ID code: '1BDH' 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' --------------------------------------------------------------------------------- 5326 C1' A B 700 beta 5322 5327 5325 5347 C1' C B 701 beta 5343 5348 5346 5366 C1' G B 702 beta 5362 5367 5365 5388 C1' C B 703 beta 5384 5389 5387 5407 C1' A B 704 beta 5403 5408 5406 5428 C1' A B 705 beta 5424 5429 5427 5449 C1' A B 706 beta 5445 5450 5448 5470 C1' C B 707 beta 5466 5471 5469 5489 C1' G B 708 beta 5485 5490 5488 5511 C1' T B 709 beta 5507 5512 5510 5531 C1' T B 710 beta 5527 5532 5530 5551 C1' T B 711 beta 5547 5552 5550 5571 C1' G B 712 beta 5567 5572 5570 5593 C1' C B 713 beta 5589 5594 5592 5612 C1' G B 714 beta 5608 5613 5611 5634 C1' T B 715 beta 5630 5635 5633 5672 C1' A D 700 beta 5668 5673 5671 5693 C1' C D 701 beta 5689 5694 5692 5712 C1' G D 702 beta 5708 5713 5711 5734 C1' C D 703 beta 5730 5735 5733 5753 C1' A D 704 beta 5749 5754 5752 5774 C1' A D 705 beta 5770 5775 5773 5795 C1' A D 706 beta 5791 5796 5794 5816 C1' C D 707 beta 5812 5817 5815 5835 C1' G D 708 beta 5831 5836 5834 5857 C1' T D 709 beta 5853 5858 5856 5877 C1' T D 710 beta 5873 5878 5876 5897 C1' T D 711 beta 5893 5898 5896 5917 C1' G D 712 beta 5913 5918 5916 5939 C1' C D 713 beta 5935 5940 5938 5958 C1' G D 714 beta 5954 5959 5957 5980 C1' T D 715 beta 5976 5981 5979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5325 C2' A B 700 5326 5323 5346 C2' C B 701 5347 5344 5365 C2' G B 702 5366 5363 5387 C2' C B 703 5388 5385 5406 C2' A B 704 5407 5404 5427 C2' A B 705 5428 5425 5448 C2' A B 706 5449 5446 5469 C2' C B 707 5470 5467 5488 C2' G B 708 5489 5486 5510 C2' T B 709 5511 5508 5530 C2' T B 710 5531 5528 5550 C2' T B 711 5551 5548 5570 C2' G B 712 5571 5568 5592 C2' C B 713 5593 5590 5611 C2' G B 714 5612 5609 5633 C2' T B 715 5634 5631 5671 C2' A D 700 5672 5669 5692 C2' C D 701 5693 5690 5711 C2' G D 702 5712 5709 5733 C2' C D 703 5734 5731 5752 C2' A D 704 5753 5750 5773 C2' A D 705 5774 5771 5794 C2' A D 706 5795 5792 5815 C2' C D 707 5816 5813 5834 C2' G D 708 5835 5832 5856 C2' T D 709 5857 5854 5876 C2' T D 710 5877 5874 5896 C2' T D 711 5897 5894 5916 C2' G D 712 5917 5914 5938 C2' C D 713 5939 5936 5957 C2' G D 714 5958 5955 5979 C2' T D 715 5980 5977 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5323 C3' A B 700 OK 5321 5324 5325 5344 C3' C B 701 OK 5342 5345 5346 5363 C3' G B 702 OK 5361 5364 5365 5385 C3' C B 703 OK 5383 5386 5387 5404 C3' A B 704 OK 5402 5405 5406 5425 C3' A B 705 OK 5423 5426 5427 5446 C3' A B 706 OK 5444 5447 5448 5467 C3' C B 707 OK 5465 5468 5469 5486 C3' G B 708 OK 5484 5487 5488 5508 C3' T B 709 OK 5506 5509 5510 5528 C3' T B 710 OK 5526 5529 5530 5548 C3' T B 711 OK 5546 5549 5550 5568 C3' G B 712 OK 5566 5569 5570 5590 C3' C B 713 OK 5588 5591 5592 5609 C3' G B 714 OK 5607 5610 5611 5631 C3' T B 715 OK 5629 5632 5633 5669 C3' A D 700 OK 5667 5670 5671 5690 C3' C D 701 OK 5688 5691 5692 5709 C3' G D 702 OK 5707 5710 5711 5731 C3' C D 703 OK 5729 5732 5733 5750 C3' A D 704 OK 5748 5751 5752 5771 C3' A D 705 OK 5769 5772 5773 5792 C3' A D 706 OK 5790 5793 5794 5813 C3' C D 707 OK 5811 5814 5815 5832 C3' G D 708 OK 5830 5833 5834 5854 C3' T D 709 OK 5852 5855 5856 5874 C3' T D 710 OK 5872 5875 5876 5894 C3' T D 711 OK 5892 5895 5896 5914 C3' G D 712 OK 5912 5915 5916 5936 C3' C D 713 OK 5934 5937 5938 5955 C3' G D 714 OK 5953 5956 5957 5977 C3' T D 715 OK 5975 5978 5979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5321 C4' A B 700 OK 5323 5320 5322 5342 C4' C B 701 OK 5344 5341 5343 5361 C4' G B 702 OK 5363 5360 5362 5383 C4' C B 703 OK 5385 5382 5384 5402 C4' A B 704 OK 5404 5401 5403 5423 C4' A B 705 OK 5425 5422 5424 5444 C4' A B 706 OK 5446 5443 5445 5465 C4' C B 707 OK 5467 5464 5466 5484 C4' G B 708 OK 5486 5483 5485 5506 C4' T B 709 OK 5508 5505 5507 5526 C4' T B 710 OK 5528 5525 5527 5546 C4' T B 711 OK 5548 5545 5547 5566 C4' G B 712 OK 5568 5565 5567 5588 C4' C B 713 OK 5590 5587 5589 5607 C4' G B 714 OK 5609 5606 5608 5629 C4' T B 715 OK 5631 5628 5630 5667 C4' A D 700 OK 5669 5666 5668 5688 C4' C D 701 OK 5690 5687 5689 5707 C4' G D 702 OK 5709 5706 5708 5729 C4' C D 703 OK 5731 5728 5730 5748 C4' A D 704 OK 5750 5747 5749 5769 C4' A D 705 OK 5771 5768 5770 5790 C4' A D 706 OK 5792 5789 5791 5811 C4' C D 707 OK 5813 5810 5812 5830 C4' G D 708 OK 5832 5829 5831 5852 C4' T D 709 OK 5854 5851 5853 5872 C4' T D 710 OK 5874 5871 5873 5892 C4' T D 711 OK 5894 5891 5893 5912 C4' G D 712 OK 5914 5911 5913 5934 C4' C D 713 OK 5936 5933 5935 5953 C4' G D 714 OK 5955 5952 5954 5975 C4' T D 715 OK 5977 5974 5976 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5320 C5' A B 700 5319 5321 5341 C5' C B 701 5340 5342 5360 C5' G B 702 5359 5361 5382 C5' C B 703 5381 5383 5401 C5' A B 704 5400 5402 5422 C5' A B 705 5421 5423 5443 C5' A B 706 5442 5444 5464 C5' C B 707 5463 5465 5483 C5' G B 708 5482 5484 5505 C5' T B 709 5504 5506 5525 C5' T B 710 5524 5526 5545 C5' T B 711 5544 5546 5565 C5' G B 712 5564 5566 5587 C5' C B 713 5586 5588 5606 C5' G B 714 5605 5607 5628 C5' T B 715 5627 5629 5666 C5' A D 700 5665 5667 5687 C5' C D 701 5686 5688 5706 C5' G D 702 5705 5707 5728 C5' C D 703 5727 5729 5747 C5' A D 704 5746 5748 5768 C5' A D 705 5767 5769 5789 C5' A D 706 5788 5790 5810 C5' C D 707 5809 5811 5829 C5' G D 708 5828 5830 5851 C5' T D 709 5850 5852 5871 C5' T D 710 5870 5872 5891 C5' T D 711 5890 5892 5911 C5' G D 712 5910 5912 5933 C5' C D 713 5932 5934 5952 C5' G D 714 5951 5953 5974 C5' T D 715 5973 5975 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5337 P C B 701 OK OK 5324 5338 5339 5340 5356 P G B 702 OK OK 5345 5357 5358 5359 5378 P C B 703 OK OK 5364 5379 5380 5381 5397 P A B 704 OK OK 5386 5398 5399 5400 5418 P A B 705 OK OK 5405 5419 5420 5421 5439 P A B 706 OK OK 5426 5440 5441 5442 5460 P C B 707 OK OK 5447 5461 5462 5463 5479 P G B 708 OK OK 5468 5480 5481 5482 5501 P T B 709 OK OK 5487 5502 5503 5504 5521 P T B 710 OK OK 5509 5522 5523 5524 5541 P T B 711 OK OK 5529 5542 5543 5544 5561 P G B 712 OK OK 5549 5562 5563 5564 5583 P C B 713 OK OK 5569 5584 5585 5586 5602 P G B 714 OK OK 5591 5603 5604 5605 5624 P T B 715 OK OK 5610 5625 5626 5627 5683 P C D 701 OK OK 5670 5684 5685 5686 5702 P G D 702 OK OK 5691 5703 5704 5705 5724 P C D 703 OK OK 5710 5725 5726 5727 5743 P A D 704 OK OK 5732 5744 5745 5746 5764 P A D 705 OK OK 5751 5765 5766 5767 5785 P A D 706 OK OK 5772 5786 5787 5788 5806 P C D 707 OK OK 5793 5807 5808 5809 5825 P G D 708 OK OK 5814 5826 5827 5828 5847 P T D 709 OK OK 5833 5848 5849 5850 5867 P T D 710 OK OK 5855 5868 5869 5870 5887 P T D 711 OK OK 5875 5888 5889 5890 5907 P G D 712 OK OK 5895 5908 5909 5910 5929 P C D 713 OK OK 5915 5930 5931 5932 5948 P G D 714 OK OK 5937 5949 5950 5951 5970 P T D 715 OK OK 5956 5971 5972 5973 ---------------------------------------------------------------------------------