ID code: '3MFI' 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' --------------------------------------------------------------------------------- 4133 C1' DG P 1 beta 4129 4134 4132 4155 C1' DT P 2 beta 4151 4156 4154 4175 C1' DC P 3 beta 4171 4176 4174 4194 C1' DC P 4 beta 4190 4195 4193 4213 C1' DT P 5 beta 4209 4214 4212 4233 C1' DC P 6 beta 4229 4234 4232 4252 C1' DC P 7 beta 4248 4253 4251 4271 C1' DC P 8 beta 4267 4272 4270 4290 C1' DC P 9 beta 4286 4291 4289 4309 C1' DT P 10 beta 4305 4310 4308 4327 C1' DOC P 11 beta 4331 4319 4328 4348 C1' DA T 4 beta 4344 4349 4347 4369 C1' TTD T 5 beta 4365 4370 4368 4409 C1' DG T 6 beta 4405 4410 4408 4431 C1' DA T 7 beta 4427 4432 4430 4452 C1' DG T 8 beta 4448 4453 4451 4474 C1' DG T 9 beta 4470 4475 4473 4496 C1' DG T 10 beta 4492 4497 4495 4518 C1' DG T 11 beta 4514 4519 4517 4540 C1' DA T 12 beta 4536 4541 4539 4561 C1' DG T 13 beta 4557 4562 4560 4583 C1' DG T 14 beta 4579 4584 4582 4605 C1' DA T 15 beta 4601 4606 4604 4626 C1' DC T 16 beta 4622 4627 4625 4655 C1' DTP A 514 beta 4651 4656 4654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4132 C2' DG P 1 4133 4130 4154 C2' DT P 2 4155 4152 4174 C2' DC P 3 4175 4172 4193 C2' DC P 4 4194 4191 4212 C2' DT P 5 4213 4210 4232 C2' DC P 6 4233 4230 4251 C2' DC P 7 4252 4249 4270 C2' DC P 8 4271 4268 4289 C2' DC P 9 4290 4287 4308 C2' DT P 10 4309 4306 4328 C2' DOC P 11 4327 4329 4347 C2' DA T 4 4348 4345 4368 C2' TTD T 5 4369 4408 C2' DG T 6 4409 4406 4430 C2' DA T 7 4431 4428 4451 C2' DG T 8 4452 4449 4473 C2' DG T 9 4474 4471 4495 C2' DG T 10 4496 4493 4517 C2' DG T 11 4518 4515 4539 C2' DA T 12 4540 4537 4560 C2' DG T 13 4561 4558 4582 C2' DG T 14 4583 4580 4604 C2' DA T 15 4605 4602 4625 C2' DC T 16 4626 4623 4654 C2' DTP A 514 4655 4652 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4130 C3' DG P 1 OK 4128 4131 4132 4152 C3' DT P 2 OK 4150 4153 4154 4172 C3' DC P 3 OK 4170 4173 4174 4191 C3' DC P 4 OK 4189 4192 4193 4210 C3' DT P 5 OK 4208 4211 4212 4230 C3' DC P 6 OK 4228 4231 4232 4249 C3' DC P 7 OK 4247 4250 4251 4268 C3' DC P 8 OK 4266 4269 4270 4287 C3' DC P 9 OK 4285 4288 4289 4306 C3' DT P 10 OK 4304 4307 4308 4329 C3' DOC P 11 4330 4328 4345 C3' DA T 4 OK 4343 4346 4347 4397 C3' TTD T 5 4396 4398 4406 C3' DG T 6 OK 4404 4407 4408 4428 C3' DA T 7 OK 4426 4429 4430 4449 C3' DG T 8 OK 4447 4450 4451 4471 C3' DG T 9 OK 4469 4472 4473 4493 C3' DG T 10 OK 4491 4494 4495 4515 C3' DG T 11 OK 4513 4516 4517 4537 C3' DA T 12 OK 4535 4538 4539 4558 C3' DG T 13 OK 4556 4559 4560 4580 C3' DG T 14 OK 4578 4581 4582 4602 C3' DA T 15 OK 4600 4603 4604 4623 C3' DC T 16 OK 4621 4624 4625 4652 C3' DTP A 514 OK 4650 4653 4654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4128 C4' DG P 1 OK 4130 4127 4129 4150 C4' DT P 2 OK 4152 4149 4151 4170 C4' DC P 3 OK 4172 4169 4171 4189 C4' DC P 4 OK 4191 4188 4190 4208 C4' DT P 5 OK 4210 4207 4209 4228 C4' DC P 6 OK 4230 4227 4229 4247 C4' DC P 7 OK 4249 4246 4248 4266 C4' DC P 8 OK 4268 4265 4267 4285 C4' DC P 9 OK 4287 4284 4286 4304 C4' DT P 10 OK 4306 4303 4305 4330 C4' DOC P 11 OK 4329 4332 4331 4343 C4' DA T 4 OK 4345 4342 4344 4396 C4' TTD T 5 4397 4404 C4' DG T 6 OK 4406 4403 4405 4426 C4' DA T 7 OK 4428 4425 4427 4447 C4' DG T 8 OK 4449 4446 4448 4469 C4' DG T 9 OK 4471 4468 4470 4491 C4' DG T 10 OK 4493 4490 4492 4513 C4' DG T 11 OK 4515 4512 4514 4535 C4' DA T 12 OK 4537 4534 4536 4556 C4' DG T 13 OK 4558 4555 4557 4578 C4' DG T 14 OK 4580 4577 4579 4600 C4' DA T 15 OK 4602 4599 4601 4621 C4' DC T 16 OK 4623 4620 4622 4650 C4' DTP A 514 OK 4652 4649 4651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4127 C5' DG P 1 4126 4128 4149 C5' DT P 2 4148 4150 4169 C5' DC P 3 4168 4170 4188 C5' DC P 4 4187 4189 4207 C5' DT P 5 4206 4208 4227 C5' DC P 6 4226 4228 4246 C5' DC P 7 4245 4247 4265 C5' DC P 8 4264 4266 4284 C5' DC P 9 4283 4285 4303 C5' DT P 10 4302 4304 4332 C5' DOC P 11 4333 4330 4342 C5' DA T 4 4341 4343 4363 C5' TTD T 5 4362 4403 C5' DG T 6 4402 4404 4425 C5' DA T 7 4424 4426 4446 C5' DG T 8 4445 4447 4468 C5' DG T 9 4467 4469 4490 C5' DG T 10 4489 4491 4512 C5' DG T 11 4511 4513 4534 C5' DA T 12 4533 4535 4555 C5' DG T 13 4554 4556 4577 C5' DG T 14 4576 4578 4599 C5' DA T 15 4598 4600 4620 C5' DC T 16 4619 4621 4649 C5' DTP A 514 4648 4650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4145 P DT P 2 distorted distorted 4131 4146 4147 4148 4165 P DC P 3 distorted distorted 4153 4166 4167 4168 4184 P DC P 4 distorted distorted 4173 4185 4186 4187 4203 P DT P 5 distorted distorted 4192 4204 4205 4206 4223 P DC P 6 distorted distorted 4211 4224 4225 4226 4242 P DC P 7 distorted distorted 4231 4243 4244 4245 4261 P DC P 8 distorted distorted 4250 4262 4263 4264 4280 P DC P 9 distorted distorted 4269 4281 4282 4283 4299 P DT P 10 distorted distorted 4288 4300 4301 4302 4334 P DOC P 11 distorted distorted 4307 4335 4336 4333 4338 P DA T 4 distorted distorted 4339 4340 4341 4359 P TTD T 5 distorted distorted 4346 4360 4361 4362 4399 P DG T 6 distorted distorted 4398 4400 4401 4402 4421 P DA T 7 distorted distorted 4407 4422 4423 4424 4442 P DG T 8 distorted distorted 4429 4443 4444 4445 4464 P DG T 9 distorted distorted 4450 4465 4466 4467 4486 P DG T 10 distorted distorted 4472 4487 4488 4489 4508 P DG T 11 distorted distorted 4494 4509 4510 4511 4530 P DA T 12 distorted distorted 4516 4531 4532 4533 4551 P DG T 13 distorted distorted 4538 4552 4553 4554 4573 P DG T 14 distorted distorted 4559 4574 4575 4576 4595 P DA T 15 distorted distorted 4581 4596 4597 4598 4616 P DC T 16 distorted distorted 4603 4617 4618 4619 ---------------------------------------------------------------------------------