ID code: '4DLE' 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' --------------------------------------------------------------------------------- 4371 C1' DG B 101 beta 4367 4372 4370 4393 C1' DA B 102 beta 4389 4394 4392 4414 C1' DC B 103 beta 4410 4415 4413 4433 C1' DC B 104 beta 4429 4434 4432 4452 C1' DA B 105 beta 4448 4453 4451 4473 C1' DC B 106 beta 4469 4474 4472 4492 C1' DG B 107 beta 4488 4493 4491 4514 C1' DG B 108 beta 4510 4515 4513 4536 C1' DC B 109 beta 4532 4537 4535 4555 C1' DG B 110 beta 4551 4556 4554 4577 C1' DC B 111 beta 4573 4578 4576 4594 C1' DOC B 112 beta 4598 4586 4595 4612 C1' DA C 201 beta 4608 4613 4611 4633 C1' DA C 202 beta 4629 4634 4632 4654 C1' DA C 203 beta 4650 4655 4653 4675 C1' DG C 204 beta 4671 4676 4674 4697 C1' DG C 205 beta 4693 4698 4696 4719 C1' DG C 206 beta 4715 4720 4718 4741 C1' DC C 207 beta 4737 4742 4740 4760 C1' DG C 208 beta 4756 4761 4759 4782 C1' DC C 209 beta 4778 4783 4781 4801 C1' DC C 210 beta 4797 4802 4800 4820 C1' DG C 211 beta 4816 4821 4819 4842 C1' DT C 212 beta 4838 4843 4841 4862 C1' DG C 213 beta 4858 4863 4861 4884 C1' DG C 214 beta 4880 4885 4883 4906 C1' DT C 215 beta 4902 4907 4905 4926 C1' DC C 216 beta 4922 4927 4925 4951 C1' DCT A 903 beta 4955 4943 4952 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4370 C2' DG B 101 4371 4368 4392 C2' DA B 102 4393 4390 4413 C2' DC B 103 4414 4411 4432 C2' DC B 104 4433 4430 4451 C2' DA B 105 4452 4449 4472 C2' DC B 106 4473 4470 4491 C2' DG B 107 4492 4489 4513 C2' DG B 108 4514 4511 4535 C2' DC B 109 4536 4533 4554 C2' DG B 110 4555 4552 4576 C2' DC B 111 4577 4574 4595 C2' DOC B 112 4594 4596 4611 C2' DA C 201 4612 4609 4632 C2' DA C 202 4633 4630 4653 C2' DA C 203 4654 4651 4674 C2' DG C 204 4675 4672 4696 C2' DG C 205 4697 4694 4718 C2' DG C 206 4719 4716 4740 C2' DC C 207 4741 4738 4759 C2' DG C 208 4760 4757 4781 C2' DC C 209 4782 4779 4800 C2' DC C 210 4801 4798 4819 C2' DG C 211 4820 4817 4841 C2' DT C 212 4842 4839 4861 C2' DG C 213 4862 4859 4883 C2' DG C 214 4884 4881 4905 C2' DT C 215 4906 4903 4925 C2' DC C 216 4926 4923 4952 C2' DCT A 903 4951 4953 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4368 C3' DG B 101 OK 4366 4369 4370 4390 C3' DA B 102 OK 4388 4391 4392 4411 C3' DC B 103 OK 4409 4412 4413 4430 C3' DC B 104 OK 4428 4431 4432 4449 C3' DA B 105 OK 4447 4450 4451 4470 C3' DC B 106 OK 4468 4471 4472 4489 C3' DG B 107 OK 4487 4490 4491 4511 C3' DG B 108 OK 4509 4512 4513 4533 C3' DC B 109 OK 4531 4534 4535 4552 C3' DG B 110 OK 4550 4553 4554 4574 C3' DC B 111 OK 4572 4575 4576 4596 C3' DOC B 112 4597 4595 4609 C3' DA C 201 OK 4607 4610 4611 4630 C3' DA C 202 OK 4628 4631 4632 4651 C3' DA C 203 OK 4649 4652 4653 4672 C3' DG C 204 OK 4670 4673 4674 4694 C3' DG C 205 OK 4692 4695 4696 4716 C3' DG C 206 OK 4714 4717 4718 4738 C3' DC C 207 OK 4736 4739 4740 4757 C3' DG C 208 OK 4755 4758 4759 4779 C3' DC C 209 OK 4777 4780 4781 4798 C3' DC C 210 OK 4796 4799 4800 4817 C3' DG C 211 OK 4815 4818 4819 4839 C3' DT C 212 OK 4837 4840 4841 4859 C3' DG C 213 OK 4857 4860 4861 4881 C3' DG C 214 OK 4879 4882 4883 4903 C3' DT C 215 OK 4901 4904 4905 4923 C3' DC C 216 OK 4921 4924 4925 4953 C3' DCT A 903 4954 4952 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4366 C4' DG B 101 OK 4368 4365 4367 4388 C4' DA B 102 OK 4390 4387 4389 4409 C4' DC B 103 OK 4411 4408 4410 4428 C4' DC B 104 OK 4430 4427 4429 4447 C4' DA B 105 OK 4449 4446 4448 4468 C4' DC B 106 OK 4470 4467 4469 4487 C4' DG B 107 OK 4489 4486 4488 4509 C4' DG B 108 OK 4511 4508 4510 4531 C4' DC B 109 OK 4533 4530 4532 4550 C4' DG B 110 OK 4552 4549 4551 4572 C4' DC B 111 OK 4574 4571 4573 4597 C4' DOC B 112 OK 4596 4599 4598 4607 C4' DA C 201 OK 4609 4606 4608 4628 C4' DA C 202 OK 4630 4627 4629 4649 C4' DA C 203 OK 4651 4648 4650 4670 C4' DG C 204 OK 4672 4669 4671 4692 C4' DG C 205 OK 4694 4691 4693 4714 C4' DG C 206 OK 4716 4713 4715 4736 C4' DC C 207 OK 4738 4735 4737 4755 C4' DG C 208 OK 4757 4754 4756 4777 C4' DC C 209 OK 4779 4776 4778 4796 C4' DC C 210 OK 4798 4795 4797 4815 C4' DG C 211 OK 4817 4814 4816 4837 C4' DT C 212 OK 4839 4836 4838 4857 C4' DG C 213 OK 4859 4856 4858 4879 C4' DG C 214 OK 4881 4878 4880 4901 C4' DT C 215 OK 4903 4900 4902 4921 C4' DC C 216 OK 4923 4920 4922 4954 C4' DCT A 903 OK 4953 4956 4955 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4365 C5' DG B 101 4364 4366 4387 C5' DA B 102 4386 4388 4408 C5' DC B 103 4407 4409 4427 C5' DC B 104 4426 4428 4446 C5' DA B 105 4445 4447 4467 C5' DC B 106 4466 4468 4486 C5' DG B 107 4485 4487 4508 C5' DG B 108 4507 4509 4530 C5' DC B 109 4529 4531 4549 C5' DG B 110 4548 4550 4571 C5' DC B 111 4570 4572 4599 C5' DOC B 112 4600 4597 4606 C5' DA C 201 4605 4607 4627 C5' DA C 202 4626 4628 4648 C5' DA C 203 4647 4649 4669 C5' DG C 204 4668 4670 4691 C5' DG C 205 4690 4692 4713 C5' DG C 206 4712 4714 4735 C5' DC C 207 4734 4736 4754 C5' DG C 208 4753 4755 4776 C5' DC C 209 4775 4777 4795 C5' DC C 210 4794 4796 4814 C5' DG C 211 4813 4815 4836 C5' DT C 212 4835 4837 4856 C5' DG C 213 4855 4857 4878 C5' DG C 214 4877 4879 4900 C5' DT C 215 4899 4901 4920 C5' DC C 216 4919 4921 4956 C5' DCT A 903 4957 4954 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4383 P DA B 102 distorted distorted 4369 4384 4385 4386 4404 P DC B 103 distorted distorted 4391 4405 4406 4407 4423 P DC B 104 distorted distorted 4412 4424 4425 4426 4442 P DA B 105 distorted distorted 4431 4443 4444 4445 4463 P DC B 106 distorted distorted 4450 4464 4465 4466 4482 P DG B 107 distorted distorted 4471 4483 4484 4485 4504 P DG B 108 distorted distorted 4490 4505 4506 4507 4526 P DC B 109 distorted distorted 4512 4527 4528 4529 4545 P DG B 110 distorted distorted 4534 4546 4547 4548 4567 P DC B 111 distorted distorted 4553 4568 4569 4570 4601 P DOC B 112 distorted distorted 4575 4602 4603 4600 4623 P DA C 202 distorted distorted 4610 4624 4625 4626 4644 P DA C 203 distorted distorted 4631 4645 4646 4647 4665 P DG C 204 distorted distorted 4652 4666 4667 4668 4687 P DG C 205 distorted distorted 4673 4688 4689 4690 4709 P DG C 206 distorted distorted 4695 4710 4711 4712 4731 P DC C 207 distorted distorted 4717 4732 4733 4734 4750 P DG C 208 distorted distorted 4739 4751 4752 4753 4772 P DC C 209 distorted distorted 4758 4773 4774 4775 4791 P DC C 210 distorted distorted 4780 4792 4793 4794 4810 P DG C 211 distorted distorted 4799 4811 4812 4813 4832 P DT C 212 distorted distorted 4818 4833 4834 4835 4852 P DG C 213 distorted distorted 4840 4853 4854 4855 4874 P DG C 214 distorted distorted 4860 4875 4876 4877 4896 P DT C 215 distorted distorted 4882 4897 4898 4899 4916 P DC C 216 distorted distorted 4904 4917 4918 4919 ---------------------------------------------------------------------------------