ID code: '4DFP' 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' --------------------------------------------------------------------------------- 4300 C1' DG B 101 beta 4296 4301 4299 4322 C1' DA B 102 beta 4318 4323 4321 4343 C1' DC B 103 beta 4339 4344 4342 4362 C1' DC B 104 beta 4358 4363 4361 4381 C1' DA B 105 beta 4377 4382 4380 4402 C1' DC B 106 beta 4398 4403 4401 4421 C1' DG B 107 beta 4417 4422 4420 4443 C1' DG B 108 beta 4439 4444 4442 4465 C1' DC B 109 beta 4461 4466 4464 4484 C1' DG B 110 beta 4480 4485 4483 4506 C1' DC B 111 beta 4502 4507 4505 4523 C1' DOC B 112 beta 4527 4515 4524 4541 C1' DA C 201 beta 4537 4542 4540 4562 C1' DA C 202 beta 4558 4563 4561 4583 C1' DA C 203 beta 4579 4584 4582 4604 C1' DC C 204 beta 4600 4605 4603 4623 C1' DG C 205 beta 4619 4624 4622 4645 C1' DG C 206 beta 4641 4646 4644 4667 C1' DC C 207 beta 4663 4668 4666 4686 C1' DG C 208 beta 4682 4687 4685 4708 C1' DC C 209 beta 4704 4709 4707 4727 C1' DC C 210 beta 4723 4728 4726 4746 C1' DG C 211 beta 4742 4747 4745 4768 C1' DT C 212 beta 4764 4769 4767 4788 C1' DG C 213 beta 4784 4789 4787 4810 C1' DG C 214 beta 4806 4811 4809 4832 C1' DT C 215 beta 4828 4833 4831 4852 C1' DC C 216 beta 4848 4853 4851 4898 C1' 0L7 A 908 beta 4902 4897 4899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4299 C2' DG B 101 4300 4297 4321 C2' DA B 102 4322 4319 4342 C2' DC B 103 4343 4340 4361 C2' DC B 104 4362 4359 4380 C2' DA B 105 4381 4378 4401 C2' DC B 106 4402 4399 4420 C2' DG B 107 4421 4418 4442 C2' DG B 108 4443 4440 4464 C2' DC B 109 4465 4462 4483 C2' DG B 110 4484 4481 4505 C2' DC B 111 4506 4503 4524 C2' DOC B 112 4523 4525 4540 C2' DA C 201 4541 4538 4561 C2' DA C 202 4562 4559 4582 C2' DA C 203 4583 4580 4603 C2' DC C 204 4604 4601 4622 C2' DG C 205 4623 4620 4644 C2' DG C 206 4645 4642 4666 C2' DC C 207 4667 4664 4685 C2' DG C 208 4686 4683 4707 C2' DC C 209 4708 4705 4726 C2' DC C 210 4727 4724 4745 C2' DG C 211 4746 4743 4767 C2' DT C 212 4768 4765 4787 C2' DG C 213 4788 4785 4809 C2' DG C 214 4810 4807 4831 C2' DT C 215 4832 4829 4851 C2' DC C 216 4852 4849 4899 C2' 0L7 A 908 4898 4900 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4297 C3' DG B 101 OK 4295 4298 4299 4319 C3' DA B 102 OK 4317 4320 4321 4340 C3' DC B 103 OK 4338 4341 4342 4359 C3' DC B 104 OK 4357 4360 4361 4378 C3' DA B 105 OK 4376 4379 4380 4399 C3' DC B 106 OK 4397 4400 4401 4418 C3' DG B 107 OK 4416 4419 4420 4440 C3' DG B 108 OK 4438 4441 4442 4462 C3' DC B 109 OK 4460 4463 4464 4481 C3' DG B 110 OK 4479 4482 4483 4503 C3' DC B 111 OK 4501 4504 4505 4525 C3' DOC B 112 4526 4524 4538 C3' DA C 201 OK 4536 4539 4540 4559 C3' DA C 202 OK 4557 4560 4561 4580 C3' DA C 203 OK 4578 4581 4582 4601 C3' DC C 204 OK 4599 4602 4603 4620 C3' DG C 205 OK 4618 4621 4622 4642 C3' DG C 206 OK 4640 4643 4644 4664 C3' DC C 207 OK 4662 4665 4666 4683 C3' DG C 208 OK 4681 4684 4685 4705 C3' DC C 209 OK 4703 4706 4707 4724 C3' DC C 210 OK 4722 4725 4726 4743 C3' DG C 211 OK 4741 4744 4745 4765 C3' DT C 212 OK 4763 4766 4767 4785 C3' DG C 213 OK 4783 4786 4787 4807 C3' DG C 214 OK 4805 4808 4809 4829 C3' DT C 215 OK 4827 4830 4831 4849 C3' DC C 216 OK 4847 4850 4851 4900 C3' 0L7 A 908 OK 4903 4901 4899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4295 C4' DG B 101 OK 4297 4294 4296 4317 C4' DA B 102 OK 4319 4316 4318 4338 C4' DC B 103 OK 4340 4337 4339 4357 C4' DC B 104 OK 4359 4356 4358 4376 C4' DA B 105 OK 4378 4375 4377 4397 C4' DC B 106 OK 4399 4396 4398 4416 C4' DG B 107 OK 4418 4415 4417 4438 C4' DG B 108 OK 4440 4437 4439 4460 C4' DC B 109 OK 4462 4459 4461 4479 C4' DG B 110 OK 4481 4478 4480 4501 C4' DC B 111 OK 4503 4500 4502 4526 C4' DOC B 112 OK 4525 4528 4527 4536 C4' DA C 201 OK 4538 4535 4537 4557 C4' DA C 202 OK 4559 4556 4558 4578 C4' DA C 203 OK 4580 4577 4579 4599 C4' DC C 204 OK 4601 4598 4600 4618 C4' DG C 205 OK 4620 4617 4619 4640 C4' DG C 206 OK 4642 4639 4641 4662 C4' DC C 207 OK 4664 4661 4663 4681 C4' DG C 208 OK 4683 4680 4682 4703 C4' DC C 209 OK 4705 4702 4704 4722 C4' DC C 210 OK 4724 4721 4723 4741 C4' DG C 211 OK 4743 4740 4742 4763 C4' DT C 212 OK 4765 4762 4764 4783 C4' DG C 213 OK 4785 4782 4784 4805 C4' DG C 214 OK 4807 4804 4806 4827 C4' DT C 215 OK 4829 4826 4828 4847 C4' DC C 216 OK 4849 4846 4848 4903 C4' 0L7 A 908 OK 4900 4904 4902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4294 C5' DG B 101 4293 4295 4316 C5' DA B 102 4315 4317 4337 C5' DC B 103 4336 4338 4356 C5' DC B 104 4355 4357 4375 C5' DA B 105 4374 4376 4396 C5' DC B 106 4395 4397 4415 C5' DG B 107 4414 4416 4437 C5' DG B 108 4436 4438 4459 C5' DC B 109 4458 4460 4478 C5' DG B 110 4477 4479 4500 C5' DC B 111 4499 4501 4528 C5' DOC B 112 4529 4526 4535 C5' DA C 201 4534 4536 4556 C5' DA C 202 4555 4557 4577 C5' DA C 203 4576 4578 4598 C5' DC C 204 4597 4599 4617 C5' DG C 205 4616 4618 4639 C5' DG C 206 4638 4640 4661 C5' DC C 207 4660 4662 4680 C5' DG C 208 4679 4681 4702 C5' DC C 209 4701 4703 4721 C5' DC C 210 4720 4722 4740 C5' DG C 211 4739 4741 4762 C5' DT C 212 4761 4763 4782 C5' DG C 213 4781 4783 4804 C5' DG C 214 4803 4805 4826 C5' DT C 215 4825 4827 4846 C5' DC C 216 4845 4847 4904 C5' 0L7 A 908 4905 4903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4312 P DA B 102 distorted distorted 4298 4313 4314 4315 4333 P DC B 103 distorted distorted 4320 4334 4335 4336 4352 P DC B 104 distorted distorted 4341 4353 4354 4355 4371 P DA B 105 distorted distorted 4360 4372 4373 4374 4392 P DC B 106 distorted distorted 4379 4393 4394 4395 4411 P DG B 107 distorted distorted 4400 4412 4413 4414 4433 P DG B 108 distorted distorted 4419 4434 4435 4436 4455 P DC B 109 distorted distorted 4441 4456 4457 4458 4474 P DG B 110 distorted distorted 4463 4475 4476 4477 4496 P DC B 111 distorted distorted 4482 4497 4498 4499 4530 P DOC B 112 distorted distorted 4504 4531 4532 4529 4552 P DA C 202 distorted distorted 4539 4553 4554 4555 4573 P DA C 203 distorted distorted 4560 4574 4575 4576 4594 P DC C 204 distorted distorted 4581 4595 4596 4597 4613 P DG C 205 distorted distorted 4602 4614 4615 4616 4635 P DG C 206 distorted distorted 4621 4636 4637 4638 4657 P DC C 207 distorted distorted 4643 4658 4659 4660 4676 P DG C 208 distorted distorted 4665 4677 4678 4679 4698 P DC C 209 distorted distorted 4684 4699 4700 4701 4717 P DC C 210 distorted distorted 4706 4718 4719 4720 4736 P DG C 211 distorted distorted 4725 4737 4738 4739 4758 P DT C 212 distorted distorted 4744 4759 4760 4761 4778 P DG C 213 distorted distorted 4766 4779 4780 4781 4800 P DG C 214 distorted distorted 4786 4801 4802 4803 4822 P DT C 215 distorted distorted 4808 4823 4824 4825 4842 P DC C 216 distorted distorted 4830 4843 4844 4845 ---------------------------------------------------------------------------------