ID code: '3K58' 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' --------------------------------------------------------------------------------- 6341 C1' DT T 802 beta 6337 6342 6340 6361 C1' DA T 803 beta 6357 6362 6360 6382 C1' DA T 804 beta 6378 6383 6381 6403 C1' DG T 805 beta 6399 6404 6402 6425 C1' DT T 806 beta 6421 6426 6424 6445 C1' DA T 807 beta 6441 6446 6444 6466 C1' DC T 808 beta 6462 6467 6465 6485 C1' DG T 809 beta 6481 6486 6484 6507 C1' DC T 810 beta 6503 6508 6506 6526 C1' DT T 811 beta 6522 6527 6525 6546 C1' DA T 812 beta 6542 6547 6545 6567 C1' DG T 813 beta 6563 6568 6566 6589 C1' DG T 814 beta 6585 6590 6588 6611 C1' DC T 815 beta 6607 6612 6610 6630 C1' DA T 816 beta 6626 6631 6629 6651 C1' DC T 817 beta 6647 6652 6650 6670 C1' DA T 818 beta 6666 6671 6669 6689 C1' DG P 901 beta 6685 6690 6688 6711 C1' DT P 902 beta 6707 6712 6710 6731 C1' DG P 903 beta 6727 6732 6730 6753 C1' DC P 904 beta 6749 6754 6752 6772 C1' DC P 905 beta 6768 6773 6771 6791 C1' DT P 906 beta 6787 6792 6790 6811 C1' DA P 907 beta 6807 6812 6810 6832 C1' DG P 908 beta 6828 6833 6831 6854 C1' DC P 909 beta 6850 6855 6853 6873 C1' DG P 910 beta 6869 6874 6872 6895 C1' DT P 911 beta 6891 6896 6894 6915 C1' DA P 912 beta 6911 6916 6914 6934 C1' DOC P 913 beta 6938 6926 6935 6964 C1' TTP A 914 beta 6960 6965 6963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6340 C2' DT T 802 6341 6338 6360 C2' DA T 803 6361 6358 6381 C2' DA T 804 6382 6379 6402 C2' DG T 805 6403 6400 6424 C2' DT T 806 6425 6422 6444 C2' DA T 807 6445 6442 6465 C2' DC T 808 6466 6463 6484 C2' DG T 809 6485 6482 6506 C2' DC T 810 6507 6504 6525 C2' DT T 811 6526 6523 6545 C2' DA T 812 6546 6543 6566 C2' DG T 813 6567 6564 6588 C2' DG T 814 6589 6586 6610 C2' DC T 815 6611 6608 6629 C2' DA T 816 6630 6627 6650 C2' DC T 817 6651 6648 6669 C2' DA T 818 6670 6667 6688 C2' DG P 901 6689 6686 6710 C2' DT P 902 6711 6708 6730 C2' DG P 903 6731 6728 6752 C2' DC P 904 6753 6750 6771 C2' DC P 905 6772 6769 6790 C2' DT P 906 6791 6788 6810 C2' DA P 907 6811 6808 6831 C2' DG P 908 6832 6829 6853 C2' DC P 909 6854 6851 6872 C2' DG P 910 6873 6870 6894 C2' DT P 911 6895 6892 6914 C2' DA P 912 6915 6912 6935 C2' DOC P 913 6934 6936 6963 C2' TTP A 914 6964 6961 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6338 C3' DT T 802 OK 6336 6339 6340 6358 C3' DA T 803 OK 6356 6359 6360 6379 C3' DA T 804 OK 6377 6380 6381 6400 C3' DG T 805 OK 6398 6401 6402 6422 C3' DT T 806 OK 6420 6423 6424 6442 C3' DA T 807 OK 6440 6443 6444 6463 C3' DC T 808 OK 6461 6464 6465 6482 C3' DG T 809 OK 6480 6483 6484 6504 C3' DC T 810 OK 6502 6505 6506 6523 C3' DT T 811 OK 6521 6524 6525 6543 C3' DA T 812 OK 6541 6544 6545 6564 C3' DG T 813 OK 6562 6565 6566 6586 C3' DG T 814 OK 6584 6587 6588 6608 C3' DC T 815 OK 6606 6609 6610 6627 C3' DA T 816 OK 6625 6628 6629 6648 C3' DC T 817 OK 6646 6649 6650 6667 C3' DA T 818 OK 6665 6668 6669 6686 C3' DG P 901 OK 6684 6687 6688 6708 C3' DT P 902 OK 6706 6709 6710 6728 C3' DG P 903 OK 6726 6729 6730 6750 C3' DC P 904 OK 6748 6751 6752 6769 C3' DC P 905 OK 6767 6770 6771 6788 C3' DT P 906 OK 6786 6789 6790 6808 C3' DA P 907 OK 6806 6809 6810 6829 C3' DG P 908 OK 6827 6830 6831 6851 C3' DC P 909 OK 6849 6852 6853 6870 C3' DG P 910 OK 6868 6871 6872 6892 C3' DT P 911 OK 6890 6893 6894 6912 C3' DA P 912 OK 6910 6913 6914 6936 C3' DOC P 913 6937 6935 6961 C3' TTP A 914 OK 6959 6962 6963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6336 C4' DT T 802 OK 6338 6335 6337 6356 C4' DA T 803 OK 6358 6355 6357 6377 C4' DA T 804 OK 6379 6376 6378 6398 C4' DG T 805 OK 6400 6397 6399 6420 C4' DT T 806 OK 6422 6419 6421 6440 C4' DA T 807 OK 6442 6439 6441 6461 C4' DC T 808 OK 6463 6460 6462 6480 C4' DG T 809 OK 6482 6479 6481 6502 C4' DC T 810 OK 6504 6501 6503 6521 C4' DT T 811 OK 6523 6520 6522 6541 C4' DA T 812 OK 6543 6540 6542 6562 C4' DG T 813 OK 6564 6561 6563 6584 C4' DG T 814 OK 6586 6583 6585 6606 C4' DC T 815 OK 6608 6605 6607 6625 C4' DA T 816 OK 6627 6624 6626 6646 C4' DC T 817 OK 6648 6645 6647 6665 C4' DA T 818 OK 6667 6664 6666 6684 C4' DG P 901 OK 6686 6683 6685 6706 C4' DT P 902 OK 6708 6705 6707 6726 C4' DG P 903 OK 6728 6725 6727 6748 C4' DC P 904 OK 6750 6747 6749 6767 C4' DC P 905 OK 6769 6766 6768 6786 C4' DT P 906 OK 6788 6785 6787 6806 C4' DA P 907 OK 6808 6805 6807 6827 C4' DG P 908 OK 6829 6826 6828 6849 C4' DC P 909 OK 6851 6848 6850 6868 C4' DG P 910 OK 6870 6867 6869 6890 C4' DT P 911 OK 6892 6889 6891 6910 C4' DA P 912 OK 6912 6909 6911 6937 C4' DOC P 913 OK 6936 6939 6938 6959 C4' TTP A 914 OK 6961 6958 6960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6335 C5' DT T 802 6334 6336 6355 C5' DA T 803 6354 6356 6376 C5' DA T 804 6375 6377 6397 C5' DG T 805 6396 6398 6419 C5' DT T 806 6418 6420 6439 C5' DA T 807 6438 6440 6460 C5' DC T 808 6459 6461 6479 C5' DG T 809 6478 6480 6501 C5' DC T 810 6500 6502 6520 C5' DT T 811 6519 6521 6540 C5' DA T 812 6539 6541 6561 C5' DG T 813 6560 6562 6583 C5' DG T 814 6582 6584 6605 C5' DC T 815 6604 6606 6624 C5' DA T 816 6623 6625 6645 C5' DC T 817 6644 6646 6664 C5' DA T 818 6663 6665 6683 C5' DG P 901 6682 6684 6705 C5' DT P 902 6704 6706 6725 C5' DG P 903 6724 6726 6747 C5' DC P 904 6746 6748 6766 C5' DC P 905 6765 6767 6785 C5' DT P 906 6784 6786 6805 C5' DA P 907 6804 6806 6826 C5' DG P 908 6825 6827 6848 C5' DC P 909 6847 6849 6867 C5' DG P 910 6866 6868 6889 C5' DT P 911 6888 6890 6909 C5' DA P 912 6908 6910 6939 C5' DOC P 913 6940 6937 6958 C5' TTP A 914 6957 6959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6351 P DA T 803 distorted distorted 6339 6352 6353 6354 6372 P DA T 804 distorted distorted 6359 6373 6374 6375 6393 P DG T 805 distorted distorted 6380 6394 6395 6396 6415 P DT T 806 distorted distorted 6401 6416 6417 6418 6435 P DA T 807 distorted distorted 6423 6436 6437 6438 6456 P DC T 808 distorted distorted 6443 6457 6458 6459 6475 P DG T 809 distorted distorted 6464 6476 6477 6478 6497 P DC T 810 distorted distorted 6483 6498 6499 6500 6516 P DT T 811 distorted distorted 6505 6517 6518 6519 6536 P DA T 812 distorted distorted 6524 6537 6538 6539 6557 P DG T 813 distorted distorted 6544 6558 6559 6560 6579 P DG T 814 distorted distorted 6565 6580 6581 6582 6601 P DC T 815 distorted distorted 6587 6602 6603 6604 6620 P DA T 816 distorted distorted 6609 6621 6622 6623 6641 P DC T 817 distorted distorted 6628 6642 6643 6644 6660 P DA T 818 distorted distorted 6649 6661 6662 6663 6701 P DT P 902 distorted distorted 6687 6702 6703 6704 6721 P DG P 903 distorted distorted 6709 6722 6723 6724 6743 P DC P 904 distorted distorted 6729 6744 6745 6746 6762 P DC P 905 distorted distorted 6751 6763 6764 6765 6781 P DT P 906 distorted distorted 6770 6782 6783 6784 6801 P DA P 907 distorted distorted 6789 6802 6803 6804 6822 P DG P 908 distorted distorted 6809 6823 6824 6825 6844 P DC P 909 distorted distorted 6830 6845 6846 6847 6863 P DG P 910 distorted distorted 6852 6864 6865 6866 6885 P DT P 911 distorted distorted 6871 6886 6887 6888 6905 P DA P 912 distorted distorted 6893 6906 6907 6908 6941 P DOC P 913 distorted distorted 6913 6942 6943 6940 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