ID code: '1RAM' 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' --------------------------------------------------------------------------------- 4382 C1' C C 1 beta 4378 4383 4381 4401 C1' G C 2 beta 4397 4402 4400 4423 C1' G C 3 beta 4419 4424 4422 4445 C1' C C 4 beta 4441 4446 4444 4464 C1' T C 5 beta 4460 4465 4463 4484 C1' G C 6 beta 4480 4485 4483 4506 C1' G C 7 beta 4502 4507 4505 4528 C1' A C 8 beta 4524 4529 4527 4549 C1' A C 9 beta 4545 4550 4548 4570 C1' A C 10 beta 4566 4571 4569 4591 C1' T C 11 beta 4587 4592 4590 4611 C1' T C 12 beta 4607 4612 4610 4631 C1' T C 13 beta 4627 4632 4630 4651 C1' C C 14 beta 4647 4652 4650 4670 C1' C C 15 beta 4666 4671 4669 4689 C1' A C 16 beta 4685 4690 4688 4710 C1' G C 17 beta 4706 4711 4709 4732 C1' C C 18 beta 4728 4733 4731 4751 C1' C C 19 beta 4747 4752 4750 4770 C1' G C 20 beta 4766 4771 4769 4790 C1' C D 1 beta 4786 4791 4789 4809 C1' G D 2 beta 4805 4810 4808 4831 C1' G D 3 beta 4827 4832 4830 4853 C1' C D 4 beta 4849 4854 4852 4872 C1' T D 5 beta 4868 4873 4871 4892 C1' G D 6 beta 4888 4893 4891 4914 C1' G D 7 beta 4910 4915 4913 4936 C1' A D 8 beta 4932 4937 4935 4957 C1' A D 9 beta 4953 4958 4956 4978 C1' A D 10 beta 4974 4979 4977 4999 C1' T D 11 beta 4995 5000 4998 5019 C1' T D 12 beta 5015 5020 5018 5039 C1' T D 13 beta 5035 5040 5038 5059 C1' C D 14 beta 5055 5060 5058 5078 C1' C D 15 beta 5074 5079 5077 5097 C1' A D 16 beta 5093 5098 5096 5118 C1' G D 17 beta 5114 5119 5117 5140 C1' C D 18 beta 5136 5141 5139 5159 C1' C D 19 beta 5155 5160 5158 5178 C1' G D 20 beta 5174 5179 5177 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4381 C2' C C 1 4382 4379 4400 C2' G C 2 4401 4398 4422 C2' G C 3 4423 4420 4444 C2' C C 4 4445 4442 4463 C2' T C 5 4464 4461 4483 C2' G C 6 4484 4481 4505 C2' G C 7 4506 4503 4527 C2' A C 8 4528 4525 4548 C2' A C 9 4549 4546 4569 C2' A C 10 4570 4567 4590 C2' T C 11 4591 4588 4610 C2' T C 12 4611 4608 4630 C2' T C 13 4631 4628 4650 C2' C C 14 4651 4648 4669 C2' C C 15 4670 4667 4688 C2' A C 16 4689 4686 4709 C2' G C 17 4710 4707 4731 C2' C C 18 4732 4729 4750 C2' C C 19 4751 4748 4769 C2' G C 20 4770 4767 4789 C2' C D 1 4790 4787 4808 C2' G D 2 4809 4806 4830 C2' G D 3 4831 4828 4852 C2' C D 4 4853 4850 4871 C2' T D 5 4872 4869 4891 C2' G D 6 4892 4889 4913 C2' G D 7 4914 4911 4935 C2' A D 8 4936 4933 4956 C2' A D 9 4957 4954 4977 C2' A D 10 4978 4975 4998 C2' T D 11 4999 4996 5018 C2' T D 12 5019 5016 5038 C2' T D 13 5039 5036 5058 C2' C D 14 5059 5056 5077 C2' C D 15 5078 5075 5096 C2' A D 16 5097 5094 5117 C2' G D 17 5118 5115 5139 C2' C D 18 5140 5137 5158 C2' C D 19 5159 5156 5177 C2' G D 20 5178 5175 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4379 C3' C C 1 OK 4377 4380 4381 4398 C3' G C 2 OK 4396 4399 4400 4420 C3' G C 3 OK 4418 4421 4422 4442 C3' C C 4 OK 4440 4443 4444 4461 C3' T C 5 OK 4459 4462 4463 4481 C3' G C 6 OK 4479 4482 4483 4503 C3' G C 7 OK 4501 4504 4505 4525 C3' A C 8 OK 4523 4526 4527 4546 C3' A C 9 OK 4544 4547 4548 4567 C3' A C 10 OK 4565 4568 4569 4588 C3' T C 11 OK 4586 4589 4590 4608 C3' T C 12 OK 4606 4609 4610 4628 C3' T C 13 OK 4626 4629 4630 4648 C3' C C 14 OK 4646 4649 4650 4667 C3' C C 15 OK 4665 4668 4669 4686 C3' A C 16 OK 4684 4687 4688 4707 C3' G C 17 OK 4705 4708 4709 4729 C3' C C 18 OK 4727 4730 4731 4748 C3' C C 19 OK 4746 4749 4750 4767 C3' G C 20 OK 4765 4768 4769 4787 C3' C D 1 OK 4785 4788 4789 4806 C3' G D 2 OK 4804 4807 4808 4828 C3' G D 3 OK 4826 4829 4830 4850 C3' C D 4 OK 4848 4851 4852 4869 C3' T D 5 OK 4867 4870 4871 4889 C3' G D 6 OK 4887 4890 4891 4911 C3' G D 7 OK 4909 4912 4913 4933 C3' A D 8 OK 4931 4934 4935 4954 C3' A D 9 OK 4952 4955 4956 4975 C3' A D 10 OK 4973 4976 4977 4996 C3' T D 11 OK 4994 4997 4998 5016 C3' T D 12 OK 5014 5017 5018 5036 C3' T D 13 OK 5034 5037 5038 5056 C3' C D 14 OK 5054 5057 5058 5075 C3' C D 15 OK 5073 5076 5077 5094 C3' A D 16 OK 5092 5095 5096 5115 C3' G D 17 OK 5113 5116 5117 5137 C3' C D 18 OK 5135 5138 5139 5156 C3' C D 19 OK 5154 5157 5158 5175 C3' G D 20 OK 5173 5176 5177 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4377 C4' C C 1 OK 4379 4376 4378 4396 C4' G C 2 OK 4398 4395 4397 4418 C4' G C 3 OK 4420 4417 4419 4440 C4' C C 4 OK 4442 4439 4441 4459 C4' T C 5 OK 4461 4458 4460 4479 C4' G C 6 OK 4481 4478 4480 4501 C4' G C 7 OK 4503 4500 4502 4523 C4' A C 8 OK 4525 4522 4524 4544 C4' A C 9 OK 4546 4543 4545 4565 C4' A C 10 OK 4567 4564 4566 4586 C4' T C 11 OK 4588 4585 4587 4606 C4' T C 12 OK 4608 4605 4607 4626 C4' T C 13 OK 4628 4625 4627 4646 C4' C C 14 OK 4648 4645 4647 4665 C4' C C 15 OK 4667 4664 4666 4684 C4' A C 16 OK 4686 4683 4685 4705 C4' G C 17 OK 4707 4704 4706 4727 C4' C C 18 OK 4729 4726 4728 4746 C4' C C 19 OK 4748 4745 4747 4765 C4' G C 20 OK 4767 4764 4766 4785 C4' C D 1 OK 4787 4784 4786 4804 C4' G D 2 OK 4806 4803 4805 4826 C4' G D 3 OK 4828 4825 4827 4848 C4' C D 4 OK 4850 4847 4849 4867 C4' T D 5 OK 4869 4866 4868 4887 C4' G D 6 OK 4889 4886 4888 4909 C4' G D 7 OK 4911 4908 4910 4931 C4' A D 8 OK 4933 4930 4932 4952 C4' A D 9 OK 4954 4951 4953 4973 C4' A D 10 OK 4975 4972 4974 4994 C4' T D 11 OK 4996 4993 4995 5014 C4' T D 12 OK 5016 5013 5015 5034 C4' T D 13 OK 5036 5033 5035 5054 C4' C D 14 OK 5056 5053 5055 5073 C4' C D 15 OK 5075 5072 5074 5092 C4' A D 16 OK 5094 5091 5093 5113 C4' G D 17 OK 5115 5112 5114 5135 C4' C D 18 OK 5137 5134 5136 5154 C4' C D 19 OK 5156 5153 5155 5173 C4' G D 20 OK 5175 5172 5174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4376 C5' C C 1 4375 4377 4395 C5' G C 2 4394 4396 4417 C5' G C 3 4416 4418 4439 C5' C C 4 4438 4440 4458 C5' T C 5 4457 4459 4478 C5' G C 6 4477 4479 4500 C5' G C 7 4499 4501 4522 C5' A C 8 4521 4523 4543 C5' A C 9 4542 4544 4564 C5' A C 10 4563 4565 4585 C5' T C 11 4584 4586 4605 C5' T C 12 4604 4606 4625 C5' T C 13 4624 4626 4645 C5' C C 14 4644 4646 4664 C5' C C 15 4663 4665 4683 C5' A C 16 4682 4684 4704 C5' G C 17 4703 4705 4726 C5' C C 18 4725 4727 4745 C5' C C 19 4744 4746 4764 C5' G C 20 4763 4765 4784 C5' C D 1 4783 4785 4803 C5' G D 2 4802 4804 4825 C5' G D 3 4824 4826 4847 C5' C D 4 4846 4848 4866 C5' T D 5 4865 4867 4886 C5' G D 6 4885 4887 4908 C5' G D 7 4907 4909 4930 C5' A D 8 4929 4931 4951 C5' A D 9 4950 4952 4972 C5' A D 10 4971 4973 4993 C5' T D 11 4992 4994 5013 C5' T D 12 5012 5014 5033 C5' T D 13 5032 5034 5053 C5' C D 14 5052 5054 5072 C5' C D 15 5071 5073 5091 C5' A D 16 5090 5092 5112 C5' G D 17 5111 5113 5134 C5' C D 18 5133 5135 5153 C5' C D 19 5152 5154 5172 C5' G D 20 5171 5173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4391 P G C 2 OK OK 4380 4392 4393 4394 4413 P G C 3 distorted distorted 4399 4414 4415 4416 4435 P C C 4 OK OK 4421 4436 4437 4438 4454 P T C 5 OK OK 4443 4455 4456 4457 4474 P G C 6 OK OK 4462 4475 4476 4477 4496 P G C 7 OK OK 4482 4497 4498 4499 4518 P A C 8 OK OK 4504 4519 4520 4521 4539 P A C 9 OK OK 4526 4540 4541 4542 4560 P A C 10 OK OK 4547 4561 4562 4563 4581 P T C 11 OK OK 4568 4582 4583 4584 4601 P T C 12 OK OK 4589 4602 4603 4604 4621 P T C 13 OK OK 4609 4622 4623 4624 4641 P C C 14 OK OK 4629 4642 4643 4644 4660 P C C 15 OK OK 4649 4661 4662 4663 4679 P A C 16 OK OK 4668 4680 4681 4682 4700 P G C 17 OK OK 4687 4701 4702 4703 4722 P C C 18 OK OK 4708 4723 4724 4725 4741 P C C 19 OK OK 4730 4742 4743 4744 4760 P G C 20 OK OK 4749 4761 4762 4763 4799 P G D 2 distorted distorted 4788 4800 4801 4802 4821 P G D 3 OK OK 4807 4822 4823 4824 4843 P C D 4 OK OK 4829 4844 4845 4846 4862 P T D 5 distorted distorted 4851 4863 4864 4865 4882 P G D 6 OK OK 4870 4883 4884 4885 4904 P G D 7 OK OK 4890 4905 4906 4907 4926 P A D 8 OK OK 4912 4927 4928 4929 4947 P A D 9 OK OK 4934 4948 4949 4950 4968 P A D 10 OK OK 4955 4969 4970 4971 4989 P T D 11 OK OK 4976 4990 4991 4992 5009 P T D 12 OK OK 4997 5010 5011 5012 5029 P T D 13 OK OK 5017 5030 5031 5032 5049 P C D 14 OK OK 5037 5050 5051 5052 5068 P C D 15 OK OK 5057 5069 5070 5071 5087 P A D 16 OK OK 5076 5088 5089 5090 5108 P G D 17 OK OK 5095 5109 5110 5111 5130 P C D 18 OK OK 5116 5131 5132 5133 5149 P C D 19 OK OK 5138 5150 5151 5152 5168 P G D 20 OK OK 5157 5169 5170 5171 ---------------------------------------------------------------------------------