ID code: '3PO5' 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' --------------------------------------------------------------------------------- 4206 C1' DG B 101 beta 4202 4207 4205 4228 C1' DA B 102 beta 4224 4229 4227 4249 C1' DC B 103 beta 4245 4250 4248 4268 C1' DC B 104 beta 4264 4269 4267 4287 C1' DA B 105 beta 4283 4288 4286 4308 C1' DC B 106 beta 4304 4309 4307 4327 C1' DG B 107 beta 4323 4328 4326 4349 C1' DG B 108 beta 4345 4350 4348 4371 C1' DC B 109 beta 4367 4372 4370 4390 C1' DG B 110 beta 4386 4391 4389 4412 C1' DC B 111 beta 4408 4413 4411 4430 C1' 2DA B 112 beta 4427 4431 4429 4450 C1' 3DR C 204 4449 4446 4463 C1' DT C 205 beta 4459 4464 4462 4483 C1' DG C 206 beta 4479 4484 4482 4505 C1' DC C 207 beta 4501 4506 4504 4524 C1' DG C 208 beta 4520 4525 4523 4546 C1' DC C 209 beta 4542 4547 4545 4565 C1' DC C 210 beta 4561 4566 4564 4584 C1' DG C 211 beta 4580 4585 4583 4606 C1' DT C 212 beta 4602 4607 4605 4626 C1' DG C 213 beta 4622 4627 4625 4648 C1' DG C 214 beta 4644 4649 4647 4670 C1' DT C 215 beta 4666 4671 4669 4690 C1' DC C 216 beta 4686 4691 4689 4722 C1' DDS A 835 beta 4735 4718 4726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4205 C2' DG B 101 4206 4203 4227 C2' DA B 102 4228 4225 4248 C2' DC B 103 4249 4246 4267 C2' DC B 104 4268 4265 4286 C2' DA B 105 4287 4284 4307 C2' DC B 106 4308 4305 4326 C2' DG B 107 4327 4324 4348 C2' DG B 108 4349 4346 4370 C2' DC B 109 4371 4368 4389 C2' DG B 110 4390 4387 4411 C2' DC B 111 4412 4409 4429 C2' 2DA B 112 4430 4428 4446 C2' 3DR C 204 4450 4451 4462 C2' DT C 205 4463 4460 4482 C2' DG C 206 4483 4480 4504 C2' DC C 207 4505 4502 4523 C2' DG C 208 4524 4521 4545 C2' DC C 209 4546 4543 4564 C2' DC C 210 4565 4562 4583 C2' DG C 211 4584 4581 4605 C2' DT C 212 4606 4603 4625 C2' DG C 213 4626 4623 4647 C2' DG C 214 4648 4645 4669 C2' DT C 215 4670 4667 4689 C2' DC C 216 4690 4687 4726 C2' DDS A 835 4722 4730 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4203 C3' DG B 101 OK 4201 4204 4205 4225 C3' DA B 102 OK 4223 4226 4227 4246 C3' DC B 103 OK 4244 4247 4248 4265 C3' DC B 104 OK 4263 4266 4267 4284 C3' DA B 105 OK 4282 4285 4286 4305 C3' DC B 106 OK 4303 4306 4307 4324 C3' DG B 107 OK 4322 4325 4326 4346 C3' DG B 108 OK 4344 4347 4348 4368 C3' DC B 109 OK 4366 4369 4370 4387 C3' DG B 110 OK 4385 4388 4389 4409 C3' DC B 111 OK 4407 4410 4411 4428 C3' 2DA B 112 4426 4429 4451 C3' 3DR C 204 OK 4448 4452 4446 4460 C3' DT C 205 OK 4458 4461 4462 4480 C3' DG C 206 OK 4478 4481 4482 4502 C3' DC C 207 OK 4500 4503 4504 4521 C3' DG C 208 OK 4519 4522 4523 4543 C3' DC C 209 OK 4541 4544 4545 4562 C3' DC C 210 OK 4560 4563 4564 4581 C3' DG C 211 OK 4579 4582 4583 4603 C3' DT C 212 OK 4601 4604 4605 4623 C3' DG C 213 OK 4621 4624 4625 4645 C3' DG C 214 OK 4643 4646 4647 4667 C3' DT C 215 OK 4665 4668 4669 4687 C3' DC C 216 OK 4685 4688 4689 4730 C3' DDS A 835 4734 4726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4201 C4' DG B 101 OK 4203 4200 4202 4223 C4' DA B 102 OK 4225 4222 4224 4244 C4' DC B 103 OK 4246 4243 4245 4263 C4' DC B 104 OK 4265 4262 4264 4282 C4' DA B 105 OK 4284 4281 4283 4303 C4' DC B 106 OK 4305 4302 4304 4322 C4' DG B 107 OK 4324 4321 4323 4344 C4' DG B 108 OK 4346 4343 4345 4366 C4' DC B 109 OK 4368 4365 4367 4385 C4' DG B 110 OK 4387 4384 4386 4407 C4' DC B 111 OK 4409 4406 4408 4426 C4' 2DA B 112 OK 4428 4425 4427 4448 C4' 3DR C 204 OK 4451 4447 4449 4458 C4' DT C 205 OK 4460 4457 4459 4478 C4' DG C 206 OK 4480 4477 4479 4500 C4' DC C 207 OK 4502 4499 4501 4519 C4' DG C 208 OK 4521 4518 4520 4541 C4' DC C 209 OK 4543 4540 4542 4560 C4' DC C 210 OK 4562 4559 4561 4579 C4' DG C 211 OK 4581 4578 4580 4601 C4' DT C 212 OK 4603 4600 4602 4621 C4' DG C 213 OK 4623 4620 4622 4643 C4' DG C 214 OK 4645 4642 4644 4665 C4' DT C 215 OK 4667 4664 4666 4685 C4' DC C 216 OK 4687 4684 4686 4734 C4' DDS A 835 OK 4730 4736 4735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4200 C5' DG B 101 4199 4201 4222 C5' DA B 102 4221 4223 4243 C5' DC B 103 4242 4244 4262 C5' DC B 104 4261 4263 4281 C5' DA B 105 4280 4282 4302 C5' DC B 106 4301 4303 4321 C5' DG B 107 4320 4322 4343 C5' DG B 108 4342 4344 4365 C5' DC B 109 4364 4366 4384 C5' DG B 110 4383 4385 4406 C5' DC B 111 4405 4407 4425 C5' 2DA B 112 4424 4426 4447 C5' 3DR C 204 4442 4448 4457 C5' DT C 205 4456 4458 4477 C5' DG C 206 4476 4478 4499 C5' DC C 207 4498 4500 4518 C5' DG C 208 4517 4519 4540 C5' DC C 209 4539 4541 4559 C5' DC C 210 4558 4560 4578 C5' DG C 211 4577 4579 4600 C5' DT C 212 4599 4601 4620 C5' DG C 213 4619 4621 4642 C5' DG C 214 4641 4643 4664 C5' DT C 215 4663 4665 4684 C5' DC C 216 4683 4685 4736 C5' DDS A 835 4737 4734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4218 P DA B 102 distorted distorted 4204 4219 4220 4221 4239 P DC B 103 distorted distorted 4226 4240 4241 4242 4258 P DC B 104 distorted distorted 4247 4259 4260 4261 4277 P DA B 105 distorted distorted 4266 4278 4279 4280 4298 P DC B 106 distorted distorted 4285 4299 4300 4301 4317 P DG B 107 distorted distorted 4306 4318 4319 4320 4339 P DG B 108 distorted distorted 4325 4340 4341 4342 4361 P DC B 109 distorted distorted 4347 4362 4363 4364 4380 P DG B 110 distorted distorted 4369 4381 4382 4383 4402 P DC B 111 distorted distorted 4388 4403 4404 4405 4421 P 2DA B 112 distorted distorted 4410 4422 4423 4424 4443 P 3DR C 204 OK OK 4444 4445 4442 4453 P DT C 205 distorted distorted 4452 4454 4455 4456 4473 P DG C 206 distorted distorted 4461 4474 4475 4476 4495 P DC C 207 distorted distorted 4481 4496 4497 4498 4514 P DG C 208 distorted distorted 4503 4515 4516 4517 4536 P DC C 209 distorted distorted 4522 4537 4538 4539 4555 P DC C 210 distorted distorted 4544 4556 4557 4558 4574 P DG C 211 distorted distorted 4563 4575 4576 4577 4596 P DT C 212 distorted distorted 4582 4597 4598 4599 4616 P DG C 213 distorted distorted 4604 4617 4618 4619 4638 P DG C 214 distorted distorted 4624 4639 4640 4641 4660 P DT C 215 distorted distorted 4646 4661 4662 4663 4680 P DC C 216 distorted distorted 4668 4681 4682 4683 ---------------------------------------------------------------------------------