ID code: '1QSY' 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' --------------------------------------------------------------------------------- 4189 C1' G B 101 beta 4185 4190 4188 4211 C1' A B 102 beta 4207 4212 4210 4232 C1' C B 103 beta 4228 4233 4231 4251 C1' C B 104 beta 4247 4252 4250 4270 C1' A B 105 beta 4266 4271 4269 4291 C1' C B 106 beta 4287 4292 4290 4310 C1' G B 107 beta 4306 4311 4309 4332 C1' G B 108 beta 4328 4333 4331 4354 C1' C B 109 beta 4350 4355 4353 4373 C1' G B 110 beta 4369 4374 4372 4395 C1' C B 111 beta 4391 4396 4394 4413 C1' A2D B 112 beta 4410 4414 4412 4473 C1' T C 205 beta 4469 4474 4472 4493 C1' G C 206 beta 4489 4494 4492 4515 C1' C C 207 beta 4511 4516 4514 4534 C1' G C 208 beta 4530 4535 4533 4556 C1' C C 209 beta 4552 4557 4555 4575 C1' C C 210 beta 4571 4576 4574 4594 C1' G C 211 beta 4590 4595 4593 4616 C1' T C 212 beta 4612 4617 4615 4636 C1' G C 213 beta 4632 4637 4635 4658 C1' G C 214 beta 4654 4659 4657 4680 C1' T C 215 beta 4676 4681 4679 4700 C1' C C 216 beta 4696 4701 4699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4188 C2' G B 101 4189 4186 4210 C2' A B 102 4211 4208 4231 C2' C B 103 4232 4229 4250 C2' C B 104 4251 4248 4269 C2' A B 105 4270 4267 4290 C2' C B 106 4291 4288 4309 C2' G B 107 4310 4307 4331 C2' G B 108 4332 4329 4353 C2' C B 109 4354 4351 4372 C2' G B 110 4373 4370 4394 C2' C B 111 4395 4392 4412 C2' A2D B 112 4413 4411 4472 C2' T C 205 4473 4470 4492 C2' G C 206 4493 4490 4514 C2' C C 207 4515 4512 4533 C2' G C 208 4534 4531 4555 C2' C C 209 4556 4553 4574 C2' C C 210 4575 4572 4593 C2' G C 211 4594 4591 4615 C2' T C 212 4616 4613 4635 C2' G C 213 4636 4633 4657 C2' G C 214 4658 4655 4679 C2' T C 215 4680 4677 4699 C2' C C 216 4700 4697 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4186 C3' G B 101 OK 4184 4187 4188 4208 C3' A B 102 OK 4206 4209 4210 4229 C3' C B 103 OK 4227 4230 4231 4248 C3' C B 104 OK 4246 4249 4250 4267 C3' A B 105 OK 4265 4268 4269 4288 C3' C B 106 OK 4286 4289 4290 4307 C3' G B 107 OK 4305 4308 4309 4329 C3' G B 108 OK 4327 4330 4331 4351 C3' C B 109 OK 4349 4352 4353 4370 C3' G B 110 OK 4368 4371 4372 4392 C3' C B 111 OK 4390 4393 4394 4411 C3' A2D B 112 4409 4412 4470 C3' T C 205 OK 4468 4471 4472 4490 C3' G C 206 OK 4488 4491 4492 4512 C3' C C 207 OK 4510 4513 4514 4531 C3' G C 208 OK 4529 4532 4533 4553 C3' C C 209 OK 4551 4554 4555 4572 C3' C C 210 OK 4570 4573 4574 4591 C3' G C 211 OK 4589 4592 4593 4613 C3' T C 212 OK 4611 4614 4615 4633 C3' G C 213 OK 4631 4634 4635 4655 C3' G C 214 OK 4653 4656 4657 4677 C3' T C 215 OK 4675 4678 4679 4697 C3' C C 216 OK 4695 4698 4699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4184 C4' G B 101 OK 4186 4183 4185 4206 C4' A B 102 OK 4208 4205 4207 4227 C4' C B 103 OK 4229 4226 4228 4246 C4' C B 104 OK 4248 4245 4247 4265 C4' A B 105 OK 4267 4264 4266 4286 C4' C B 106 OK 4288 4285 4287 4305 C4' G B 107 OK 4307 4304 4306 4327 C4' G B 108 OK 4329 4326 4328 4349 C4' C B 109 OK 4351 4348 4350 4368 C4' G B 110 OK 4370 4367 4369 4390 C4' C B 111 OK 4392 4389 4391 4409 C4' A2D B 112 OK 4411 4408 4410 4468 C4' T C 205 OK 4470 4467 4469 4488 C4' G C 206 OK 4490 4487 4489 4510 C4' C C 207 OK 4512 4509 4511 4529 C4' G C 208 OK 4531 4528 4530 4551 C4' C C 209 OK 4553 4550 4552 4570 C4' C C 210 OK 4572 4569 4571 4589 C4' G C 211 OK 4591 4588 4590 4611 C4' T C 212 OK 4613 4610 4612 4631 C4' G C 213 OK 4633 4630 4632 4653 C4' G C 214 OK 4655 4652 4654 4675 C4' T C 215 OK 4677 4674 4676 4695 C4' C C 216 OK 4697 4694 4696 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4183 C5' G B 101 4182 4184 4205 C5' A B 102 4204 4206 4226 C5' C B 103 4225 4227 4245 C5' C B 104 4244 4246 4264 C5' A B 105 4263 4265 4285 C5' C B 106 4284 4286 4304 C5' G B 107 4303 4305 4326 C5' G B 108 4325 4327 4348 C5' C B 109 4347 4349 4367 C5' G B 110 4366 4368 4389 C5' C B 111 4388 4390 4408 C5' A2D B 112 4407 4409 4467 C5' T C 205 4466 4468 4487 C5' G C 206 4486 4488 4509 C5' C C 207 4508 4510 4528 C5' G C 208 4527 4529 4550 C5' C C 209 4549 4551 4569 C5' C C 210 4568 4570 4588 C5' G C 211 4587 4589 4610 C5' T C 212 4609 4611 4630 C5' G C 213 4629 4631 4652 C5' G C 214 4651 4653 4674 C5' T C 215 4673 4675 4694 C5' C C 216 4693 4695 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4201 P A B 102 distorted distorted 4187 4202 4203 4204 4222 P C B 103 distorted distorted 4209 4223 4224 4225 4241 P C B 104 distorted distorted 4230 4242 4243 4244 4260 P A B 105 distorted distorted 4249 4261 4262 4263 4281 P C B 106 distorted distorted 4268 4282 4283 4284 4300 P G B 107 distorted distorted 4289 4301 4302 4303 4322 P G B 108 distorted distorted 4308 4323 4324 4325 4344 P C B 109 distorted distorted 4330 4345 4346 4347 4363 P G B 110 distorted distorted 4352 4364 4365 4366 4385 P C B 111 distorted distorted 4371 4386 4387 4388 4404 P A2D B 112 OK OK 4393 4405 4406 4407 4483 P G C 206 distorted distorted 4471 4484 4485 4486 4505 P C C 207 distorted distorted 4491 4506 4507 4508 4524 P G C 208 distorted distorted 4513 4525 4526 4527 4546 P C C 209 distorted distorted 4532 4547 4548 4549 4565 P C C 210 distorted distorted 4554 4566 4567 4568 4584 P G C 211 distorted distorted 4573 4585 4586 4587 4606 P T C 212 distorted distorted 4592 4607 4608 4609 4626 P G C 213 distorted distorted 4614 4627 4628 4629 4648 P G C 214 distorted distorted 4634 4649 4650 4651 4670 P T C 215 distorted distorted 4656 4671 4672 4673 4690 P C C 216 distorted distorted 4678 4691 4692 4693 ---------------------------------------------------------------------------------