ID code: '5KLA' 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' --------------------------------------------------------------------------------- 5540 C1' U B 1 alpha beta 5535 5555 5541 5538 5571 C1' G B 2 alpha beta 5566 5589 5572 5569 5605 C1' U B 3 alpha beta 5600 5620 5606 5603 5635 C1' A B 4 alpha beta 5630 5652 5636 5633 5668 C1' C B 5 alpha beta 5663 5683 5669 5666 5699 C1' A B 6 alpha beta 5694 5716 5700 5697 5732 C1' U B 7 alpha beta 5727 5747 5733 5730 5762 C1' A B 8 alpha beta 5757 5780 5763 5760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5538 C2' U B 1 OK OK 5540 5536 5553 5539 5569 C2' G B 2 OK OK 5571 5567 5587 5570 5603 C2' U B 3 OK OK 5605 5601 5618 5604 5633 C2' A B 4 OK OK 5635 5631 5650 5634 5666 C2' C B 5 OK OK 5668 5664 5681 5667 5697 C2' A B 6 OK OK 5699 5695 5714 5698 5730 C2' U B 7 OK OK 5732 5728 5745 5731 5760 C2' A B 8 OK OK 5762 5758 5778 5761 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5536 C3' U B 1 OK OK 5534 5552 5537 5538 5567 C3' G B 2 OK OK 5565 5586 5568 5569 5601 C3' U B 3 OK OK 5599 5617 5602 5603 5631 C3' A B 4 OK OK 5629 5649 5632 5633 5664 C3' C B 5 OK OK 5662 5680 5665 5666 5695 C3' A B 6 OK OK 5693 5713 5696 5697 5728 C3' U B 7 OK OK 5726 5744 5729 5730 5758 C3' A B 8 OK OK 5756 5776 5759 5760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5534 C4' U B 1 OK OK 5536 5551 5533 5535 5565 C4' G B 2 OK OK 5567 5585 5564 5566 5599 C4' U B 3 OK OK 5601 5616 5598 5600 5629 C4' A B 4 OK OK 5631 5648 5628 5630 5662 C4' C B 5 OK OK 5664 5679 5661 5663 5693 C4' A B 6 OK OK 5695 5712 5692 5694 5726 C4' U B 7 OK OK 5728 5743 5725 5727 5756 C4' A B 8 OK OK 5758 5775 5755 5757 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5533 C5' U B 1 OK OK 5532 5549 5550 5534 5564 C5' G B 2 OK OK 5563 5583 5584 5565 5598 C5' U B 3 OK OK 5597 5614 5615 5599 5628 C5' A B 4 OK OK 5627 5646 5647 5629 5661 C5' C B 5 OK OK 5660 5677 5678 5662 5692 C5' A B 6 OK OK 5691 5710 5711 5693 5725 C5' U B 7 OK OK 5724 5741 5742 5726 5755 C5' A B 8 OK OK 5754 5773 5774 5756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5560 P G B 2 distorted distorted 5537 5561 5562 5563 5594 P U B 3 distorted distorted 5568 5595 5596 5597 5624 P A B 4 distorted distorted 5602 5625 5626 5627 5657 P C B 5 distorted distorted 5632 5658 5659 5660 5688 P A B 6 distorted distorted 5665 5689 5690 5691 5721 P U B 7 distorted distorted 5696 5722 5723 5724 5751 P A B 8 distorted distorted 5729 5752 5753 5754 ---------------------------------------------------------------------------------