 OK 5880 5883 5884 5902 C3' T D 711 OK 5900 5903 5904 5922 C3' G D 712 OK 5920 5923 5924 5944 C3' C D 713 OK 5942 5945 5946 5963 C3' G D 714 OK 5961 5964 5965 5985 C3' T D 715 OK 5983 5986 5987 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5329 C4' A B 700 OK 5331 5328 5330 5350 C4' C B 701 OK 5352 5349 5351 5369 C4' G B 702 OK 5371 5368 5370 5391 C4' C B 703 OK 5393 5390 5392 5410 C4' A B 704 OK 5412 5409 5411 5431 C4' A B 705 OK 5433 5430 5432 5452 C4' A B 706 OK 5454 5451 5453 5473 C4' C B 707 OK 5475 5472 5474 5492 C4' G B 708 OK 5494 5491 5493 5514 C4' T B 709 OK 5516 5513 5515 5534 C4' T B 710 OK 5536 5533 5535 5554 C4' T B 711 OK 5556 5553 5555 5574 C4' G B 712 OK 5576 5573 5575 5596 C4' C B 713 OK 5598 5595 5597 5615 C4' G B 714 OK 5617 5614 5616 5637 C4' T B 715 OK 5639 5636 5638 5675 C4' A D 700 OK 5677 5674 5676 5696 C4' C D 701 OK 5698 5695 5697 5715 C4' G D 702 OK 5717 5714 5716 5737 C4' C D 703 OK 5739 5736 5738 5756 C4' A D 704 OK 5758 5755 5757 5777 C4' A D 705 OK 5779 5776 5778 5798 C4' A D 706 OK 5800 5797 5799 5819 C4' C D 707 OK 5821 5818 5820 5838 C4' G D 708 OK 5840 5837 5839 5860 C4' T D 709 OK 5862 5859 5861 5880 C4' T D 710 OK 5882 5879 5881 5900 C4' T D 711 OK 5902 5899 5901 5920 C4' G D 712 OK 5922 5919 5921 5942 C4' C D 713 OK 5944 5941 5943 5961 C4' G D 714 OK 5963 5960 5962 5983 C4' T D 715 OK 5985 5982 5984 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5328 C5' A B 700 5327 5329 5349 C5' C B 701 5348 5350 5368 C5' G B 702 5367 5369 5390 C5' C B 703 5389 5391 5409 C5' A B 704 5408 5410 5430 C5' A B 705 5429 5431 5451 C5' A B 706 5450 5452 5472 C5' C B 707 5471 5473 5491 C5' G B 708 5490 5492 5513 C5' T B 709 5512 5514 5533 C5' T B 710 5532 5534 5553 C5' T B 711 5552 5554 5573 C5' G B 712 5572 5574 5595 C5' C B 713 5594 5596 5614 C5' G B 714 5613 5615 5636 C5' T B 715 5635 5637 5674 C5' A D 700 5673 5675 5695 C5' C D 701 5694 5696 5714 C5' G D 702 5713 5715 5736 C5' C D 703 5735 5737 5755 C5' A D 704 5754 5756 5776 C5' A D 705 5775 5777 5797 C5' A D 706 5796 5798 5818 C5' C D 707 5817 5819 5837 C5' G D 708 5836 5838 5859 C5' T D 709 5858 5860 5879 C5' T D 710 5878 5880 5899 C5' T D 711 5898 5900 5919 C5' G D 712 5918 5920 5941 C5' C D 713 5940 5942 5960 C5' G D 714 5959 5961 5982 C5' T D 715 5981 5983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5345 P C B 701 distorted distorted 5332 5346 5347 5348 5364 P G B 702 distorted distorted 5353 5365 5366 5367 5386 P C B 703 distorted distorted 5372 5387 5388 5389 5405 P A B 704 distorted distorted 5394 5406 5407 5408 5426 P A B 705 OK OK 5413 5427 5428 5429 5447 P A B 706 distorted distorted 5434 5448 5449 5450 5468 P C B 707 OK OK 5455 5469 5470 5471 5487 P G B 708 distorted distorted 5476 5488 5489 5490 5509 P T B 709 distorted distorted 5495 5510 5511 5512 5529 P T B 710 distorted distorted 5517 5530 5531 5532 5549 P T B 711 distorted distorted 5537 5550 5551 5552 5569 P G B 712 distorted distorted 5557 5570 5571 5572 5591 P C B 713 OK OK 5577 5592 5593 5594 5610 P G B 714 OK OK 5599 5611 5612 5613 5632 P T B 715 OK OK 5618 5633 5634 5635 5691 P C D 701 distorted distorted 5678 5692 5693 5694 5710 P G D 702 distorted distorted 5699 5711 5712 5713 5732 P C D 703 distorted distorted 5718 5733 5734 5735 5751 P A D 704 distorted distorted 5740 5752 5753 5754 5772 P A D 705 OK OK 5759 5773 5774 5775 5793 P A D 706 distorted distorted 5780 5794 5795 5796 5814 P C D 707 OK OK 5801 5815 5816 5817 5833 P G D 708 distorted distorted 5822 5834 5835 5836 5855 P T D 709 distorted distorted 5841 5856 5857 5858 5875 P T D 710 distorted distorted 5863 5876 5877 5878 5895 P T D 711 distorted distorted 5883 5896 5897 5898 5915 P G D 712 distorted distorted 5903 5916 5917 5918 5937 P C D 713 OK OK 5923 5938 5939 5940 5956 P G D 714 OK OK 5945 5957 5958 5959 5978 P T D 715 OK OK 5964 5979 5980 5981 ---------------------------------------------------------------------------------