ID code: '4DFJ' 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' --------------------------------------------------------------------------------- 4364 C1' DG B 101 beta 4360 4365 4363 4386 C1' DA B 102 beta 4382 4387 4385 4407 C1' DC B 103 beta 4403 4408 4406 4426 C1' DC B 104 beta 4422 4427 4425 4445 C1' DA B 105 beta 4441 4446 4444 4466 C1' DC B 106 beta 4462 4467 4465 4485 C1' DG B 107 beta 4481 4486 4484 4507 C1' DG B 108 beta 4503 4508 4506 4529 C1' DC B 109 beta 4525 4530 4528 4548 C1' DG B 110 beta 4544 4549 4547 4570 C1' DC B 111 beta 4566 4571 4569 4587 C1' DOC B 112 beta 4591 4579 4588 4605 C1' DA C 201 beta 4601 4606 4604 4626 C1' DA C 202 beta 4622 4627 4625 4647 C1' DA C 203 beta 4643 4648 4646 4668 C1' DA C 204 beta 4664 4669 4667 4689 C1' DG C 205 beta 4685 4690 4688 4711 C1' DG C 206 beta 4707 4712 4710 4733 C1' DC C 207 beta 4729 4734 4732 4752 C1' DG C 208 beta 4748 4753 4751 4774 C1' DC C 209 beta 4770 4775 4773 4793 C1' DC C 210 beta 4789 4794 4792 4812 C1' DG C 211 beta 4808 4813 4811 4834 C1' DT C 212 beta 4830 4835 4833 4854 C1' DG C 213 beta 4850 4855 4853 4876 C1' DG C 214 beta 4872 4877 4875 4898 C1' DT C 215 beta 4894 4899 4897 4918 C1' DC C 216 beta 4914 4919 4917 4949 C1' 0KL A 903 beta 4948 4950 4947 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4363 C2' DG B 101 4364 4361 4385 C2' DA B 102 4386 4383 4406 C2' DC B 103 4407 4404 4425 C2' DC B 104 4426 4423 4444 C2' DA B 105 4445 4442 4465 C2' DC B 106 4466 4463 4484 C2' DG B 107 4485 4482 4506 C2' DG B 108 4507 4504 4528 C2' DC B 109 4529 4526 4547 C2' DG B 110 4548 4545 4569 C2' DC B 111 4570 4567 4588 C2' DOC B 112 4587 4589 4604 C2' DA C 201 4605 4602 4625 C2' DA C 202 4626 4623 4646 C2' DA C 203 4647 4644 4667 C2' DA C 204 4668 4665 4688 C2' DG C 205 4689 4686 4710 C2' DG C 206 4711 4708 4732 C2' DC C 207 4733 4730 4751 C2' DG C 208 4752 4749 4773 C2' DC C 209 4774 4771 4792 C2' DC C 210 4793 4790 4811 C2' DG C 211 4812 4809 4833 C2' DT C 212 4834 4831 4853 C2' DG C 213 4854 4851 4875 C2' DG C 214 4876 4873 4897 C2' DT C 215 4898 4895 4917 C2' DC C 216 4918 4915 4947 C2' 0KL A 903 4949 4945 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4361 C3' DG B 101 OK 4359 4362 4363 4383 C3' DA B 102 OK 4381 4384 4385 4404 C3' DC B 103 OK 4402 4405 4406 4423 C3' DC B 104 OK 4421 4424 4425 4442 C3' DA B 105 OK 4440 4443 4444 4463 C3' DC B 106 OK 4461 4464 4465 4482 C3' DG B 107 OK 4480 4483 4484 4504 C3' DG B 108 OK 4502 4505 4506 4526 C3' DC B 109 OK 4524 4527 4528 4545 C3' DG B 110 OK 4543 4546 4547 4567 C3' DC B 111 OK 4565 4568 4569 4589 C3' DOC B 112 4590 4588 4602 C3' DA C 201 OK 4600 4603 4604 4623 C3' DA C 202 OK 4621 4624 4625 4644 C3' DA C 203 OK 4642 4645 4646 4665 C3' DA C 204 OK 4663 4666 4667 4686 C3' DG C 205 OK 4684 4687 4688 4708 C3' DG C 206 OK 4706 4709 4710 4730 C3' DC C 207 OK 4728 4731 4732 4749 C3' DG C 208 OK 4747 4750 4751 4771 C3' DC C 209 OK 4769 4772 4773 4790 C3' DC C 210 OK 4788 4791 4792 4809 C3' DG C 211 OK 4807 4810 4811 4831 C3' DT C 212 OK 4829 4832 4833 4851 C3' DG C 213 OK 4849 4852 4853 4873 C3' DG C 214 OK 4871 4874 4875 4895 C3' DT C 215 OK 4893 4896 4897 4915 C3' DC C 216 OK 4913 4916 4917 4945 C3' 0KL A 903 OK 4944 4946 4947 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4359 C4' DG B 101 OK 4361 4358 4360 4381 C4' DA B 102 OK 4383 4380 4382 4402 C4' DC B 103 OK 4404 4401 4403 4421 C4' DC B 104 OK 4423 4420 4422 4440 C4' DA B 105 OK 4442 4439 4441 4461 C4' DC B 106 OK 4463 4460 4462 4480 C4' DG B 107 OK 4482 4479 4481 4502 C4' DG B 108 OK 4504 4501 4503 4524 C4' DC B 109 OK 4526 4523 4525 4543 C4' DG B 110 OK 4545 4542 4544 4565 C4' DC B 111 OK 4567 4564 4566 4590 C4' DOC B 112 OK 4589 4592 4591 4600 C4' DA C 201 OK 4602 4599 4601 4621 C4' DA C 202 OK 4623 4620 4622 4642 C4' DA C 203 OK 4644 4641 4643 4663 C4' DA C 204 OK 4665 4662 4664 4684 C4' DG C 205 OK 4686 4683 4685 4706 C4' DG C 206 OK 4708 4705 4707 4728 C4' DC C 207 OK 4730 4727 4729 4747 C4' DG C 208 OK 4749 4746 4748 4769 C4' DC C 209 OK 4771 4768 4770 4788 C4' DC C 210 OK 4790 4787 4789 4807 C4' DG C 211 OK 4809 4806 4808 4829 C4' DT C 212 OK 4831 4828 4830 4849 C4' DG C 213 OK 4851 4848 4850 4871 C4' DG C 214 OK 4873 4870 4872 4893 C4' DT C 215 OK 4895 4892 4894 4913 C4' DC C 216 OK 4915 4912 4914 4944 C4' 0KL A 903 OK 4945 4943 4948 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4358 C5' DG B 101 4357 4359 4380 C5' DA B 102 4379 4381 4401 C5' DC B 103 4400 4402 4420 C5' DC B 104 4419 4421 4439 C5' DA B 105 4438 4440 4460 C5' DC B 106 4459 4461 4479 C5' DG B 107 4478 4480 4501 C5' DG B 108 4500 4502 4523 C5' DC B 109 4522 4524 4542 C5' DG B 110 4541 4543 4564 C5' DC B 111 4563 4565 4592 C5' DOC B 112 4593 4590 4599 C5' DA C 201 4598 4600 4620 C5' DA C 202 4619 4621 4641 C5' DA C 203 4640 4642 4662 C5' DA C 204 4661 4663 4683 C5' DG C 205 4682 4684 4705 C5' DG C 206 4704 4706 4727 C5' DC C 207 4726 4728 4746 C5' DG C 208 4745 4747 4768 C5' DC C 209 4767 4769 4787 C5' DC C 210 4786 4788 4806 C5' DG C 211 4805 4807 4828 C5' DT C 212 4827 4829 4848 C5' DG C 213 4847 4849 4870 C5' DG C 214 4869 4871 4892 C5' DT C 215 4891 4893 4912 C5' DC C 216 4911 4913 4943 C5' 0KL A 903 4942 4944 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4376 P DA B 102 distorted distorted 4362 4377 4378 4379 4397 P DC B 103 distorted distorted 4384 4398 4399 4400 4416 P DC B 104 distorted distorted 4405 4417 4418 4419 4435 P DA B 105 distorted distorted 4424 4436 4437 4438 4456 P DC B 106 distorted distorted 4443 4457 4458 4459 4475 P DG B 107 distorted distorted 4464 4476 4477 4478 4497 P DG B 108 distorted distorted 4483 4498 4499 4500 4519 P DC B 109 distorted distorted 4505 4520 4521 4522 4538 P DG B 110 distorted distorted 4527 4539 4540 4541 4560 P DC B 111 distorted distorted 4546 4561 4562 4563 4594 P DOC B 112 OK OK 4568 4595 4596 4593 4616 P DA C 202 distorted distorted 4603 4617 4618 4619 4637 P DA C 203 distorted distorted 4624 4638 4639 4640 4658 P DA C 204 distorted distorted 4645 4659 4660 4661 4679 P DG C 205 distorted distorted 4666 4680 4681 4682 4701 P DG C 206 distorted distorted 4687 4702 4703 4704 4723 P DC C 207 distorted distorted 4709 4724 4725 4726 4742 P DG C 208 distorted distorted 4731 4743 4744 4745 4764 P DC C 209 distorted distorted 4750 4765 4766 4767 4783 P DC C 210 distorted distorted 4772 4784 4785 4786 4802 P DG C 211 distorted distorted 4791 4803 4804 4805 4824 P DT C 212 distorted distorted 4810 4825 4826 4827 4844 P DG C 213 distorted distorted 4832 4845 4846 4847 4866 P DG C 214 distorted distorted 4852 4867 4868 4869 4888 P DT C 215 distorted distorted 4874 4889 4890 4891 4908 P DC C 216 distorted distorted 4896 4909 4910 4911 ---------------------------------------------------------------------------------