ID code: '2PUE' 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' --------------------------------------------------------------------------------- 5330 C1' A B 700 beta 5326 5331 5329 5351 C1' C B 701 beta 5347 5352 5350 5370 C1' G B 702 beta 5366 5371 5369 5392 C1' C B 703 beta 5388 5393 5391 5411 C1' A B 704 beta 5407 5412 5410 5432 C1' A B 705 beta 5428 5433 5431 5453 C1' A B 706 beta 5449 5454 5452 5474 C1' C B 707 beta 5470 5475 5473 5493 C1' G B 708 beta 5489 5494 5492 5515 C1' T B 709 beta 5511 5516 5514 5535 C1' T B 710 beta 5531 5536 5534 5555 C1' T B 711 beta 5551 5556 5554 5575 C1' G B 712 beta 5571 5576 5574 5597 C1' C B 713 beta 5593 5598 5596 5616 C1' G B 714 beta 5612 5617 5615 5638 C1' T B 715 beta 5634 5639 5637 5676 C1' A E 700 beta 5672 5677 5675 5697 C1' C E 701 beta 5693 5698 5696 5716 C1' G E 702 beta 5712 5717 5715 5738 C1' C E 703 beta 5734 5739 5737 5757 C1' A E 704 beta 5753 5758 5756 5778 C1' A E 705 beta 5774 5779 5777 5799 C1' A E 706 beta 5795 5800 5798 5820 C1' C E 707 beta 5816 5821 5819 5839 C1' G E 708 beta 5835 5840 5838 5861 C1' T E 709 beta 5857 5862 5860 5881 C1' T E 710 beta 5877 5882 5880 5901 C1' T E 711 beta 5897 5902 5900 5921 C1' G E 712 beta 5917 5922 5920 5943 C1' C E 713 beta 5939 5944 5942 5962 C1' G E 714 beta 5958 5963 5961 5984 C1' T E 715 beta 5980 5985 5983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5329 C2' A B 700 5330 5327 5350 C2' C B 701 5351 5348 5369 C2' G B 702 5370 5367 5391 C2' C B 703 5392 5389 5410 C2' A B 704 5411 5408 5431 C2' A B 705 5432 5429 5452 C2' A B 706 5453 5450 5473 C2' C B 707 5474 5471 5492 C2' G B 708 5493 5490 5514 C2' T B 709 5515 5512 5534 C2' T B 710 5535 5532 5554 C2' T B 711 5555 5552 5574 C2' G B 712 5575 5572 5596 C2' C B 713 5597 5594 5615 C2' G B 714 5616 5613 5637 C2' T B 715 5638 5635 5675 C2' A E 700 5676 5673 5696 C2' C E 701 5697 5694 5715 C2' G E 702 5716 5713 5737 C2' C E 703 5738 5735 5756 C2' A E 704 5757 5754 5777 C2' A E 705 5778 5775 5798 C2' A E 706 5799 5796 5819 C2' C E 707 5820 5817 5838 C2' G E 708 5839 5836 5860 C2' T E 709 5861 5858 5880 C2' T E 710 5881 5878 5900 C2' T E 711 5901 5898 5920 C2' G E 712 5921 5918 5942 C2' C E 713 5943 5940 5961 C2' G E 714 5962 5959 5983 C2' T E 715 5984 5981 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5327 C3' A B 700 OK 5325 5328 5329 5348 C3' C B 701 OK 5346 5349 5350 5367 C3' G B 702 OK 5365 5368 5369 5389 C3' C B 703 OK 5387 5390 5391 5408 C3' A B 704 OK 5406 5409 5410 5429 C3' A B 705 OK 5427 5430 5431 5450 C3' A B 706 OK 5448 5451 5452 5471 C3' C B 707 OK 5469 5472 5473 5490 C3' G B 708 OK 5488 5491 5492 5512 C3' T B 709 OK 5510 5513 5514 5532 C3' T B 710 OK 5530 5533 5534 5552 C3' T B 711 OK 5550 5553 5554 5572 C3' G B 712 OK 5570 5573 5574 5594 C3' C B 713 OK 5592 5595 5596 5613 C3' G B 714 OK 5611 5614 5615 5635 C3' T B 715 OK 5633 5636 5637 5673 C3' A E 700 OK 5671 5674 5675 5694 C3' C E 701 OK 5692 5695 5696 5713 C3' G E 702 OK 5711 5714 5715 5735 C3' C E 703 OK 5733 5736 5737 5754 C3' A E 704 OK 5752 5755 5756 5775 C3' A E 705 OK 5773 5776 5777 5796 C3' A E 706 OK 5794 5797 5798 5817 C3' C E 707 OK 5815 5818 5819 5836 C3' G E 708 OK 5834 5837 5838 5858 C3' T E 709 OK 5856 5859 5860 5878 C3' T E 710 OK 5876 5879 5880 5898 C3' T E 711 OK 5896 5899 5900 5918 C3' G E 712 OK 5916 5919 5920 5940 C3' C E 713 OK 5938 5941 5942 5959 C3' G E 714 OK 5957 5960 5961 5981 C3' T E 715 OK 5979 5982 5983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5325 C4' A B 700 OK 5327 5324 5326 5346 C4' C B 701 OK 5348 5345 5347 5365 C4' G B 702 OK 5367 5364 5366 5387 C4' C B 703 OK 5389 5386 5388 5406 C4' A B 704 OK 5408 5405 5407 5427 C4' A B 705 OK 5429 5426 5428 5448 C4' A B 706 OK 5450 5447 5449 5469 C4' C B 707 OK 5471 5468 5470 5488 C4' G B 708 OK 5490 5487 5489 5510 C4' T B 709 OK 5512 5509 5511 5530 C4' T B 710 OK 5532 5529 5531 5550 C4' T B 711 OK 5552 5549 5551 5570 C4' G B 712 OK 5572 5569 5571 5592 C4' C B 713 OK 5594 5591 5593 5611 C4' G B 714 OK 5613 5610 5612 5633 C4' T B 715 OK 5635 5632 5634 5671 C4' A E 700 OK 5673 5670 5672 5692 C4' C E 701 OK 5694 5691 5693 5711 C4' G E 702 OK 5713 5710 5712 5733 C4' C E 703 OK 5735 5732 5734 5752 C4' A E 704 OK 5754 5751 5753 5773 C4' A E 705 OK 5775 5772 5774 5794 C4' A E 706 OK 5796 5793 5795 5815 C4' C E 707 OK 5817 5814 5816 5834 C4' G E 708 OK 5836 5833 5835 5856 C4' T E 709 OK 5858 5855 5857 5876 C4' T E 710 OK 5878 5875 5877 5896 C4' T E 711 OK 5898 5895 5897 5916 C4' G E 712 OK 5918 5915 5917 5938 C4' C E 713 OK 5940 5937 5939 5957 C4' G E 714 OK 5959 5956 5958 5979 C4' T E 715 OK 5981 5978 5980 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5324 C5' A B 700 5323 5325 5345 C5' C B 701 5344 5346 5364 C5' G B 702 5363 5365 5386 C5' C B 703 5385 5387 5405 C5' A B 704 5404 5406 5426 C5' A B 705 5425 5427 5447 C5' A B 706 5446 5448 5468 C5' C B 707 5467 5469 5487 C5' G B 708 5486 5488 5509 C5' T B 709 5508 5510 5529 C5' T B 710 5528 5530 5549 C5' T B 711 5548 5550 5569 C5' G B 712 5568 5570 5591 C5' C B 713 5590 5592 5610 C5' G B 714 5609 5611 5632 C5' T B 715 5631 5633 5670 C5' A E 700 5669 5671 5691 C5' C E 701 5690 5692 5710 C5' G E 702 5709 5711 5732 C5' C E 703 5731 5733 5751 C5' A E 704 5750 5752 5772 C5' A E 705 5771 5773 5793 C5' A E 706 5792 5794 5814 C5' C E 707 5813 5815 5833 C5' G E 708 5832 5834 5855 C5' T E 709 5854 5856 5875 C5' T E 710 5874 5876 5895 C5' T E 711 5894 5896 5915 C5' G E 712 5914 5916 5937 C5' C E 713 5936 5938 5956 C5' G E 714 5955 5957 5978 C5' T E 715 5977 5979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5341 P C B 701 distorted distorted 5328 5342 5343 5344 5360 P G B 702 distorted distorted 5349 5361 5362 5363 5382 P C B 703 distorted distorted 5368 5383 5384 5385 5401 P A B 704 distorted distorted 5390 5402 5403 5404 5422 P A B 705 distorted distorted 5409 5423 5424 5425 5443 P A B 706 distorted distorted 5430 5444 5445 5446 5464 P C B 707 distorted distorted 5451 5465 5466 5467 5483 P G B 708 distorted distorted 5472 5484 5485 5486 5505 P T B 709 distorted distorted 5491 5506 5507 5508 5525 P T B 710 distorted distorted 5513 5526 5527 5528 5545 P T B 711 distorted distorted 5533 5546 5547 5548 5565 P G B 712 distorted distorted 5553 5566 5567 5568 5587 P C B 713 distorted distorted 5573 5588 5589 5590 5606 P G B 714 distorted distorted 5595 5607 5608 5609 5628 P T B 715 distorted distorted 5614 5629 5630 5631 5687 P C E 701 distorted distorted 5674 5688 5689 5690 5706 P G E 702 distorted distorted 5695 5707 5708 5709 5728 P C E 703 distorted distorted 5714 5729 5730 5731 5747 P A E 704 distorted distorted 5736 5748 5749 5750 5768 P A E 705 distorted distorted 5755 5769 5770 5771 5789 P A E 706 distorted distorted 5776 5790 5791 5792 5810 P C E 707 distorted distorted 5797 5811 5812 5813 5829 P G E 708 distorted distorted 5818 5830 5831 5832 5851 P T E 709 distorted distorted 5837 5852 5853 5854 5871 P T E 710 distorted distorted 5859 5872 5873 5874 5891 P T E 711 distorted distorted 5879 5892 5893 5894 5911 P G E 712 distorted distorted 5899 5912 5913 5914 5933 P C E 713 distorted distorted 5919 5934 5935 5936 5952 P G E 714 distorted distorted 5941 5953 5954 5955 5974 P T E 715 distorted distorted 5960 5975 5976 5977 ---------------------------------------------------------------------------------