ID code: '4ELT' 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' --------------------------------------------------------------------------------- 4315 C1' DG B 101 beta 4311 4316 4314 4337 C1' DA B 102 beta 4333 4338 4336 4358 C1' DC B 103 beta 4354 4359 4357 4377 C1' DC B 104 beta 4373 4378 4376 4396 C1' DA B 105 beta 4392 4397 4395 4417 C1' DC B 106 beta 4413 4418 4416 4436 C1' DG B 107 beta 4432 4437 4435 4458 C1' DG B 108 beta 4454 4459 4457 4480 C1' DC B 109 beta 4476 4481 4479 4499 C1' DG B 110 beta 4495 4500 4498 4521 C1' DC B 111 beta 4517 4522 4520 4538 C1' DOC B 112 beta 4542 4530 4539 4556 C1' DA C 201 beta 4552 4557 4555 4577 C1' DA C 202 beta 4573 4578 4576 4598 C1' DA C 203 beta 4594 4599 4597 4619 C1' DA C 204 beta 4615 4620 4618 4640 C1' DG C 205 beta 4636 4641 4639 4662 C1' DG C 206 beta 4658 4663 4661 4684 C1' DC C 207 beta 4680 4685 4683 4703 C1' DG C 208 beta 4699 4704 4702 4725 C1' DC C 209 beta 4721 4726 4724 4744 C1' DC C 210 beta 4740 4745 4743 4763 C1' DG C 211 beta 4759 4764 4762 4785 C1' DT C 212 beta 4781 4786 4784 4805 C1' DG C 213 beta 4801 4806 4804 4827 C1' DG C 214 beta 4823 4828 4826 4849 C1' DT C 215 beta 4845 4850 4848 4869 C1' DC C 216 beta 4865 4870 4868 4898 C1' 0R5 A 901 beta 4897 4899 4896 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4314 C2' DG B 101 4315 4312 4336 C2' DA B 102 4337 4334 4357 C2' DC B 103 4358 4355 4376 C2' DC B 104 4377 4374 4395 C2' DA B 105 4396 4393 4416 C2' DC B 106 4417 4414 4435 C2' DG B 107 4436 4433 4457 C2' DG B 108 4458 4455 4479 C2' DC B 109 4480 4477 4498 C2' DG B 110 4499 4496 4520 C2' DC B 111 4521 4518 4539 C2' DOC B 112 4538 4540 4555 C2' DA C 201 4556 4553 4576 C2' DA C 202 4577 4574 4597 C2' DA C 203 4598 4595 4618 C2' DA C 204 4619 4616 4639 C2' DG C 205 4640 4637 4661 C2' DG C 206 4662 4659 4683 C2' DC C 207 4684 4681 4702 C2' DG C 208 4703 4700 4724 C2' DC C 209 4725 4722 4743 C2' DC C 210 4744 4741 4762 C2' DG C 211 4763 4760 4784 C2' DT C 212 4785 4782 4804 C2' DG C 213 4805 4802 4826 C2' DG C 214 4827 4824 4848 C2' DT C 215 4849 4846 4868 C2' DC C 216 4869 4866 4896 C2' 0R5 A 901 4898 4894 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4312 C3' DG B 101 OK 4310 4313 4314 4334 C3' DA B 102 OK 4332 4335 4336 4355 C3' DC B 103 OK 4353 4356 4357 4374 C3' DC B 104 OK 4372 4375 4376 4393 C3' DA B 105 OK 4391 4394 4395 4414 C3' DC B 106 OK 4412 4415 4416 4433 C3' DG B 107 OK 4431 4434 4435 4455 C3' DG B 108 OK 4453 4456 4457 4477 C3' DC B 109 OK 4475 4478 4479 4496 C3' DG B 110 OK 4494 4497 4498 4518 C3' DC B 111 OK 4516 4519 4520 4540 C3' DOC B 112 4541 4539 4553 C3' DA C 201 OK 4551 4554 4555 4574 C3' DA C 202 OK 4572 4575 4576 4595 C3' DA C 203 OK 4593 4596 4597 4616 C3' DA C 204 OK 4614 4617 4618 4637 C3' DG C 205 OK 4635 4638 4639 4659 C3' DG C 206 OK 4657 4660 4661 4681 C3' DC C 207 OK 4679 4682 4683 4700 C3' DG C 208 OK 4698 4701 4702 4722 C3' DC C 209 OK 4720 4723 4724 4741 C3' DC C 210 OK 4739 4742 4743 4760 C3' DG C 211 OK 4758 4761 4762 4782 C3' DT C 212 OK 4780 4783 4784 4802 C3' DG C 213 OK 4800 4803 4804 4824 C3' DG C 214 OK 4822 4825 4826 4846 C3' DT C 215 OK 4844 4847 4848 4866 C3' DC C 216 OK 4864 4867 4868 4894 C3' 0R5 A 901 OK 4893 4895 4896 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4310 C4' DG B 101 OK 4312 4309 4311 4332 C4' DA B 102 OK 4334 4331 4333 4353 C4' DC B 103 OK 4355 4352 4354 4372 C4' DC B 104 OK 4374 4371 4373 4391 C4' DA B 105 OK 4393 4390 4392 4412 C4' DC B 106 OK 4414 4411 4413 4431 C4' DG B 107 OK 4433 4430 4432 4453 C4' DG B 108 OK 4455 4452 4454 4475 C4' DC B 109 OK 4477 4474 4476 4494 C4' DG B 110 OK 4496 4493 4495 4516 C4' DC B 111 OK 4518 4515 4517 4541 C4' DOC B 112 OK 4540 4543 4542 4551 C4' DA C 201 OK 4553 4550 4552 4572 C4' DA C 202 OK 4574 4571 4573 4593 C4' DA C 203 OK 4595 4592 4594 4614 C4' DA C 204 OK 4616 4613 4615 4635 C4' DG C 205 OK 4637 4634 4636 4657 C4' DG C 206 OK 4659 4656 4658 4679 C4' DC C 207 OK 4681 4678 4680 4698 C4' DG C 208 OK 4700 4697 4699 4720 C4' DC C 209 OK 4722 4719 4721 4739 C4' DC C 210 OK 4741 4738 4740 4758 C4' DG C 211 OK 4760 4757 4759 4780 C4' DT C 212 OK 4782 4779 4781 4800 C4' DG C 213 OK 4802 4799 4801 4822 C4' DG C 214 OK 4824 4821 4823 4844 C4' DT C 215 OK 4846 4843 4845 4864 C4' DC C 216 OK 4866 4863 4865 4893 C4' 0R5 A 901 OK 4894 4892 4897 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4309 C5' DG B 101 4308 4310 4331 C5' DA B 102 4330 4332 4352 C5' DC B 103 4351 4353 4371 C5' DC B 104 4370 4372 4390 C5' DA B 105 4389 4391 4411 C5' DC B 106 4410 4412 4430 C5' DG B 107 4429 4431 4452 C5' DG B 108 4451 4453 4474 C5' DC B 109 4473 4475 4493 C5' DG B 110 4492 4494 4515 C5' DC B 111 4514 4516 4543 C5' DOC B 112 4544 4541 4550 C5' DA C 201 4549 4551 4571 C5' DA C 202 4570 4572 4592 C5' DA C 203 4591 4593 4613 C5' DA C 204 4612 4614 4634 C5' DG C 205 4633 4635 4656 C5' DG C 206 4655 4657 4678 C5' DC C 207 4677 4679 4697 C5' DG C 208 4696 4698 4719 C5' DC C 209 4718 4720 4738 C5' DC C 210 4737 4739 4757 C5' DG C 211 4756 4758 4779 C5' DT C 212 4778 4780 4799 C5' DG C 213 4798 4800 4821 C5' DG C 214 4820 4822 4843 C5' DT C 215 4842 4844 4863 C5' DC C 216 4862 4864 4892 C5' 0R5 A 901 4891 4893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4327 P DA B 102 distorted distorted 4313 4328 4329 4330 4348 P DC B 103 distorted distorted 4335 4349 4350 4351 4367 P DC B 104 distorted distorted 4356 4368 4369 4370 4386 P DA B 105 distorted distorted 4375 4387 4388 4389 4407 P DC B 106 distorted distorted 4394 4408 4409 4410 4426 P DG B 107 distorted distorted 4415 4427 4428 4429 4448 P DG B 108 distorted distorted 4434 4449 4450 4451 4470 P DC B 109 distorted distorted 4456 4471 4472 4473 4489 P DG B 110 distorted distorted 4478 4490 4491 4492 4511 P DC B 111 distorted distorted 4497 4512 4513 4514 4545 P DOC B 112 OK OK 4519 4546 4547 4544 4567 P DA C 202 distorted distorted 4554 4568 4569 4570 4588 P DA C 203 distorted distorted 4575 4589 4590 4591 4609 P DA C 204 distorted distorted 4596 4610 4611 4612 4630 P DG C 205 distorted distorted 4617 4631 4632 4633 4652 P DG C 206 distorted distorted 4638 4653 4654 4655 4674 P DC C 207 distorted distorted 4660 4675 4676 4677 4693 P DG C 208 distorted distorted 4682 4694 4695 4696 4715 P DC C 209 distorted distorted 4701 4716 4717 4718 4734 P DC C 210 distorted distorted 4723 4735 4736 4737 4753 P DG C 211 distorted distorted 4742 4754 4755 4756 4775 P DT C 212 distorted distorted 4761 4776 4777 4778 4795 P DG C 213 distorted distorted 4783 4796 4797 4798 4817 P DG C 214 distorted distorted 4803 4818 4819 4820 4839 P DT C 215 distorted distorted 4825 4840 4841 4842 4859 P DC C 216 distorted distorted 4847 4860 4861 4862 ---------------------------------------------------------------------------------