ID code: '4PUQ' 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' --------------------------------------------------------------------------------- 4375 C1' C C 1 beta 4370 4376 4373 4476 C1' DA C 4 beta 4472 4477 4475 4497 C1' DA C 5 beta 4493 4498 4496 4518 C1' DT C 6 beta 4514 4519 4517 4538 C1' DT C 7 beta 4534 4539 4537 4558 C1' DC C 8 beta 4554 4559 4557 4577 C1' DG C 9 beta 4573 4578 4576 4602 C1' C D 1 beta 4597 4603 4600 4703 C1' DA D 4 beta 4699 4704 4702 4724 C1' DA D 5 beta 4720 4725 4723 4745 C1' DT D 6 beta 4741 4746 4744 4765 C1' DT D 7 beta 4761 4766 4764 4785 C1' DC D 8 beta 4781 4786 4784 4804 C1' DG D 9 beta 4800 4805 4803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4373 C2' C C 1 OK 4375 4371 4374 4475 C2' DA C 4 4476 4473 4496 C2' DA C 5 4497 4494 4517 C2' DT C 6 4518 4515 4537 C2' DT C 7 4538 4535 4557 C2' DC C 8 4558 4555 4576 C2' DG C 9 4577 4574 4600 C2' C D 1 OK 4602 4598 4601 4702 C2' DA D 4 4703 4700 4723 C2' DA D 5 4724 4721 4744 C2' DT D 6 4745 4742 4764 C2' DT D 7 4765 4762 4784 C2' DC D 8 4785 4782 4803 C2' DG D 9 4804 4801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4371 C3' C C 1 OK 4369 4372 4373 4473 C3' DA C 4 OK 4471 4474 4475 4494 C3' DA C 5 OK 4492 4495 4496 4515 C3' DT C 6 OK 4513 4516 4517 4535 C3' DT C 7 OK 4533 4536 4537 4555 C3' DC C 8 OK 4553 4556 4557 4574 C3' DG C 9 OK 4572 4575 4576 4598 C3' C D 1 OK 4596 4599 4600 4700 C3' DA D 4 OK 4698 4701 4702 4721 C3' DA D 5 OK 4719 4722 4723 4742 C3' DT D 6 OK 4740 4743 4744 4762 C3' DT D 7 OK 4760 4763 4764 4782 C3' DC D 8 OK 4780 4783 4784 4801 C3' DG D 9 OK 4799 4802 4803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4369 C4' C C 1 OK 4371 4368 4370 4471 C4' DA C 4 OK 4473 4470 4472 4492 C4' DA C 5 OK 4494 4491 4493 4513 C4' DT C 6 OK 4515 4512 4514 4533 C4' DT C 7 OK 4535 4532 4534 4553 C4' DC C 8 OK 4555 4552 4554 4572 C4' DG C 9 OK 4574 4571 4573 4596 C4' C D 1 OK 4598 4595 4597 4698 C4' DA D 4 OK 4700 4697 4699 4719 C4' DA D 5 OK 4721 4718 4720 4740 C4' DT D 6 OK 4742 4739 4741 4760 C4' DT D 7 OK 4762 4759 4761 4780 C4' DC D 8 OK 4782 4779 4781 4799 C4' DG D 9 OK 4801 4798 4800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4368 C5' C C 1 4367 4369 4470 C5' DA C 4 4469 4471 4491 C5' DA C 5 4490 4492 4512 C5' DT C 6 4511 4513 4532 C5' DT C 7 4531 4533 4552 C5' DC C 8 4551 4553 4571 C5' DG C 9 4570 4572 4595 C5' C D 1 4594 4596 4697 C5' DA D 4 4696 4698 4718 C5' DA D 5 4717 4719 4739 C5' DT D 6 4738 4740 4759 C5' DT D 7 4758 4760 4779 C5' DC D 8 4778 4780 4798 C5' DG D 9 4797 4799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4364 P C C 1 distorted distorted 4365 4366 4367 4384 P DC C 2 4372 4385 P DC C 2 4372 4422 P DG C 3 4423 P DG C 3 4466 P DA C 4 distorted distorted 4467 4468 4469 4487 P DA C 5 distorted distorted 4474 4488 4489 4490 4508 P DT C 6 distorted distorted 4495 4509 4510 4511 4528 P DT C 7 distorted distorted 4516 4529 4530 4531 4548 P DC C 8 distorted distorted 4536 4549 4550 4551 4567 P DG C 9 distorted distorted 4556 4568 4569 4570 4591 P C D 1 distorted distorted 4592 4593 4594 4611 P DC D 2 4599 4612 P DC D 2 4599 4649 P DG D 3 4650 P DG D 3 4693 P DA D 4 distorted distorted 4694 4695 4696 4714 P DA D 5 distorted distorted 4701 4715 4716 4717 4735 P DT D 6 distorted distorted 4722 4736 4737 4738 4755 P DT D 7 distorted distorted 4743 4756 4757 4758 4775 P DC D 8 distorted distorted 4763 4776 4777 4778 4794 P DG D 9 distorted distorted 4783 4795 4796 4797 ---------------------------------------------------------------------------------