ID code: '3LWM' 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' --------------------------------------------------------------------------------- 4288 C1' DG B 101 beta 4284 4289 4287 4310 C1' DA B 102 beta 4306 4311 4309 4331 C1' DC B 103 beta 4327 4332 4330 4350 C1' DC B 104 beta 4346 4351 4349 4369 C1' DA B 105 beta 4365 4370 4368 4390 C1' DC B 106 beta 4386 4391 4389 4409 C1' DG B 107 beta 4405 4410 4408 4431 C1' DG B 108 beta 4427 4432 4430 4453 C1' DC B 109 beta 4449 4454 4452 4472 C1' DG B 110 beta 4468 4473 4471 4494 C1' DC B 111 beta 4490 4495 4493 4512 C1' 2DA B 112 beta 4509 4513 4511 4531 C1' DT C 205 beta 4527 4532 4530 4551 C1' DG C 206 beta 4547 4552 4550 4573 C1' DC C 207 beta 4569 4574 4572 4592 C1' DG C 208 beta 4588 4593 4591 4614 C1' DC C 209 beta 4610 4615 4613 4633 C1' DC C 210 beta 4629 4634 4632 4652 C1' DG C 211 beta 4648 4653 4651 4674 C1' DT C 212 beta 4670 4675 4673 4694 C1' DG C 213 beta 4690 4695 4693 4716 C1' DG C 214 beta 4712 4717 4715 4738 C1' DT C 215 beta 4734 4739 4737 4758 C1' DC C 216 beta 4754 4759 4757 4781 C1' DDS A 1 beta 4794 4777 4785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4287 C2' DG B 101 4288 4285 4309 C2' DA B 102 4310 4307 4330 C2' DC B 103 4331 4328 4349 C2' DC B 104 4350 4347 4368 C2' DA B 105 4369 4366 4389 C2' DC B 106 4390 4387 4408 C2' DG B 107 4409 4406 4430 C2' DG B 108 4431 4428 4452 C2' DC B 109 4453 4450 4471 C2' DG B 110 4472 4469 4493 C2' DC B 111 4494 4491 4511 C2' 2DA B 112 4512 4510 4530 C2' DT C 205 4531 4528 4550 C2' DG C 206 4551 4548 4572 C2' DC C 207 4573 4570 4591 C2' DG C 208 4592 4589 4613 C2' DC C 209 4614 4611 4632 C2' DC C 210 4633 4630 4651 C2' DG C 211 4652 4649 4673 C2' DT C 212 4674 4671 4693 C2' DG C 213 4694 4691 4715 C2' DG C 214 4716 4713 4737 C2' DT C 215 4738 4735 4757 C2' DC C 216 4758 4755 4785 C2' DDS A 1 4781 4789 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4285 C3' DG B 101 OK 4283 4286 4287 4307 C3' DA B 102 OK 4305 4308 4309 4328 C3' DC B 103 OK 4326 4329 4330 4347 C3' DC B 104 OK 4345 4348 4349 4366 C3' DA B 105 OK 4364 4367 4368 4387 C3' DC B 106 OK 4385 4388 4389 4406 C3' DG B 107 OK 4404 4407 4408 4428 C3' DG B 108 OK 4426 4429 4430 4450 C3' DC B 109 OK 4448 4451 4452 4469 C3' DG B 110 OK 4467 4470 4471 4491 C3' DC B 111 OK 4489 4492 4493 4510 C3' 2DA B 112 4508 4511 4528 C3' DT C 205 OK 4526 4529 4530 4548 C3' DG C 206 OK 4546 4549 4550 4570 C3' DC C 207 OK 4568 4571 4572 4589 C3' DG C 208 OK 4587 4590 4591 4611 C3' DC C 209 OK 4609 4612 4613 4630 C3' DC C 210 OK 4628 4631 4632 4649 C3' DG C 211 OK 4647 4650 4651 4671 C3' DT C 212 OK 4669 4672 4673 4691 C3' DG C 213 OK 4689 4692 4693 4713 C3' DG C 214 OK 4711 4714 4715 4735 C3' DT C 215 OK 4733 4736 4737 4755 C3' DC C 216 OK 4753 4756 4757 4789 C3' DDS A 1 4793 4785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4283 C4' DG B 101 OK 4285 4282 4284 4305 C4' DA B 102 OK 4307 4304 4306 4326 C4' DC B 103 OK 4328 4325 4327 4345 C4' DC B 104 OK 4347 4344 4346 4364 C4' DA B 105 OK 4366 4363 4365 4385 C4' DC B 106 OK 4387 4384 4386 4404 C4' DG B 107 OK 4406 4403 4405 4426 C4' DG B 108 OK 4428 4425 4427 4448 C4' DC B 109 OK 4450 4447 4449 4467 C4' DG B 110 OK 4469 4466 4468 4489 C4' DC B 111 OK 4491 4488 4490 4508 C4' 2DA B 112 OK 4510 4507 4509 4526 C4' DT C 205 OK 4528 4525 4527 4546 C4' DG C 206 OK 4548 4545 4547 4568 C4' DC C 207 OK 4570 4567 4569 4587 C4' DG C 208 OK 4589 4586 4588 4609 C4' DC C 209 OK 4611 4608 4610 4628 C4' DC C 210 OK 4630 4627 4629 4647 C4' DG C 211 OK 4649 4646 4648 4669 C4' DT C 212 OK 4671 4668 4670 4689 C4' DG C 213 OK 4691 4688 4690 4711 C4' DG C 214 OK 4713 4710 4712 4733 C4' DT C 215 OK 4735 4732 4734 4753 C4' DC C 216 OK 4755 4752 4754 4793 C4' DDS A 1 OK 4789 4795 4794 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4282 C5' DG B 101 4281 4283 4304 C5' DA B 102 4303 4305 4325 C5' DC B 103 4324 4326 4344 C5' DC B 104 4343 4345 4363 C5' DA B 105 4362 4364 4384 C5' DC B 106 4383 4385 4403 C5' DG B 107 4402 4404 4425 C5' DG B 108 4424 4426 4447 C5' DC B 109 4446 4448 4466 C5' DG B 110 4465 4467 4488 C5' DC B 111 4487 4489 4507 C5' 2DA B 112 4506 4508 4525 C5' DT C 205 4524 4526 4545 C5' DG C 206 4544 4546 4567 C5' DC C 207 4566 4568 4586 C5' DG C 208 4585 4587 4608 C5' DC C 209 4607 4609 4627 C5' DC C 210 4626 4628 4646 C5' DG C 211 4645 4647 4668 C5' DT C 212 4667 4669 4688 C5' DG C 213 4687 4689 4710 C5' DG C 214 4709 4711 4732 C5' DT C 215 4731 4733 4752 C5' DC C 216 4751 4753 4795 C5' DDS A 1 4796 4793 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4300 P DA B 102 distorted distorted 4286 4301 4302 4303 4321 P DC B 103 distorted distorted 4308 4322 4323 4324 4340 P DC B 104 distorted distorted 4329 4341 4342 4343 4359 P DA B 105 distorted distorted 4348 4360 4361 4362 4380 P DC B 106 distorted distorted 4367 4381 4382 4383 4399 P DG B 107 distorted distorted 4388 4400 4401 4402 4421 P DG B 108 distorted distorted 4407 4422 4423 4424 4443 P DC B 109 distorted distorted 4429 4444 4445 4446 4462 P DG B 110 distorted distorted 4451 4463 4464 4465 4484 P DC B 111 distorted distorted 4470 4485 4486 4487 4503 P 2DA B 112 OK OK 4492 4504 4505 4506 4541 P DG C 206 distorted distorted 4529 4542 4543 4544 4563 P DC C 207 distorted distorted 4549 4564 4565 4566 4582 P DG C 208 distorted distorted 4571 4583 4584 4585 4604 P DC C 209 distorted distorted 4590 4605 4606 4607 4623 P DC C 210 distorted distorted 4612 4624 4625 4626 4642 P DG C 211 distorted distorted 4631 4643 4644 4645 4664 P DT C 212 distorted distorted 4650 4665 4666 4667 4684 P DG C 213 distorted distorted 4672 4685 4686 4687 4706 P DG C 214 distorted distorted 4692 4707 4708 4709 4728 P DT C 215 distorted distorted 4714 4729 4730 4731 4748 P DC C 216 distorted distorted 4736 4749 4750 4751 ---------------------------------------------------------------------------------