ID code: '4DLG' 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' --------------------------------------------------------------------------------- 4425 C1' DG B 101 beta 4421 4426 4424 4447 C1' DA B 102 beta 4443 4448 4446 4468 C1' DC B 103 beta 4464 4469 4467 4487 C1' DC B 104 beta 4483 4488 4486 4506 C1' DA B 105 beta 4502 4507 4505 4527 C1' DC B 106 beta 4523 4528 4526 4546 C1' DG B 107 beta 4542 4547 4545 4568 C1' DG B 108 beta 4564 4569 4567 4590 C1' DC B 109 beta 4586 4591 4589 4609 C1' DG B 110 beta 4605 4610 4608 4631 C1' DC B 111 beta 4627 4632 4630 4648 C1' DOC B 112 beta 4652 4640 4649 4669 C1' DA C 203 beta 4665 4670 4668 4690 C1' DG C 204 beta 4686 4691 4689 4712 C1' DG C 205 beta 4708 4713 4711 4734 C1' DG C 206 beta 4730 4735 4733 4756 C1' DC C 207 beta 4752 4757 4755 4775 C1' DG C 208 beta 4771 4776 4774 4797 C1' DC C 209 beta 4793 4798 4796 4816 C1' DC C 210 beta 4812 4817 4815 4835 C1' DG C 211 beta 4831 4836 4834 4857 C1' DT C 212 beta 4853 4858 4856 4877 C1' DG C 213 beta 4873 4878 4876 4899 C1' DG C 214 beta 4895 4900 4898 4921 C1' DT C 215 beta 4917 4922 4920 4941 C1' DC C 216 beta 4937 4942 4940 4959 C1' DCT A 901 beta 4963 4951 4960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4424 C2' DG B 101 4425 4422 4446 C2' DA B 102 4447 4444 4467 C2' DC B 103 4468 4465 4486 C2' DC B 104 4487 4484 4505 C2' DA B 105 4506 4503 4526 C2' DC B 106 4527 4524 4545 C2' DG B 107 4546 4543 4567 C2' DG B 108 4568 4565 4589 C2' DC B 109 4590 4587 4608 C2' DG B 110 4609 4606 4630 C2' DC B 111 4631 4628 4649 C2' DOC B 112 4648 4650 4668 C2' DA C 203 4669 4666 4689 C2' DG C 204 4690 4687 4711 C2' DG C 205 4712 4709 4733 C2' DG C 206 4734 4731 4755 C2' DC C 207 4756 4753 4774 C2' DG C 208 4775 4772 4796 C2' DC C 209 4797 4794 4815 C2' DC C 210 4816 4813 4834 C2' DG C 211 4835 4832 4856 C2' DT C 212 4857 4854 4876 C2' DG C 213 4877 4874 4898 C2' DG C 214 4899 4896 4920 C2' DT C 215 4921 4918 4940 C2' DC C 216 4941 4938 4960 C2' DCT A 901 4959 4961 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4422 C3' DG B 101 OK 4420 4423 4424 4444 C3' DA B 102 OK 4442 4445 4446 4465 C3' DC B 103 OK 4463 4466 4467 4484 C3' DC B 104 OK 4482 4485 4486 4503 C3' DA B 105 OK 4501 4504 4505 4524 C3' DC B 106 OK 4522 4525 4526 4543 C3' DG B 107 OK 4541 4544 4545 4565 C3' DG B 108 OK 4563 4566 4567 4587 C3' DC B 109 OK 4585 4588 4589 4606 C3' DG B 110 OK 4604 4607 4608 4628 C3' DC B 111 OK 4626 4629 4630 4650 C3' DOC B 112 4651 4649 4666 C3' DA C 203 OK 4664 4667 4668 4687 C3' DG C 204 OK 4685 4688 4689 4709 C3' DG C 205 OK 4707 4710 4711 4731 C3' DG C 206 OK 4729 4732 4733 4753 C3' DC C 207 OK 4751 4754 4755 4772 C3' DG C 208 OK 4770 4773 4774 4794 C3' DC C 209 OK 4792 4795 4796 4813 C3' DC C 210 OK 4811 4814 4815 4832 C3' DG C 211 OK 4830 4833 4834 4854 C3' DT C 212 OK 4852 4855 4856 4874 C3' DG C 213 OK 4872 4875 4876 4896 C3' DG C 214 OK 4894 4897 4898 4918 C3' DT C 215 OK 4916 4919 4920 4938 C3' DC C 216 OK 4936 4939 4940 4961 C3' DCT A 901 4962 4960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4420 C4' DG B 101 OK 4422 4419 4421 4442 C4' DA B 102 OK 4444 4441 4443 4463 C4' DC B 103 OK 4465 4462 4464 4482 C4' DC B 104 OK 4484 4481 4483 4501 C4' DA B 105 OK 4503 4500 4502 4522 C4' DC B 106 OK 4524 4521 4523 4541 C4' DG B 107 OK 4543 4540 4542 4563 C4' DG B 108 OK 4565 4562 4564 4585 C4' DC B 109 OK 4587 4584 4586 4604 C4' DG B 110 OK 4606 4603 4605 4626 C4' DC B 111 OK 4628 4625 4627 4651 C4' DOC B 112 OK 4650 4653 4652 4664 C4' DA C 203 OK 4666 4663 4665 4685 C4' DG C 204 OK 4687 4684 4686 4707 C4' DG C 205 OK 4709 4706 4708 4729 C4' DG C 206 OK 4731 4728 4730 4751 C4' DC C 207 OK 4753 4750 4752 4770 C4' DG C 208 OK 4772 4769 4771 4792 C4' DC C 209 OK 4794 4791 4793 4811 C4' DC C 210 OK 4813 4810 4812 4830 C4' DG C 211 OK 4832 4829 4831 4852 C4' DT C 212 OK 4854 4851 4853 4872 C4' DG C 213 OK 4874 4871 4873 4894 C4' DG C 214 OK 4896 4893 4895 4916 C4' DT C 215 OK 4918 4915 4917 4936 C4' DC C 216 OK 4938 4935 4937 4962 C4' DCT A 901 OK 4961 4964 4963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4419 C5' DG B 101 4418 4420 4441 C5' DA B 102 4440 4442 4462 C5' DC B 103 4461 4463 4481 C5' DC B 104 4480 4482 4500 C5' DA B 105 4499 4501 4521 C5' DC B 106 4520 4522 4540 C5' DG B 107 4539 4541 4562 C5' DG B 108 4561 4563 4584 C5' DC B 109 4583 4585 4603 C5' DG B 110 4602 4604 4625 C5' DC B 111 4624 4626 4653 C5' DOC B 112 4654 4651 4663 C5' DA C 203 4662 4664 4684 C5' DG C 204 4683 4685 4706 C5' DG C 205 4705 4707 4728 C5' DG C 206 4727 4729 4750 C5' DC C 207 4749 4751 4769 C5' DG C 208 4768 4770 4791 C5' DC C 209 4790 4792 4810 C5' DC C 210 4809 4811 4829 C5' DG C 211 4828 4830 4851 C5' DT C 212 4850 4852 4871 C5' DG C 213 4870 4872 4893 C5' DG C 214 4892 4894 4915 C5' DT C 215 4914 4916 4935 C5' DC C 216 4934 4936 4964 C5' DCT A 901 4965 4962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4437 P DA B 102 distorted distorted 4423 4438 4439 4440 4458 P DC B 103 distorted distorted 4445 4459 4460 4461 4477 P DC B 104 distorted distorted 4466 4478 4479 4480 4496 P DA B 105 distorted distorted 4485 4497 4498 4499 4517 P DC B 106 distorted distorted 4504 4518 4519 4520 4536 P DG B 107 distorted distorted 4525 4537 4538 4539 4558 P DG B 108 distorted distorted 4544 4559 4560 4561 4580 P DC B 109 distorted distorted 4566 4581 4582 4583 4599 P DG B 110 distorted distorted 4588 4600 4601 4602 4621 P DC B 111 distorted distorted 4607 4622 4623 4624 4655 P DOC B 112 OK OK 4629 4656 4657 4654 4659 P DA C 203 distorted distorted 4660 4661 4662 4680 P DG C 204 distorted distorted 4667 4681 4682 4683 4702 P DG C 205 distorted distorted 4688 4703 4704 4705 4724 P DG C 206 distorted distorted 4710 4725 4726 4727 4746 P DC C 207 distorted distorted 4732 4747 4748 4749 4765 P DG C 208 distorted distorted 4754 4766 4767 4768 4787 P DC C 209 distorted distorted 4773 4788 4789 4790 4806 P DC C 210 distorted distorted 4795 4807 4808 4809 4825 P DG C 211 distorted distorted 4814 4826 4827 4828 4847 P DT C 212 distorted distorted 4833 4848 4849 4850 4867 P DG C 213 distorted distorted 4855 4868 4869 4870 4889 P DG C 214 distorted distorted 4875 4890 4891 4892 4911 P DT C 215 distorted distorted 4897 4912 4913 4914 4931 P DC C 216 distorted distorted 4919 4932 4933 4934 ---------------------------------------------------------------------------------