ID code: '1B95' 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' --------------------------------------------------------------------------------- 4129 C1' A C 2 beta 4125 4130 4128 4150 C1' A C 3 beta 4146 4151 4149 4171 C1' G C 4 beta 4167 4172 4170 4193 C1' A C 5 beta 4189 4194 4192 4214 C1' T C 6 beta 4210 4215 4213 4234 C1' A C 7 beta 4230 4235 4233 4255 C1' T C 8 beta 4251 4256 4254 4275 C1' C C 9 beta 4271 4276 4274 4294 C1' T C 10 beta 4290 4295 4293 4314 C1' T C 11 beta 4310 4315 4313 4353 C1' A D 2 beta 4349 4354 4352 4374 C1' A D 3 beta 4370 4375 4373 4395 C1' G D 4 beta 4391 4396 4394 4417 C1' A D 5 beta 4413 4418 4416 4438 C1' T D 6 beta 4434 4439 4437 4458 C1' A D 7 beta 4454 4459 4457 4479 C1' T D 8 beta 4475 4480 4478 4499 C1' C D 9 beta 4495 4500 4498 4518 C1' T D 10 beta 4514 4519 4517 4538 C1' T D 11 beta 4534 4539 4537 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4128 C2' A C 2 4129 4126 4149 C2' A C 3 4150 4147 4170 C2' G C 4 4171 4168 4192 C2' A C 5 4193 4190 4213 C2' T C 6 4214 4211 4233 C2' A C 7 4234 4231 4254 C2' T C 8 4255 4252 4274 C2' C C 9 4275 4272 4293 C2' T C 10 4294 4291 4313 C2' T C 11 4314 4311 4352 C2' A D 2 4353 4350 4373 C2' A D 3 4374 4371 4394 C2' G D 4 4395 4392 4416 C2' A D 5 4417 4414 4437 C2' T D 6 4438 4435 4457 C2' A D 7 4458 4455 4478 C2' T D 8 4479 4476 4498 C2' C D 9 4499 4496 4517 C2' T D 10 4518 4515 4537 C2' T D 11 4538 4535 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4126 C3' A C 2 OK 4124 4127 4128 4147 C3' A C 3 OK 4145 4148 4149 4168 C3' G C 4 OK 4166 4169 4170 4190 C3' A C 5 OK 4188 4191 4192 4211 C3' T C 6 OK 4209 4212 4213 4231 C3' A C 7 OK 4229 4232 4233 4252 C3' T C 8 OK 4250 4253 4254 4272 C3' C C 9 OK 4270 4273 4274 4291 C3' T C 10 OK 4289 4292 4293 4311 C3' T C 11 OK 4309 4312 4313 4350 C3' A D 2 OK 4348 4351 4352 4371 C3' A D 3 OK 4369 4372 4373 4392 C3' G D 4 OK 4390 4393 4394 4414 C3' A D 5 OK 4412 4415 4416 4435 C3' T D 6 OK 4433 4436 4437 4455 C3' A D 7 OK 4453 4456 4457 4476 C3' T D 8 OK 4474 4477 4478 4496 C3' C D 9 OK 4494 4497 4498 4515 C3' T D 10 OK 4513 4516 4517 4535 C3' T D 11 OK 4533 4536 4537 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4124 C4' A C 2 OK 4126 4123 4125 4145 C4' A C 3 OK 4147 4144 4146 4166 C4' G C 4 OK 4168 4165 4167 4188 C4' A C 5 OK 4190 4187 4189 4209 C4' T C 6 OK 4211 4208 4210 4229 C4' A C 7 OK 4231 4228 4230 4250 C4' T C 8 OK 4252 4249 4251 4270 C4' C C 9 OK 4272 4269 4271 4289 C4' T C 10 OK 4291 4288 4290 4309 C4' T C 11 OK 4311 4308 4310 4348 C4' A D 2 OK 4350 4347 4349 4369 C4' A D 3 OK 4371 4368 4370 4390 C4' G D 4 OK 4392 4389 4391 4412 C4' A D 5 OK 4414 4411 4413 4433 C4' T D 6 OK 4435 4432 4434 4453 C4' A D 7 OK 4455 4452 4454 4474 C4' T D 8 OK 4476 4473 4475 4494 C4' C D 9 OK 4496 4493 4495 4513 C4' T D 10 OK 4515 4512 4514 4533 C4' T D 11 OK 4535 4532 4534 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4123 C5' A C 2 4122 4124 4144 C5' A C 3 4143 4145 4165 C5' G C 4 4164 4166 4187 C5' A C 5 4186 4188 4208 C5' T C 6 4207 4209 4228 C5' A C 7 4227 4229 4249 C5' T C 8 4248 4250 4269 C5' C C 9 4268 4270 4288 C5' T C 10 4287 4289 4308 C5' T C 11 4307 4309 4347 C5' A D 2 4346 4348 4368 C5' A D 3 4367 4369 4389 C5' G D 4 4388 4390 4411 C5' A D 5 4410 4412 4432 C5' T D 6 4431 4433 4452 C5' A D 7 4451 4453 4473 C5' T D 8 4472 4474 4493 C5' C D 9 4492 4494 4512 C5' T D 10 4511 4513 4532 C5' T D 11 4531 4533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4140 P A C 3 distorted distorted 4127 4141 4142 4143 4161 P G C 4 distorted distorted 4148 4162 4163 4164 4183 P A C 5 distorted distorted 4169 4184 4185 4186 4204 P T C 6 distorted distorted 4191 4205 4206 4207 4224 P A C 7 distorted distorted 4212 4225 4226 4227 4245 P T C 8 distorted distorted 4232 4246 4247 4248 4265 P C C 9 distorted distorted 4253 4266 4267 4268 4284 P T C 10 distorted distorted 4273 4285 4286 4287 4304 P T C 11 distorted distorted 4292 4305 4306 4307 4364 P A D 3 distorted distorted 4351 4365 4366 4367 4385 P G D 4 distorted distorted 4372 4386 4387 4388 4407 P A D 5 distorted distorted 4393 4408 4409 4410 4428 P T D 6 distorted distorted 4415 4429 4430 4431 4448 P A D 7 distorted distorted 4436 4449 4450 4451 4469 P T D 8 distorted distorted 4456 4470 4471 4472 4489 P C D 9 distorted distorted 4477 4490 4491 4492 4508 P T D 10 distorted distorted 4497 4509 4510 4511 4528 P T D 11 distorted distorted 4516 4529 4530 4531 ---------------------------------------------------------------------------------