ID code: '3PY8' 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' --------------------------------------------------------------------------------- 4296 C1' DG B 101 beta 4292 4297 4295 4318 C1' DA B 102 beta 4314 4319 4317 4339 C1' DC B 103 beta 4335 4340 4338 4358 C1' DC B 104 beta 4354 4359 4357 4377 C1' DA B 105 beta 4373 4378 4376 4398 C1' DC B 106 beta 4394 4399 4397 4417 C1' DG B 107 beta 4413 4418 4416 4439 C1' DG B 108 beta 4435 4440 4438 4461 C1' DC B 109 beta 4457 4462 4460 4480 C1' DG B 110 beta 4476 4481 4479 4502 C1' DC B 111 beta 4498 4503 4501 4519 C1' DOC B 112 beta 4523 4511 4520 4537 C1' DA C 203 beta 4533 4538 4536 4558 C1' DG C 204 beta 4554 4559 4557 4580 C1' DG C 205 beta 4576 4581 4579 4602 C1' DG C 206 beta 4598 4603 4601 4624 C1' DC C 207 beta 4620 4625 4623 4643 C1' DG C 208 beta 4639 4644 4642 4665 C1' DC C 209 beta 4661 4666 4664 4684 C1' DC C 210 beta 4680 4685 4683 4703 C1' DG C 211 beta 4699 4704 4702 4725 C1' DT C 212 beta 4721 4726 4724 4745 C1' DG C 213 beta 4741 4746 4744 4767 C1' DG C 214 beta 4763 4768 4766 4789 C1' DT C 215 beta 4785 4790 4788 4809 C1' DC C 216 beta 4805 4810 4808 4827 C1' DCT A 113 beta 4831 4819 4828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4295 C2' DG B 101 4296 4293 4317 C2' DA B 102 4318 4315 4338 C2' DC B 103 4339 4336 4357 C2' DC B 104 4358 4355 4376 C2' DA B 105 4377 4374 4397 C2' DC B 106 4398 4395 4416 C2' DG B 107 4417 4414 4438 C2' DG B 108 4439 4436 4460 C2' DC B 109 4461 4458 4479 C2' DG B 110 4480 4477 4501 C2' DC B 111 4502 4499 4520 C2' DOC B 112 4519 4521 4536 C2' DA C 203 4537 4534 4557 C2' DG C 204 4558 4555 4579 C2' DG C 205 4580 4577 4601 C2' DG C 206 4602 4599 4623 C2' DC C 207 4624 4621 4642 C2' DG C 208 4643 4640 4664 C2' DC C 209 4665 4662 4683 C2' DC C 210 4684 4681 4702 C2' DG C 211 4703 4700 4724 C2' DT C 212 4725 4722 4744 C2' DG C 213 4745 4742 4766 C2' DG C 214 4767 4764 4788 C2' DT C 215 4789 4786 4808 C2' DC C 216 4809 4806 4828 C2' DCT A 113 4827 4829 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4293 C3' DG B 101 OK 4291 4294 4295 4315 C3' DA B 102 OK 4313 4316 4317 4336 C3' DC B 103 OK 4334 4337 4338 4355 C3' DC B 104 OK 4353 4356 4357 4374 C3' DA B 105 OK 4372 4375 4376 4395 C3' DC B 106 OK 4393 4396 4397 4414 C3' DG B 107 OK 4412 4415 4416 4436 C3' DG B 108 OK 4434 4437 4438 4458 C3' DC B 109 OK 4456 4459 4460 4477 C3' DG B 110 OK 4475 4478 4479 4499 C3' DC B 111 OK 4497 4500 4501 4521 C3' DOC B 112 4522 4520 4534 C3' DA C 203 OK 4532 4535 4536 4555 C3' DG C 204 OK 4553 4556 4557 4577 C3' DG C 205 OK 4575 4578 4579 4599 C3' DG C 206 OK 4597 4600 4601 4621 C3' DC C 207 OK 4619 4622 4623 4640 C3' DG C 208 OK 4638 4641 4642 4662 C3' DC C 209 OK 4660 4663 4664 4681 C3' DC C 210 OK 4679 4682 4683 4700 C3' DG C 211 OK 4698 4701 4702 4722 C3' DT C 212 OK 4720 4723 4724 4742 C3' DG C 213 OK 4740 4743 4744 4764 C3' DG C 214 OK 4762 4765 4766 4786 C3' DT C 215 OK 4784 4787 4788 4806 C3' DC C 216 OK 4804 4807 4808 4829 C3' DCT A 113 4830 4828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4291 C4' DG B 101 OK 4293 4290 4292 4313 C4' DA B 102 OK 4315 4312 4314 4334 C4' DC B 103 OK 4336 4333 4335 4353 C4' DC B 104 OK 4355 4352 4354 4372 C4' DA B 105 OK 4374 4371 4373 4393 C4' DC B 106 OK 4395 4392 4394 4412 C4' DG B 107 OK 4414 4411 4413 4434 C4' DG B 108 OK 4436 4433 4435 4456 C4' DC B 109 OK 4458 4455 4457 4475 C4' DG B 110 OK 4477 4474 4476 4497 C4' DC B 111 OK 4499 4496 4498 4522 C4' DOC B 112 OK 4521 4524 4523 4532 C4' DA C 203 OK 4534 4531 4533 4553 C4' DG C 204 OK 4555 4552 4554 4575 C4' DG C 205 OK 4577 4574 4576 4597 C4' DG C 206 OK 4599 4596 4598 4619 C4' DC C 207 OK 4621 4618 4620 4638 C4' DG C 208 OK 4640 4637 4639 4660 C4' DC C 209 OK 4662 4659 4661 4679 C4' DC C 210 OK 4681 4678 4680 4698 C4' DG C 211 OK 4700 4697 4699 4720 C4' DT C 212 OK 4722 4719 4721 4740 C4' DG C 213 OK 4742 4739 4741 4762 C4' DG C 214 OK 4764 4761 4763 4784 C4' DT C 215 OK 4786 4783 4785 4804 C4' DC C 216 OK 4806 4803 4805 4830 C4' DCT A 113 OK 4829 4832 4831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4290 C5' DG B 101 4289 4291 4312 C5' DA B 102 4311 4313 4333 C5' DC B 103 4332 4334 4352 C5' DC B 104 4351 4353 4371 C5' DA B 105 4370 4372 4392 C5' DC B 106 4391 4393 4411 C5' DG B 107 4410 4412 4433 C5' DG B 108 4432 4434 4455 C5' DC B 109 4454 4456 4474 C5' DG B 110 4473 4475 4496 C5' DC B 111 4495 4497 4524 C5' DOC B 112 4525 4522 4531 C5' DA C 203 4530 4532 4552 C5' DG C 204 4551 4553 4574 C5' DG C 205 4573 4575 4596 C5' DG C 206 4595 4597 4618 C5' DC C 207 4617 4619 4637 C5' DG C 208 4636 4638 4659 C5' DC C 209 4658 4660 4678 C5' DC C 210 4677 4679 4697 C5' DG C 211 4696 4698 4719 C5' DT C 212 4718 4720 4739 C5' DG C 213 4738 4740 4761 C5' DG C 214 4760 4762 4783 C5' DT C 215 4782 4784 4803 C5' DC C 216 4802 4804 4832 C5' DCT A 113 4833 4830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4308 P DA B 102 distorted distorted 4294 4309 4310 4311 4329 P DC B 103 distorted distorted 4316 4330 4331 4332 4348 P DC B 104 distorted distorted 4337 4349 4350 4351 4367 P DA B 105 distorted distorted 4356 4368 4369 4370 4388 P DC B 106 distorted distorted 4375 4389 4390 4391 4407 P DG B 107 distorted distorted 4396 4408 4409 4410 4429 P DG B 108 distorted distorted 4415 4430 4431 4432 4451 P DC B 109 distorted distorted 4437 4452 4453 4454 4470 P DG B 110 distorted distorted 4459 4471 4472 4473 4492 P DC B 111 distorted distorted 4478 4493 4494 4495 4526 P DOC B 112 distorted distorted 4500 4527 4528 4525 4548 P DG C 204 distorted distorted 4535 4549 4550 4551 4570 P DG C 205 distorted distorted 4556 4571 4572 4573 4592 P DG C 206 distorted distorted 4578 4593 4594 4595 4614 P DC C 207 distorted distorted 4600 4615 4616 4617 4633 P DG C 208 distorted distorted 4622 4634 4635 4636 4655 P DC C 209 distorted distorted 4641 4656 4657 4658 4674 P DC C 210 distorted distorted 4663 4675 4676 4677 4693 P DG C 211 distorted distorted 4682 4694 4695 4696 4715 P DT C 212 distorted distorted 4701 4716 4717 4718 4735 P DG C 213 distorted distorted 4723 4736 4737 4738 4757 P DG C 214 distorted distorted 4743 4758 4759 4760 4779 P DT C 215 distorted distorted 4765 4780 4781 4782 4799 P DC C 216 distorted distorted 4787 4800 4801 4802 ---------------------------------------------------------------------------------