ID code: '3LWL' 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' --------------------------------------------------------------------------------- 4245 C1' DG B 101 beta 4241 4246 4244 4267 C1' DA B 102 beta 4263 4268 4266 4288 C1' DC B 103 beta 4284 4289 4287 4307 C1' DC B 104 beta 4303 4308 4306 4326 C1' DA B 105 beta 4322 4327 4325 4347 C1' DC B 106 beta 4343 4348 4346 4366 C1' DG B 107 beta 4362 4367 4365 4388 C1' DG B 108 beta 4384 4389 4387 4410 C1' DC B 109 beta 4406 4411 4409 4429 C1' DG B 110 beta 4425 4430 4428 4451 C1' DC B 111 beta 4447 4452 4450 4469 C1' 2DA B 112 beta 4466 4470 4468 4491 C1' DA C 203 beta 4487 4492 4490 4510 C1' 3DR C 204 4509 4506 4523 C1' DT C 205 beta 4519 4524 4522 4543 C1' DG C 206 beta 4539 4544 4542 4565 C1' DC C 207 beta 4561 4566 4564 4584 C1' DG C 208 beta 4580 4585 4583 4606 C1' DC C 209 beta 4602 4607 4605 4625 C1' DC C 210 beta 4621 4626 4624 4644 C1' DG C 211 beta 4640 4645 4643 4666 C1' DT C 212 beta 4662 4667 4665 4686 C1' DG C 213 beta 4682 4687 4685 4708 C1' DG C 214 beta 4704 4709 4707 4730 C1' DT C 215 beta 4726 4731 4729 4750 C1' DC C 216 beta 4746 4751 4749 4773 C1' DDS A 1 beta 4786 4769 4777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4244 C2' DG B 101 4245 4242 4266 C2' DA B 102 4267 4264 4287 C2' DC B 103 4288 4285 4306 C2' DC B 104 4307 4304 4325 C2' DA B 105 4326 4323 4346 C2' DC B 106 4347 4344 4365 C2' DG B 107 4366 4363 4387 C2' DG B 108 4388 4385 4409 C2' DC B 109 4410 4407 4428 C2' DG B 110 4429 4426 4450 C2' DC B 111 4451 4448 4468 C2' 2DA B 112 4469 4467 4490 C2' DA C 203 4491 4488 4506 C2' 3DR C 204 4510 4511 4522 C2' DT C 205 4523 4520 4542 C2' DG C 206 4543 4540 4564 C2' DC C 207 4565 4562 4583 C2' DG C 208 4584 4581 4605 C2' DC C 209 4606 4603 4624 C2' DC C 210 4625 4622 4643 C2' DG C 211 4644 4641 4665 C2' DT C 212 4666 4663 4685 C2' DG C 213 4686 4683 4707 C2' DG C 214 4708 4705 4729 C2' DT C 215 4730 4727 4749 C2' DC C 216 4750 4747 4777 C2' DDS A 1 4773 4781 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4242 C3' DG B 101 OK 4240 4243 4244 4264 C3' DA B 102 OK 4262 4265 4266 4285 C3' DC B 103 OK 4283 4286 4287 4304 C3' DC B 104 OK 4302 4305 4306 4323 C3' DA B 105 OK 4321 4324 4325 4344 C3' DC B 106 OK 4342 4345 4346 4363 C3' DG B 107 OK 4361 4364 4365 4385 C3' DG B 108 OK 4383 4386 4387 4407 C3' DC B 109 OK 4405 4408 4409 4426 C3' DG B 110 OK 4424 4427 4428 4448 C3' DC B 111 OK 4446 4449 4450 4467 C3' 2DA B 112 4465 4468 4488 C3' DA C 203 OK 4486 4489 4490 4511 C3' 3DR C 204 OK 4508 4512 4506 4520 C3' DT C 205 OK 4518 4521 4522 4540 C3' DG C 206 OK 4538 4541 4542 4562 C3' DC C 207 OK 4560 4563 4564 4581 C3' DG C 208 OK 4579 4582 4583 4603 C3' DC C 209 OK 4601 4604 4605 4622 C3' DC C 210 OK 4620 4623 4624 4641 C3' DG C 211 OK 4639 4642 4643 4663 C3' DT C 212 OK 4661 4664 4665 4683 C3' DG C 213 OK 4681 4684 4685 4705 C3' DG C 214 OK 4703 4706 4707 4727 C3' DT C 215 OK 4725 4728 4729 4747 C3' DC C 216 OK 4745 4748 4749 4781 C3' DDS A 1 4785 4777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4240 C4' DG B 101 OK 4242 4239 4241 4262 C4' DA B 102 OK 4264 4261 4263 4283 C4' DC B 103 OK 4285 4282 4284 4302 C4' DC B 104 OK 4304 4301 4303 4321 C4' DA B 105 OK 4323 4320 4322 4342 C4' DC B 106 OK 4344 4341 4343 4361 C4' DG B 107 OK 4363 4360 4362 4383 C4' DG B 108 OK 4385 4382 4384 4405 C4' DC B 109 OK 4407 4404 4406 4424 C4' DG B 110 OK 4426 4423 4425 4446 C4' DC B 111 OK 4448 4445 4447 4465 C4' 2DA B 112 OK 4467 4464 4466 4486 C4' DA C 203 OK 4488 4485 4487 4508 C4' 3DR C 204 OK 4511 4507 4509 4518 C4' DT C 205 OK 4520 4517 4519 4538 C4' DG C 206 OK 4540 4537 4539 4560 C4' DC C 207 OK 4562 4559 4561 4579 C4' DG C 208 OK 4581 4578 4580 4601 C4' DC C 209 OK 4603 4600 4602 4620 C4' DC C 210 OK 4622 4619 4621 4639 C4' DG C 211 OK 4641 4638 4640 4661 C4' DT C 212 OK 4663 4660 4662 4681 C4' DG C 213 OK 4683 4680 4682 4703 C4' DG C 214 OK 4705 4702 4704 4725 C4' DT C 215 OK 4727 4724 4726 4745 C4' DC C 216 OK 4747 4744 4746 4785 C4' DDS A 1 OK 4781 4787 4786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4239 C5' DG B 101 4238 4240 4261 C5' DA B 102 4260 4262 4282 C5' DC B 103 4281 4283 4301 C5' DC B 104 4300 4302 4320 C5' DA B 105 4319 4321 4341 C5' DC B 106 4340 4342 4360 C5' DG B 107 4359 4361 4382 C5' DG B 108 4381 4383 4404 C5' DC B 109 4403 4405 4423 C5' DG B 110 4422 4424 4445 C5' DC B 111 4444 4446 4464 C5' 2DA B 112 4463 4465 4485 C5' DA C 203 4484 4486 4507 C5' 3DR C 204 4502 4508 4517 C5' DT C 205 4516 4518 4537 C5' DG C 206 4536 4538 4559 C5' DC C 207 4558 4560 4578 C5' DG C 208 4577 4579 4600 C5' DC C 209 4599 4601 4619 C5' DC C 210 4618 4620 4638 C5' DG C 211 4637 4639 4660 C5' DT C 212 4659 4661 4680 C5' DG C 213 4679 4681 4702 C5' DG C 214 4701 4703 4724 C5' DT C 215 4723 4725 4744 C5' DC C 216 4743 4745 4787 C5' DDS A 1 4788 4785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4257 P DA B 102 distorted distorted 4243 4258 4259 4260 4278 P DC B 103 distorted distorted 4265 4279 4280 4281 4297 P DC B 104 distorted distorted 4286 4298 4299 4300 4316 P DA B 105 distorted distorted 4305 4317 4318 4319 4337 P DC B 106 distorted distorted 4324 4338 4339 4340 4356 P DG B 107 distorted distorted 4345 4357 4358 4359 4378 P DG B 108 distorted distorted 4364 4379 4380 4381 4400 P DC B 109 distorted distorted 4386 4401 4402 4403 4419 P DG B 110 distorted distorted 4408 4420 4421 4422 4441 P DC B 111 distorted distorted 4427 4442 4443 4444 4460 P 2DA B 112 distorted distorted 4449 4461 4462 4463 4481 P DA C 203 OK OK 4482 4483 4484 4503 P 3DR C 204 OK OK 4489 4504 4505 4502 4513 P DT C 205 distorted distorted 4512 4514 4515 4516 4533 P DG C 206 distorted distorted 4521 4534 4535 4536 4555 P DC C 207 distorted distorted 4541 4556 4557 4558 4574 P DG C 208 distorted distorted 4563 4575 4576 4577 4596 P DC C 209 distorted distorted 4582 4597 4598 4599 4615 P DC C 210 distorted distorted 4604 4616 4617 4618 4634 P DG C 211 distorted distorted 4623 4635 4636 4637 4656 P DT C 212 distorted distorted 4642 4657 4658 4659 4676 P DG C 213 distorted distorted 4664 4677 4678 4679 4698 P DG C 214 distorted distorted 4684 4699 4700 4701 4720 P DT C 215 distorted distorted 4706 4721 4722 4723 4740 P DC C 216 distorted distorted 4728 4741 4742 4743 ---------------------------------------------------------------------------------