ID code: '3M8S' 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' --------------------------------------------------------------------------------- 4292 C1' DG B 101 beta 4288 4293 4291 4314 C1' DA B 102 beta 4310 4315 4313 4335 C1' DC B 103 beta 4331 4336 4334 4354 C1' DC B 104 beta 4350 4355 4353 4373 C1' DA B 105 beta 4369 4374 4372 4394 C1' DC B 106 beta 4390 4395 4393 4413 C1' DG B 107 beta 4409 4414 4412 4435 C1' DG B 108 beta 4431 4436 4434 4457 C1' DC B 109 beta 4453 4458 4456 4476 C1' DG B 110 beta 4472 4477 4475 4498 C1' DC B 111 beta 4494 4499 4497 4515 C1' DOC B 112 beta 4519 4507 4516 4533 C1' DA C 201 beta 4529 4534 4532 4554 C1' DA C 202 beta 4550 4555 4553 4575 C1' DA C 203 beta 4571 4576 4574 4596 C1' DA C 204 beta 4592 4597 4595 4617 C1' DG C 205 beta 4613 4618 4616 4639 C1' DG C 206 beta 4635 4640 4638 4661 C1' DC C 207 beta 4657 4662 4660 4680 C1' DG C 208 beta 4676 4681 4679 4702 C1' DC C 209 beta 4698 4703 4701 4721 C1' DC C 210 beta 4717 4722 4720 4740 C1' DG C 211 beta 4736 4741 4739 4762 C1' DT C 212 beta 4758 4763 4761 4782 C1' DG C 213 beta 4778 4783 4781 4804 C1' DG C 214 beta 4800 4805 4803 4826 C1' DT C 215 beta 4822 4827 4825 4846 C1' DC C 216 beta 4842 4847 4845 4875 C1' HXB A 113 beta 4882 4857 4878 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4291 C2' DG B 101 4292 4289 4313 C2' DA B 102 4314 4311 4334 C2' DC B 103 4335 4332 4353 C2' DC B 104 4354 4351 4372 C2' DA B 105 4373 4370 4393 C2' DC B 106 4394 4391 4412 C2' DG B 107 4413 4410 4434 C2' DG B 108 4435 4432 4456 C2' DC B 109 4457 4454 4475 C2' DG B 110 4476 4473 4497 C2' DC B 111 4498 4495 4516 C2' DOC B 112 4515 4517 4532 C2' DA C 201 4533 4530 4553 C2' DA C 202 4554 4551 4574 C2' DA C 203 4575 4572 4595 C2' DA C 204 4596 4593 4616 C2' DG C 205 4617 4614 4638 C2' DG C 206 4639 4636 4660 C2' DC C 207 4661 4658 4679 C2' DG C 208 4680 4677 4701 C2' DC C 209 4702 4699 4720 C2' DC C 210 4721 4718 4739 C2' DG C 211 4740 4737 4761 C2' DT C 212 4762 4759 4781 C2' DG C 213 4782 4779 4803 C2' DG C 214 4804 4801 4825 C2' DT C 215 4826 4823 4845 C2' DC C 216 4846 4843 4878 C2' HXB A 113 4875 4879 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4289 C3' DG B 101 OK 4287 4290 4291 4311 C3' DA B 102 OK 4309 4312 4313 4332 C3' DC B 103 OK 4330 4333 4334 4351 C3' DC B 104 OK 4349 4352 4353 4370 C3' DA B 105 OK 4368 4371 4372 4391 C3' DC B 106 OK 4389 4392 4393 4410 C3' DG B 107 OK 4408 4411 4412 4432 C3' DG B 108 OK 4430 4433 4434 4454 C3' DC B 109 OK 4452 4455 4456 4473 C3' DG B 110 OK 4471 4474 4475 4495 C3' DC B 111 OK 4493 4496 4497 4517 C3' DOC B 112 4518 4516 4530 C3' DA C 201 OK 4528 4531 4532 4551 C3' DA C 202 OK 4549 4552 4553 4572 C3' DA C 203 OK 4570 4573 4574 4593 C3' DA C 204 OK 4591 4594 4595 4614 C3' DG C 205 OK 4612 4615 4616 4636 C3' DG C 206 OK 4634 4637 4638 4658 C3' DC C 207 OK 4656 4659 4660 4677 C3' DG C 208 OK 4675 4678 4679 4699 C3' DC C 209 OK 4697 4700 4701 4718 C3' DC C 210 OK 4716 4719 4720 4737 C3' DG C 211 OK 4735 4738 4739 4759 C3' DT C 212 OK 4757 4760 4761 4779 C3' DG C 213 OK 4777 4780 4781 4801 C3' DG C 214 OK 4799 4802 4803 4823 C3' DT C 215 OK 4821 4824 4825 4843 C3' DC C 216 OK 4841 4844 4845 4879 C3' HXB A 113 OK 4881 4880 4878 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4287 C4' DG B 101 OK 4289 4286 4288 4309 C4' DA B 102 OK 4311 4308 4310 4330 C4' DC B 103 OK 4332 4329 4331 4349 C4' DC B 104 OK 4351 4348 4350 4368 C4' DA B 105 OK 4370 4367 4369 4389 C4' DC B 106 OK 4391 4388 4390 4408 C4' DG B 107 OK 4410 4407 4409 4430 C4' DG B 108 OK 4432 4429 4431 4452 C4' DC B 109 OK 4454 4451 4453 4471 C4' DG B 110 OK 4473 4470 4472 4493 C4' DC B 111 OK 4495 4492 4494 4518 C4' DOC B 112 OK 4517 4520 4519 4528 C4' DA C 201 OK 4530 4527 4529 4549 C4' DA C 202 OK 4551 4548 4550 4570 C4' DA C 203 OK 4572 4569 4571 4591 C4' DA C 204 OK 4593 4590 4592 4612 C4' DG C 205 OK 4614 4611 4613 4634 C4' DG C 206 OK 4636 4633 4635 4656 C4' DC C 207 OK 4658 4655 4657 4675 C4' DG C 208 OK 4677 4674 4676 4697 C4' DC C 209 OK 4699 4696 4698 4716 C4' DC C 210 OK 4718 4715 4717 4735 C4' DG C 211 OK 4737 4734 4736 4757 C4' DT C 212 OK 4759 4756 4758 4777 C4' DG C 213 OK 4779 4776 4778 4799 C4' DG C 214 OK 4801 4798 4800 4821 C4' DT C 215 OK 4823 4820 4822 4841 C4' DC C 216 OK 4843 4840 4842 4881 C4' HXB A 113 OK 4879 4883 4882 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4286 C5' DG B 101 4285 4287 4308 C5' DA B 102 4307 4309 4329 C5' DC B 103 4328 4330 4348 C5' DC B 104 4347 4349 4367 C5' DA B 105 4366 4368 4388 C5' DC B 106 4387 4389 4407 C5' DG B 107 4406 4408 4429 C5' DG B 108 4428 4430 4451 C5' DC B 109 4450 4452 4470 C5' DG B 110 4469 4471 4492 C5' DC B 111 4491 4493 4520 C5' DOC B 112 4521 4518 4527 C5' DA C 201 4526 4528 4548 C5' DA C 202 4547 4549 4569 C5' DA C 203 4568 4570 4590 C5' DA C 204 4589 4591 4611 C5' DG C 205 4610 4612 4633 C5' DG C 206 4632 4634 4655 C5' DC C 207 4654 4656 4674 C5' DG C 208 4673 4675 4696 C5' DC C 209 4695 4697 4715 C5' DC C 210 4714 4716 4734 C5' DG C 211 4733 4735 4756 C5' DT C 212 4755 4757 4776 C5' DG C 213 4775 4777 4798 C5' DG C 214 4797 4799 4820 C5' DT C 215 4819 4821 4840 C5' DC C 216 4839 4841 4883 C5' HXB A 113 4884 4881 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4304 P DA B 102 distorted distorted 4290 4305 4306 4307 4325 P DC B 103 distorted distorted 4312 4326 4327 4328 4344 P DC B 104 distorted distorted 4333 4345 4346 4347 4363 P DA B 105 OK OK 4352 4364 4365 4366 4384 P DC B 106 distorted distorted 4371 4385 4386 4387 4403 P DG B 107 distorted distorted 4392 4404 4405 4406 4425 P DG B 108 distorted distorted 4411 4426 4427 4428 4447 P DC B 109 distorted distorted 4433 4448 4449 4450 4466 P DG B 110 distorted distorted 4455 4467 4468 4469 4488 P DC B 111 distorted distorted 4474 4489 4490 4491 4522 P DOC B 112 OK OK 4496 4523 4524 4521 4544 P DA C 202 distorted distorted 4531 4545 4546 4547 4565 P DA C 203 distorted distorted 4552 4566 4567 4568 4586 P DA C 204 distorted distorted 4573 4587 4588 4589 4607 P DG C 205 distorted distorted 4594 4608 4609 4610 4629 P DG C 206 distorted distorted 4615 4630 4631 4632 4651 P DC C 207 distorted distorted 4637 4652 4653 4654 4670 P DG C 208 distorted distorted 4659 4671 4672 4673 4692 P DC C 209 distorted distorted 4678 4693 4694 4695 4711 P DC C 210 distorted distorted 4700 4712 4713 4714 4730 P DG C 211 distorted distorted 4719 4731 4732 4733 4752 P DT C 212 distorted distorted 4738 4753 4754 4755 4772 P DG C 213 distorted distorted 4760 4773 4774 4775 4794 P DG C 214 distorted distorted 4780 4795 4796 4797 4816 P DT C 215 distorted distorted 4802 4817 4818 4819 4836 P DC C 216 distorted distorted 4824 4837 4838 4839 ---------------------------------------------------------------------------------