ID code: '4DFK' 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' --------------------------------------------------------------------------------- 4281 C1' DG B 101 beta 4277 4282 4280 4303 C1' DA B 102 beta 4299 4304 4302 4324 C1' DC B 103 beta 4320 4325 4323 4343 C1' DC B 104 beta 4339 4344 4342 4362 C1' DA B 105 beta 4358 4363 4361 4383 C1' DC B 106 beta 4379 4384 4382 4402 C1' DG B 107 beta 4398 4403 4401 4424 C1' DG B 108 beta 4420 4425 4423 4446 C1' DC B 109 beta 4442 4447 4445 4465 C1' DG B 110 beta 4461 4466 4464 4487 C1' DC B 111 beta 4483 4488 4486 4504 C1' DOC B 112 beta 4508 4496 4505 4522 C1' DA C 201 beta 4518 4523 4521 4543 C1' DA C 202 beta 4539 4544 4542 4564 C1' DA C 203 beta 4560 4565 4563 4585 C1' DA C 204 beta 4581 4586 4584 4606 C1' DG C 205 beta 4602 4607 4605 4628 C1' DG C 206 beta 4624 4629 4627 4650 C1' DC C 207 beta 4646 4651 4649 4669 C1' DG C 208 beta 4665 4670 4668 4691 C1' DC C 209 beta 4687 4692 4690 4710 C1' DC C 210 beta 4706 4711 4709 4729 C1' DG C 211 beta 4725 4730 4728 4751 C1' DT C 212 beta 4747 4752 4750 4771 C1' DG C 213 beta 4767 4772 4770 4793 C1' DG C 214 beta 4789 4794 4792 4815 C1' DT C 215 beta 4811 4816 4814 4835 C1' DC C 216 beta 4831 4836 4834 4871 C1' 0L5 A 901 beta 4872 4865 4876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4280 C2' DG B 101 4281 4278 4302 C2' DA B 102 4303 4300 4323 C2' DC B 103 4324 4321 4342 C2' DC B 104 4343 4340 4361 C2' DA B 105 4362 4359 4382 C2' DC B 106 4383 4380 4401 C2' DG B 107 4402 4399 4423 C2' DG B 108 4424 4421 4445 C2' DC B 109 4446 4443 4464 C2' DG B 110 4465 4462 4486 C2' DC B 111 4487 4484 4505 C2' DOC B 112 4504 4506 4521 C2' DA C 201 4522 4519 4542 C2' DA C 202 4543 4540 4563 C2' DA C 203 4564 4561 4584 C2' DA C 204 4585 4582 4605 C2' DG C 205 4606 4603 4627 C2' DG C 206 4628 4625 4649 C2' DC C 207 4650 4647 4668 C2' DG C 208 4669 4666 4690 C2' DC C 209 4691 4688 4709 C2' DC C 210 4710 4707 4728 C2' DG C 211 4729 4726 4750 C2' DT C 212 4751 4748 4770 C2' DG C 213 4771 4768 4792 C2' DG C 214 4793 4790 4814 C2' DT C 215 4815 4812 4834 C2' DC C 216 4835 4832 4876 C2' 0L5 A 901 4871 4874 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4278 C3' DG B 101 OK 4276 4279 4280 4300 C3' DA B 102 OK 4298 4301 4302 4321 C3' DC B 103 OK 4319 4322 4323 4340 C3' DC B 104 OK 4338 4341 4342 4359 C3' DA B 105 OK 4357 4360 4361 4380 C3' DC B 106 OK 4378 4381 4382 4399 C3' DG B 107 OK 4397 4400 4401 4421 C3' DG B 108 OK 4419 4422 4423 4443 C3' DC B 109 OK 4441 4444 4445 4462 C3' DG B 110 OK 4460 4463 4464 4484 C3' DC B 111 OK 4482 4485 4486 4506 C3' DOC B 112 4507 4505 4519 C3' DA C 201 OK 4517 4520 4521 4540 C3' DA C 202 OK 4538 4541 4542 4561 C3' DA C 203 OK 4559 4562 4563 4582 C3' DA C 204 OK 4580 4583 4584 4603 C3' DG C 205 OK 4601 4604 4605 4625 C3' DG C 206 OK 4623 4626 4627 4647 C3' DC C 207 OK 4645 4648 4649 4666 C3' DG C 208 OK 4664 4667 4668 4688 C3' DC C 209 OK 4686 4689 4690 4707 C3' DC C 210 OK 4705 4708 4709 4726 C3' DG C 211 OK 4724 4727 4728 4748 C3' DT C 212 OK 4746 4749 4750 4768 C3' DG C 213 OK 4766 4769 4770 4790 C3' DG C 214 OK 4788 4791 4792 4812 C3' DT C 215 OK 4810 4813 4814 4832 C3' DC C 216 OK 4830 4833 4834 4874 C3' 0L5 A 901 OK 4873 4875 4876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4276 C4' DG B 101 OK 4278 4275 4277 4298 C4' DA B 102 OK 4300 4297 4299 4319 C4' DC B 103 OK 4321 4318 4320 4338 C4' DC B 104 OK 4340 4337 4339 4357 C4' DA B 105 OK 4359 4356 4358 4378 C4' DC B 106 OK 4380 4377 4379 4397 C4' DG B 107 OK 4399 4396 4398 4419 C4' DG B 108 OK 4421 4418 4420 4441 C4' DC B 109 OK 4443 4440 4442 4460 C4' DG B 110 OK 4462 4459 4461 4482 C4' DC B 111 OK 4484 4481 4483 4507 C4' DOC B 112 OK 4506 4509 4508 4517 C4' DA C 201 OK 4519 4516 4518 4538 C4' DA C 202 OK 4540 4537 4539 4559 C4' DA C 203 OK 4561 4558 4560 4580 C4' DA C 204 OK 4582 4579 4581 4601 C4' DG C 205 OK 4603 4600 4602 4623 C4' DG C 206 OK 4625 4622 4624 4645 C4' DC C 207 OK 4647 4644 4646 4664 C4' DG C 208 OK 4666 4663 4665 4686 C4' DC C 209 OK 4688 4685 4687 4705 C4' DC C 210 OK 4707 4704 4706 4724 C4' DG C 211 OK 4726 4723 4725 4746 C4' DT C 212 OK 4748 4745 4747 4766 C4' DG C 213 OK 4768 4765 4767 4788 C4' DG C 214 OK 4790 4787 4789 4810 C4' DT C 215 OK 4812 4809 4811 4830 C4' DC C 216 OK 4832 4829 4831 4873 C4' 0L5 A 901 OK 4874 4877 4872 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4275 C5' DG B 101 4274 4276 4297 C5' DA B 102 4296 4298 4318 C5' DC B 103 4317 4319 4337 C5' DC B 104 4336 4338 4356 C5' DA B 105 4355 4357 4377 C5' DC B 106 4376 4378 4396 C5' DG B 107 4395 4397 4418 C5' DG B 108 4417 4419 4440 C5' DC B 109 4439 4441 4459 C5' DG B 110 4458 4460 4481 C5' DC B 111 4480 4482 4509 C5' DOC B 112 4510 4507 4516 C5' DA C 201 4515 4517 4537 C5' DA C 202 4536 4538 4558 C5' DA C 203 4557 4559 4579 C5' DA C 204 4578 4580 4600 C5' DG C 205 4599 4601 4622 C5' DG C 206 4621 4623 4644 C5' DC C 207 4643 4645 4663 C5' DG C 208 4662 4664 4685 C5' DC C 209 4684 4686 4704 C5' DC C 210 4703 4705 4723 C5' DG C 211 4722 4724 4745 C5' DT C 212 4744 4746 4765 C5' DG C 213 4764 4766 4787 C5' DG C 214 4786 4788 4809 C5' DT C 215 4808 4810 4829 C5' DC C 216 4828 4830 4877 C5' 0L5 A 901 4878 4873 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4293 P DA B 102 distorted distorted 4279 4294 4295 4296 4314 P DC B 103 distorted distorted 4301 4315 4316 4317 4333 P DC B 104 distorted distorted 4322 4334 4335 4336 4352 P DA B 105 distorted distorted 4341 4353 4354 4355 4373 P DC B 106 distorted distorted 4360 4374 4375 4376 4392 P DG B 107 distorted distorted 4381 4393 4394 4395 4414 P DG B 108 distorted distorted 4400 4415 4416 4417 4436 P DC B 109 distorted distorted 4422 4437 4438 4439 4455 P DG B 110 distorted distorted 4444 4456 4457 4458 4477 P DC B 111 distorted distorted 4463 4478 4479 4480 4511 P DOC B 112 distorted distorted 4485 4512 4513 4510 4533 P DA C 202 distorted distorted 4520 4534 4535 4536 4554 P DA C 203 distorted distorted 4541 4555 4556 4557 4575 P DA C 204 distorted distorted 4562 4576 4577 4578 4596 P DG C 205 distorted distorted 4583 4597 4598 4599 4618 P DG C 206 distorted distorted 4604 4619 4620 4621 4640 P DC C 207 distorted distorted 4626 4641 4642 4643 4659 P DG C 208 distorted distorted 4648 4660 4661 4662 4681 P DC C 209 distorted distorted 4667 4682 4683 4684 4700 P DC C 210 distorted distorted 4689 4701 4702 4703 4719 P DG C 211 distorted distorted 4708 4720 4721 4722 4741 P DT C 212 distorted distorted 4727 4742 4743 4744 4761 P DG C 213 distorted distorted 4749 4762 4763 4764 4783 P DG C 214 distorted distorted 4769 4784 4785 4786 4805 P DT C 215 distorted distorted 4791 4806 4807 4808 4825 P DC C 216 distorted distorted 4813 4826 4827 4828 ---------------------------------------------------------------------------------