ID code: '3PO4' 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' --------------------------------------------------------------------------------- 4322 C1' DG B 101 beta 4318 4323 4321 4344 C1' DA B 102 beta 4340 4345 4343 4365 C1' DC B 103 beta 4361 4366 4364 4384 C1' DC B 104 beta 4380 4385 4383 4403 C1' DA B 105 beta 4399 4404 4402 4424 C1' DC B 106 beta 4420 4425 4423 4443 C1' DG B 107 beta 4439 4444 4442 4465 C1' DG B 108 beta 4461 4466 4464 4487 C1' DC B 109 beta 4483 4488 4486 4506 C1' DG B 110 beta 4502 4507 4505 4528 C1' DC B 111 beta 4524 4529 4527 4546 C1' 2DA B 112 beta 4543 4547 4545 4565 C1' DT C 205 beta 4561 4566 4564 4585 C1' DG C 206 beta 4581 4586 4584 4607 C1' DC C 207 beta 4603 4608 4606 4626 C1' DG C 208 beta 4622 4627 4625 4648 C1' DC C 209 beta 4644 4649 4647 4667 C1' DC C 210 beta 4663 4668 4666 4686 C1' DG C 211 beta 4682 4687 4685 4708 C1' DT C 212 beta 4704 4709 4707 4728 C1' DG C 213 beta 4724 4729 4727 4750 C1' DG C 214 beta 4746 4751 4749 4772 C1' DT C 215 beta 4768 4773 4771 4792 C1' DC C 216 beta 4788 4793 4791 4823 C1' DDS A 835 beta 4836 4819 4827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4321 C2' DG B 101 4322 4319 4343 C2' DA B 102 4344 4341 4364 C2' DC B 103 4365 4362 4383 C2' DC B 104 4384 4381 4402 C2' DA B 105 4403 4400 4423 C2' DC B 106 4424 4421 4442 C2' DG B 107 4443 4440 4464 C2' DG B 108 4465 4462 4486 C2' DC B 109 4487 4484 4505 C2' DG B 110 4506 4503 4527 C2' DC B 111 4528 4525 4545 C2' 2DA B 112 4546 4544 4564 C2' DT C 205 4565 4562 4584 C2' DG C 206 4585 4582 4606 C2' DC C 207 4607 4604 4625 C2' DG C 208 4626 4623 4647 C2' DC C 209 4648 4645 4666 C2' DC C 210 4667 4664 4685 C2' DG C 211 4686 4683 4707 C2' DT C 212 4708 4705 4727 C2' DG C 213 4728 4725 4749 C2' DG C 214 4750 4747 4771 C2' DT C 215 4772 4769 4791 C2' DC C 216 4792 4789 4827 C2' DDS A 835 4823 4831 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4319 C3' DG B 101 OK 4317 4320 4321 4341 C3' DA B 102 OK 4339 4342 4343 4362 C3' DC B 103 OK 4360 4363 4364 4381 C3' DC B 104 OK 4379 4382 4383 4400 C3' DA B 105 OK 4398 4401 4402 4421 C3' DC B 106 OK 4419 4422 4423 4440 C3' DG B 107 OK 4438 4441 4442 4462 C3' DG B 108 OK 4460 4463 4464 4484 C3' DC B 109 OK 4482 4485 4486 4503 C3' DG B 110 OK 4501 4504 4505 4525 C3' DC B 111 OK 4523 4526 4527 4544 C3' 2DA B 112 4542 4545 4562 C3' DT C 205 OK 4560 4563 4564 4582 C3' DG C 206 OK 4580 4583 4584 4604 C3' DC C 207 OK 4602 4605 4606 4623 C3' DG C 208 OK 4621 4624 4625 4645 C3' DC C 209 OK 4643 4646 4647 4664 C3' DC C 210 OK 4662 4665 4666 4683 C3' DG C 211 OK 4681 4684 4685 4705 C3' DT C 212 OK 4703 4706 4707 4725 C3' DG C 213 OK 4723 4726 4727 4747 C3' DG C 214 OK 4745 4748 4749 4769 C3' DT C 215 OK 4767 4770 4771 4789 C3' DC C 216 OK 4787 4790 4791 4831 C3' DDS A 835 4835 4827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4317 C4' DG B 101 OK 4319 4316 4318 4339 C4' DA B 102 OK 4341 4338 4340 4360 C4' DC B 103 OK 4362 4359 4361 4379 C4' DC B 104 OK 4381 4378 4380 4398 C4' DA B 105 OK 4400 4397 4399 4419 C4' DC B 106 OK 4421 4418 4420 4438 C4' DG B 107 OK 4440 4437 4439 4460 C4' DG B 108 OK 4462 4459 4461 4482 C4' DC B 109 OK 4484 4481 4483 4501 C4' DG B 110 OK 4503 4500 4502 4523 C4' DC B 111 OK 4525 4522 4524 4542 C4' 2DA B 112 OK 4544 4541 4543 4560 C4' DT C 205 OK 4562 4559 4561 4580 C4' DG C 206 OK 4582 4579 4581 4602 C4' DC C 207 OK 4604 4601 4603 4621 C4' DG C 208 OK 4623 4620 4622 4643 C4' DC C 209 OK 4645 4642 4644 4662 C4' DC C 210 OK 4664 4661 4663 4681 C4' DG C 211 OK 4683 4680 4682 4703 C4' DT C 212 OK 4705 4702 4704 4723 C4' DG C 213 OK 4725 4722 4724 4745 C4' DG C 214 OK 4747 4744 4746 4767 C4' DT C 215 OK 4769 4766 4768 4787 C4' DC C 216 OK 4789 4786 4788 4835 C4' DDS A 835 OK 4831 4837 4836 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4316 C5' DG B 101 4315 4317 4338 C5' DA B 102 4337 4339 4359 C5' DC B 103 4358 4360 4378 C5' DC B 104 4377 4379 4397 C5' DA B 105 4396 4398 4418 C5' DC B 106 4417 4419 4437 C5' DG B 107 4436 4438 4459 C5' DG B 108 4458 4460 4481 C5' DC B 109 4480 4482 4500 C5' DG B 110 4499 4501 4522 C5' DC B 111 4521 4523 4541 C5' 2DA B 112 4540 4542 4559 C5' DT C 205 4558 4560 4579 C5' DG C 206 4578 4580 4601 C5' DC C 207 4600 4602 4620 C5' DG C 208 4619 4621 4642 C5' DC C 209 4641 4643 4661 C5' DC C 210 4660 4662 4680 C5' DG C 211 4679 4681 4702 C5' DT C 212 4701 4703 4722 C5' DG C 213 4721 4723 4744 C5' DG C 214 4743 4745 4766 C5' DT C 215 4765 4767 4786 C5' DC C 216 4785 4787 4837 C5' DDS A 835 4838 4835 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4334 P DA B 102 distorted distorted 4320 4335 4336 4337 4355 P DC B 103 distorted distorted 4342 4356 4357 4358 4374 P DC B 104 distorted distorted 4363 4375 4376 4377 4393 P DA B 105 distorted distorted 4382 4394 4395 4396 4414 P DC B 106 distorted distorted 4401 4415 4416 4417 4433 P DG B 107 distorted distorted 4422 4434 4435 4436 4455 P DG B 108 distorted distorted 4441 4456 4457 4458 4477 P DC B 109 distorted distorted 4463 4478 4479 4480 4496 P DG B 110 distorted distorted 4485 4497 4498 4499 4518 P DC B 111 distorted distorted 4504 4519 4520 4521 4537 P 2DA B 112 OK OK 4526 4538 4539 4540 4575 P DG C 206 distorted distorted 4563 4576 4577 4578 4597 P DC C 207 distorted distorted 4583 4598 4599 4600 4616 P DG C 208 distorted distorted 4605 4617 4618 4619 4638 P DC C 209 distorted distorted 4624 4639 4640 4641 4657 P DC C 210 distorted distorted 4646 4658 4659 4660 4676 P DG C 211 distorted distorted 4665 4677 4678 4679 4698 P DT C 212 distorted distorted 4684 4699 4700 4701 4718 P DG C 213 distorted distorted 4706 4719 4720 4721 4740 P DG C 214 distorted distorted 4726 4741 4742 4743 4762 P DT C 215 distorted distorted 4748 4763 4764 4765 4782 P DC C 216 distorted distorted 4770 4783 4784 4785 ---------------------------------------------------------------------------------