ID code: '1ERI' 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' --------------------------------------------------------------------------------- 4132 C1' C B 2 beta 4128 4133 4131 4151 C1' G B 3 beta 4147 4152 4150 4173 C1' C B 4 beta 4169 4174 4172 4192 C1' G B 5 beta 4188 4193 4191 4214 C1' A B 6 beta 4210 4215 4213 4235 C1' A B 7 beta 4231 4236 4234 4256 C1' T B 8 beta 4252 4257 4255 4276 C1' T B 9 beta 4272 4277 4275 4296 C1' C B 10 beta 4292 4297 4295 4315 C1' G B 11 beta 4311 4316 4314 4337 C1' C B 12 beta 4333 4338 4336 4356 C1' G B 13 beta 4352 4357 4355 4396 C1' C D 2 beta 4392 4397 4395 4415 C1' G D 3 beta 4411 4416 4414 4437 C1' C D 4 beta 4433 4438 4436 4456 C1' G D 5 beta 4452 4457 4455 4478 C1' A D 6 beta 4474 4479 4477 4499 C1' A D 7 beta 4495 4500 4498 4520 C1' T D 8 beta 4516 4521 4519 4540 C1' T D 9 beta 4536 4541 4539 4560 C1' C D 10 beta 4556 4561 4559 4579 C1' G D 11 beta 4575 4580 4578 4601 C1' C D 12 beta 4597 4602 4600 4620 C1' G D 13 beta 4616 4621 4619 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4131 C2' C B 2 4132 4129 4150 C2' G B 3 4151 4148 4172 C2' C B 4 4173 4170 4191 C2' G B 5 4192 4189 4213 C2' A B 6 4214 4211 4234 C2' A B 7 4235 4232 4255 C2' T B 8 4256 4253 4275 C2' T B 9 4276 4273 4295 C2' C B 10 4296 4293 4314 C2' G B 11 4315 4312 4336 C2' C B 12 4337 4334 4355 C2' G B 13 4356 4353 4395 C2' C D 2 4396 4393 4414 C2' G D 3 4415 4412 4436 C2' C D 4 4437 4434 4455 C2' G D 5 4456 4453 4477 C2' A D 6 4478 4475 4498 C2' A D 7 4499 4496 4519 C2' T D 8 4520 4517 4539 C2' T D 9 4540 4537 4559 C2' C D 10 4560 4557 4578 C2' G D 11 4579 4576 4600 C2' C D 12 4601 4598 4619 C2' G D 13 4620 4617 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4129 C3' C B 2 OK 4127 4130 4131 4148 C3' G B 3 OK 4146 4149 4150 4170 C3' C B 4 OK 4168 4171 4172 4189 C3' G B 5 OK 4187 4190 4191 4211 C3' A B 6 OK 4209 4212 4213 4232 C3' A B 7 OK 4230 4233 4234 4253 C3' T B 8 OK 4251 4254 4255 4273 C3' T B 9 OK 4271 4274 4275 4293 C3' C B 10 OK 4291 4294 4295 4312 C3' G B 11 OK 4310 4313 4314 4334 C3' C B 12 OK 4332 4335 4336 4353 C3' G B 13 OK 4351 4354 4355 4393 C3' C D 2 OK 4391 4394 4395 4412 C3' G D 3 OK 4410 4413 4414 4434 C3' C D 4 OK 4432 4435 4436 4453 C3' G D 5 OK 4451 4454 4455 4475 C3' A D 6 OK 4473 4476 4477 4496 C3' A D 7 OK 4494 4497 4498 4517 C3' T D 8 OK 4515 4518 4519 4537 C3' T D 9 OK 4535 4538 4539 4557 C3' C D 10 OK 4555 4558 4559 4576 C3' G D 11 OK 4574 4577 4578 4598 C3' C D 12 OK 4596 4599 4600 4617 C3' G D 13 OK 4615 4618 4619 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4127 C4' C B 2 OK 4129 4126 4128 4146 C4' G B 3 OK 4148 4145 4147 4168 C4' C B 4 OK 4170 4167 4169 4187 C4' G B 5 OK 4189 4186 4188 4209 C4' A B 6 OK 4211 4208 4210 4230 C4' A B 7 OK 4232 4229 4231 4251 C4' T B 8 OK 4253 4250 4252 4271 C4' T B 9 OK 4273 4270 4272 4291 C4' C B 10 OK 4293 4290 4292 4310 C4' G B 11 OK 4312 4309 4311 4332 C4' C B 12 OK 4334 4331 4333 4351 C4' G B 13 OK 4353 4350 4352 4391 C4' C D 2 OK 4393 4390 4392 4410 C4' G D 3 OK 4412 4409 4411 4432 C4' C D 4 OK 4434 4431 4433 4451 C4' G D 5 OK 4453 4450 4452 4473 C4' A D 6 OK 4475 4472 4474 4494 C4' A D 7 OK 4496 4493 4495 4515 C4' T D 8 OK 4517 4514 4516 4535 C4' T D 9 OK 4537 4534 4536 4555 C4' C D 10 OK 4557 4554 4556 4574 C4' G D 11 OK 4576 4573 4575 4596 C4' C D 12 OK 4598 4595 4597 4615 C4' G D 13 OK 4617 4614 4616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4126 C5' C B 2 4125 4127 4145 C5' G B 3 4144 4146 4167 C5' C B 4 4166 4168 4186 C5' G B 5 4185 4187 4208 C5' A B 6 4207 4209 4229 C5' A B 7 4228 4230 4250 C5' T B 8 4249 4251 4270 C5' T B 9 4269 4271 4290 C5' C B 10 4289 4291 4309 C5' G B 11 4308 4310 4331 C5' C B 12 4330 4332 4350 C5' G B 13 4349 4351 4390 C5' C D 2 4389 4391 4409 C5' G D 3 4408 4410 4431 C5' C D 4 4430 4432 4450 C5' G D 5 4449 4451 4472 C5' A D 6 4471 4473 4493 C5' A D 7 4492 4494 4514 C5' T D 8 4513 4515 4534 C5' T D 9 4533 4535 4554 C5' C D 10 4553 4555 4573 C5' G D 11 4572 4574 4595 C5' C D 12 4594 4596 4614 C5' G D 13 4613 4615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4141 P G B 3 distorted distorted 4130 4142 4143 4144 4163 P C B 4 OK OK 4149 4164 4165 4166 4182 P G B 5 OK OK 4171 4183 4184 4185 4204 P A B 6 OK OK 4190 4205 4206 4207 4225 P A B 7 OK OK 4212 4226 4227 4228 4246 P T B 8 OK OK 4233 4247 4248 4249 4266 P T B 9 OK OK 4254 4267 4268 4269 4286 P C B 10 OK OK 4274 4287 4288 4289 4305 P G B 11 OK OK 4294 4306 4307 4308 4327 P C B 12 OK OK 4313 4328 4329 4330 4346 P G B 13 OK OK 4335 4347 4348 4349 4405 P G D 3 distorted distorted 4394 4406 4407 4408 4427 P C D 4 OK OK 4413 4428 4429 4430 4446 P G D 5 OK OK 4435 4447 4448 4449 4468 P A D 6 OK OK 4454 4469 4470 4471 4489 P A D 7 OK OK 4476 4490 4491 4492 4510 P T D 8 OK OK 4497 4511 4512 4513 4530 P T D 9 OK OK 4518 4531 4532 4533 4550 P C D 10 OK OK 4538 4551 4552 4553 4569 P G D 11 OK OK 4558 4570 4571 4572 4591 P C D 12 OK OK 4577 4592 4593 4594 4610 P G D 13 OK OK 4599 4611 4612 4613 ---------------------------------------------------------------------------------