ID code: '4B3G' 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' --------------------------------------------------------------------------------- 9474 C1' A G 1 beta 9469 9475 9472 9496 C1' A G 2 beta 9491 9497 9494 9518 C1' A G 3 beta 9513 9519 9516 9540 C1' A G 4 beta 9535 9541 9538 9562 C1' A G 5 beta 9557 9563 9560 9584 C1' A G 6 beta 9579 9585 9582 9606 C1' A G 7 beta 9601 9607 9604 9628 C1' A G 8 beta 9623 9629 9626 9650 C1' A G 9 beta 9645 9651 9648 9673 C1' A H 2 beta 9668 9674 9671 9695 C1' A H 3 beta 9690 9696 9693 9717 C1' A H 4 beta 9712 9718 9715 9739 C1' A H 5 beta 9734 9740 9737 9761 C1' A H 6 beta 9756 9762 9759 9783 C1' A H 7 beta 9778 9784 9781 9805 C1' A H 8 beta 9800 9806 9803 9827 C1' A H 9 beta 9822 9828 9825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 9472 C2' A G 1 OK 9474 9470 9473 9494 C2' A G 2 OK 9496 9492 9495 9516 C2' A G 3 OK 9518 9514 9517 9538 C2' A G 4 OK 9540 9536 9539 9560 C2' A G 5 OK 9562 9558 9561 9582 C2' A G 6 OK 9584 9580 9583 9604 C2' A G 7 OK 9606 9602 9605 9626 C2' A G 8 OK 9628 9624 9627 9648 C2' A G 9 OK 9650 9646 9649 9671 C2' A H 2 OK 9673 9669 9672 9693 C2' A H 3 OK 9695 9691 9694 9715 C2' A H 4 OK 9717 9713 9716 9737 C2' A H 5 OK 9739 9735 9738 9759 C2' A H 6 OK 9761 9757 9760 9781 C2' A H 7 OK 9783 9779 9782 9803 C2' A H 8 OK 9805 9801 9804 9825 C2' A H 9 OK 9827 9823 9826 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9470 C3' A G 1 OK 9468 9471 9472 9492 C3' A G 2 OK 9490 9493 9494 9514 C3' A G 3 OK 9512 9515 9516 9536 C3' A G 4 OK 9534 9537 9538 9558 C3' A G 5 OK 9556 9559 9560 9580 C3' A G 6 OK 9578 9581 9582 9602 C3' A G 7 OK 9600 9603 9604 9624 C3' A G 8 OK 9622 9625 9626 9646 C3' A G 9 OK 9644 9647 9648 9669 C3' A H 2 OK 9667 9670 9671 9691 C3' A H 3 OK 9689 9692 9693 9713 C3' A H 4 OK 9711 9714 9715 9735 C3' A H 5 OK 9733 9736 9737 9757 C3' A H 6 OK 9755 9758 9759 9779 C3' A H 7 OK 9777 9780 9781 9801 C3' A H 8 OK 9799 9802 9803 9823 C3' A H 9 OK 9821 9824 9825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 9468 C4' A G 1 OK 9470 9467 9469 9490 C4' A G 2 OK 9492 9489 9491 9512 C4' A G 3 OK 9514 9511 9513 9534 C4' A G 4 OK 9536 9533 9535 9556 C4' A G 5 OK 9558 9555 9557 9578 C4' A G 6 OK 9580 9577 9579 9600 C4' A G 7 OK 9602 9599 9601 9622 C4' A G 8 OK 9624 9621 9623 9644 C4' A G 9 OK 9646 9643 9645 9667 C4' A H 2 OK 9669 9666 9668 9689 C4' A H 3 OK 9691 9688 9690 9711 C4' A H 4 OK 9713 9710 9712 9733 C4' A H 5 OK 9735 9732 9734 9755 C4' A H 6 OK 9757 9754 9756 9777 C4' A H 7 OK 9779 9776 9778 9799 C4' A H 8 OK 9801 9798 9800 9821 C4' A H 9 OK 9823 9820 9822 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 9467 C5' A G 1 9466 9468 9489 C5' A G 2 9488 9490 9511 C5' A G 3 9510 9512 9533 C5' A G 4 9532 9534 9555 C5' A G 5 9554 9556 9577 C5' A G 6 9576 9578 9599 C5' A G 7 9598 9600 9621 C5' A G 8 9620 9622 9643 C5' A G 9 9642 9644 9666 C5' A H 2 9665 9667 9688 C5' A H 3 9687 9689 9710 C5' A H 4 9709 9711 9732 C5' A H 5 9731 9733 9754 C5' A H 6 9753 9755 9776 C5' A H 7 9775 9777 9798 C5' A H 8 9797 9799 9820 C5' A H 9 9819 9821 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 9463 P A G 1 distorted distorted 9464 9465 9466 9485 P A G 2 distorted distorted 9471 9486 9487 9488 9507 P A G 3 OK OK 9493 9508 9509 9510 9529 P A G 4 distorted distorted 9515 9530 9531 9532 9551 P A G 5 OK OK 9537 9552 9553 9554 9573 P A G 6 distorted distorted 9559 9574 9575 9576 9595 P A G 7 distorted distorted 9581 9596 9597 9598 9617 P A G 8 distorted distorted 9603 9618 9619 9620 9639 P A G 9 OK OK 9625 9640 9641 9642 9662 P A H 2 distorted distorted 9663 9664 9665 9684 P A H 3 distorted distorted 9670 9685 9686 9687 9706 P A H 4 distorted distorted 9692 9707 9708 9709 9728 P A H 5 OK OK 9714 9729 9730 9731 9750 P A H 6 distorted distorted 9736 9751 9752 9753 9772 P A H 7 distorted distorted 9758 9773 9774 9775 9794 P A H 8 distorted distorted 9780 9795 9796 9797 9816 P A H 9 OK OK 9802 9817 9818 9819 ---------------------------------------------------------------------------------