ID code: '4Y91' 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' --------------------------------------------------------------------------------- 6548 C1' U N 1 beta 6543 6549 6546 6568 C1' U N 2 beta 6563 6569 6566 6588 C1' U N 3 beta 6583 6589 6586 6608 C1' U N 4 beta 6603 6609 6606 6628 C1' U N 5 beta 6623 6629 6626 6648 C1' U N 6 beta 6643 6649 6646 6669 C1' U O 1 beta 6664 6670 6667 6689 C1' U O 2 beta 6684 6690 6687 6709 C1' U O 3 beta 6704 6710 6707 6729 C1' U O 4 beta 6724 6730 6727 6749 C1' U O 5 beta 6744 6750 6747 6769 C1' U O 6 beta 6764 6770 6767 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6546 C2' U N 1 OK 6548 6544 6547 6566 C2' U N 2 OK 6568 6564 6567 6586 C2' U N 3 OK 6588 6584 6587 6606 C2' U N 4 OK 6608 6604 6607 6626 C2' U N 5 OK 6628 6624 6627 6646 C2' U N 6 OK 6648 6644 6647 6667 C2' U O 1 OK 6669 6665 6668 6687 C2' U O 2 OK 6689 6685 6688 6707 C2' U O 3 OK 6709 6705 6708 6727 C2' U O 4 OK 6729 6725 6728 6747 C2' U O 5 OK 6749 6745 6748 6767 C2' U O 6 OK 6769 6765 6768 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6544 C3' U N 1 OK 6542 6545 6546 6564 C3' U N 2 OK 6562 6565 6566 6584 C3' U N 3 OK 6582 6585 6586 6604 C3' U N 4 OK 6602 6605 6606 6624 C3' U N 5 OK 6622 6625 6626 6644 C3' U N 6 OK 6642 6645 6646 6665 C3' U O 1 OK 6663 6666 6667 6685 C3' U O 2 OK 6683 6686 6687 6705 C3' U O 3 OK 6703 6706 6707 6725 C3' U O 4 OK 6723 6726 6727 6745 C3' U O 5 OK 6743 6746 6747 6765 C3' U O 6 OK 6763 6766 6767 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6542 C4' U N 1 OK 6544 6541 6543 6562 C4' U N 2 OK 6564 6561 6563 6582 C4' U N 3 OK 6584 6581 6583 6602 C4' U N 4 OK 6604 6601 6603 6622 C4' U N 5 OK 6624 6621 6623 6642 C4' U N 6 OK 6644 6641 6643 6663 C4' U O 1 OK 6665 6662 6664 6683 C4' U O 2 OK 6685 6682 6684 6703 C4' U O 3 OK 6705 6702 6704 6723 C4' U O 4 OK 6725 6722 6724 6743 C4' U O 5 OK 6745 6742 6744 6763 C4' U O 6 OK 6765 6762 6764 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6541 C5' U N 1 6540 6542 6561 C5' U N 2 6560 6562 6581 C5' U N 3 6580 6582 6601 C5' U N 4 6600 6602 6621 C5' U N 5 6620 6622 6641 C5' U N 6 6640 6642 6662 C5' U O 1 6661 6663 6682 C5' U O 2 6681 6683 6702 C5' U O 3 6701 6703 6722 C5' U O 4 6721 6723 6742 C5' U O 5 6741 6743 6762 C5' U O 6 6761 6763 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6537 P U N 1 OK OK 6538 6539 6540 6557 P U N 2 distorted distorted 6545 6558 6559 6560 6577 P U N 3 distorted distorted 6565 6578 6579 6580 6597 P U N 4 distorted distorted 6585 6598 6599 6600 6617 P U N 5 distorted distorted 6605 6618 6619 6620 6637 P U N 6 distorted distorted 6625 6638 6639 6640 6658 P U O 1 OK OK 6659 6660 6661 6678 P U O 2 distorted distorted 6666 6679 6680 6681 6698 P U O 3 distorted distorted 6686 6699 6700 6701 6718 P U O 4 distorted distorted 6706 6719 6720 6721 6738 P U O 5 distorted distorted 6726 6739 6740 6741 6758 P U O 6 distorted distorted 6746 6759 6760 6761 ---------------------------------------------------------------------------------