ID code: '4W5N' 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' --------------------------------------------------------------------------------- 6475 C1' U B 1 beta 6470 6476 6473 6495 C1' U B 2 beta 6490 6496 6493 6515 C1' C B 3 beta 6510 6516 6513 6535 C1' A B 4 beta 6530 6536 6533 6557 C1' C B 5 beta 6552 6558 6555 6577 C1' A B 6 beta 6572 6578 6575 6599 C1' U B 7 beta 6594 6600 6597 6622 C1' C B 12 beta 6617 6623 6620 6642 C1' A B 13 beta 6637 6643 6640 6664 C1' A B 14 beta 6659 6665 6662 6686 C1' G B 15 beta 6681 6687 6684 6709 C1' U B 16 beta 6704 6710 6707 6729 C1' C B 17 beta 6724 6730 6727 6749 C1' U B 18 beta 6744 6750 6747 6769 C1' C B 19 beta 6764 6770 6767 6789 C1' U B 20 beta 6784 6790 6787 6809 C1' U B 21 beta 6804 6810 6807 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6473 C2' U B 1 OK 6475 6471 6474 6493 C2' U B 2 OK 6495 6491 6494 6513 C2' C B 3 OK 6515 6511 6514 6533 C2' A B 4 OK 6535 6531 6534 6555 C2' C B 5 OK 6557 6553 6556 6575 C2' A B 6 OK 6577 6573 6576 6597 C2' U B 7 OK 6599 6595 6598 6620 C2' C B 12 OK 6622 6618 6621 6640 C2' A B 13 OK 6642 6638 6641 6662 C2' A B 14 OK 6664 6660 6663 6684 C2' G B 15 OK 6686 6682 6685 6707 C2' U B 16 OK 6709 6705 6708 6727 C2' C B 17 OK 6729 6725 6728 6747 C2' U B 18 OK 6749 6745 6748 6767 C2' C B 19 OK 6769 6765 6768 6787 C2' U B 20 OK 6789 6785 6788 6807 C2' U B 21 OK 6809 6805 6808 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6471 C3' U B 1 OK 6469 6472 6473 6491 C3' U B 2 OK 6489 6492 6493 6511 C3' C B 3 OK 6509 6512 6513 6531 C3' A B 4 OK 6529 6532 6533 6553 C3' C B 5 OK 6551 6554 6555 6573 C3' A B 6 OK 6571 6574 6575 6595 C3' U B 7 OK 6593 6596 6597 6618 C3' C B 12 OK 6616 6619 6620 6638 C3' A B 13 OK 6636 6639 6640 6660 C3' A B 14 OK 6658 6661 6662 6682 C3' G B 15 OK 6680 6683 6684 6705 C3' U B 16 OK 6703 6706 6707 6725 C3' C B 17 OK 6723 6726 6727 6745 C3' U B 18 OK 6743 6746 6747 6765 C3' C B 19 OK 6763 6766 6767 6785 C3' U B 20 OK 6783 6786 6787 6805 C3' U B 21 OK 6803 6806 6807 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6469 C4' U B 1 OK 6471 6468 6470 6489 C4' U B 2 OK 6491 6488 6490 6509 C4' C B 3 OK 6511 6508 6510 6529 C4' A B 4 OK 6531 6528 6530 6551 C4' C B 5 OK 6553 6550 6552 6571 C4' A B 6 OK 6573 6570 6572 6593 C4' U B 7 OK 6595 6592 6594 6616 C4' C B 12 OK 6618 6615 6617 6636 C4' A B 13 OK 6638 6635 6637 6658 C4' A B 14 OK 6660 6657 6659 6680 C4' G B 15 OK 6682 6679 6681 6703 C4' U B 16 OK 6705 6702 6704 6723 C4' C B 17 OK 6725 6722 6724 6743 C4' U B 18 OK 6745 6742 6744 6763 C4' C B 19 OK 6765 6762 6764 6783 C4' U B 20 OK 6785 6782 6784 6803 C4' U B 21 OK 6805 6802 6804 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6468 C5' U B 1 6467 6469 6488 C5' U B 2 6487 6489 6508 C5' C B 3 6507 6509 6528 C5' A B 4 6527 6529 6550 C5' C B 5 6549 6551 6570 C5' A B 6 6569 6571 6592 C5' U B 7 6591 6593 6615 C5' C B 12 6614 6616 6635 C5' A B 13 6634 6636 6657 C5' A B 14 6656 6658 6679 C5' G B 15 6678 6680 6702 C5' U B 16 6701 6703 6722 C5' C B 17 6721 6723 6742 C5' U B 18 6741 6743 6762 C5' C B 19 6761 6763 6782 C5' U B 20 6781 6783 6802 C5' U B 21 6801 6803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6464 P U B 1 OK OK 6465 6466 6467 6484 P U B 2 distorted distorted 6472 6485 6486 6487 6504 P C B 3 distorted distorted 6492 6505 6506 6507 6524 P A B 4 distorted distorted 6512 6525 6526 6527 6546 P C B 5 distorted distorted 6532 6547 6548 6549 6566 P A B 6 distorted distorted 6554 6567 6568 6569 6588 P U B 7 distorted distorted 6574 6589 6590 6591 6608 P U B 8 distorted distorted 6596 6609 6610 6611 P C B 12 distorted distorted 6612 6613 6614 6631 P A B 13 distorted distorted 6619 6632 6633 6634 6653 P A B 14 distorted distorted 6639 6654 6655 6656 6675 P G B 15 distorted distorted 6661 6676 6677 6678 6698 P U B 16 distorted distorted 6683 6699 6700 6701 6718 P C B 17 distorted distorted 6706 6719 6720 6721 6738 P U B 18 distorted distorted 6726 6739 6740 6741 6758 P C B 19 distorted distorted 6746 6759 6760 6761 6778 P U B 20 distorted distorted 6766 6779 6780 6781 6798 P U B 21 distorted distorted 6786 6799 6800 6801 ---------------------------------------------------------------------------------