ID code: '1B97' 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' --------------------------------------------------------------------------------- 4119 C1' A C 2 beta 4115 4120 4118 4140 C1' A C 3 beta 4136 4141 4139 4161 C1' G C 4 beta 4157 4162 4160 4183 C1' A C 5 beta 4179 4184 4182 4204 C1' T C 6 beta 4200 4205 4203 4224 C1' A C 7 beta 4220 4225 4223 4245 C1' T C 8 beta 4241 4246 4244 4265 C1' C C 9 beta 4261 4266 4264 4284 C1' T C 10 beta 4280 4285 4283 4304 C1' T C 11 beta 4300 4305 4303 4343 C1' A D 2 beta 4339 4344 4342 4364 C1' A D 3 beta 4360 4365 4363 4385 C1' G D 4 beta 4381 4386 4384 4407 C1' A D 5 beta 4403 4408 4406 4428 C1' T D 6 beta 4424 4429 4427 4448 C1' A D 7 beta 4444 4449 4447 4469 C1' T D 8 beta 4465 4470 4468 4489 C1' C D 9 beta 4485 4490 4488 4508 C1' T D 10 beta 4504 4509 4507 4528 C1' T D 11 beta 4524 4529 4527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4118 C2' A C 2 4119 4116 4139 C2' A C 3 4140 4137 4160 C2' G C 4 4161 4158 4182 C2' A C 5 4183 4180 4203 C2' T C 6 4204 4201 4223 C2' A C 7 4224 4221 4244 C2' T C 8 4245 4242 4264 C2' C C 9 4265 4262 4283 C2' T C 10 4284 4281 4303 C2' T C 11 4304 4301 4342 C2' A D 2 4343 4340 4363 C2' A D 3 4364 4361 4384 C2' G D 4 4385 4382 4406 C2' A D 5 4407 4404 4427 C2' T D 6 4428 4425 4447 C2' A D 7 4448 4445 4468 C2' T D 8 4469 4466 4488 C2' C D 9 4489 4486 4507 C2' T D 10 4508 4505 4527 C2' T D 11 4528 4525 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4116 C3' A C 2 OK 4114 4117 4118 4137 C3' A C 3 OK 4135 4138 4139 4158 C3' G C 4 OK 4156 4159 4160 4180 C3' A C 5 OK 4178 4181 4182 4201 C3' T C 6 OK 4199 4202 4203 4221 C3' A C 7 OK 4219 4222 4223 4242 C3' T C 8 OK 4240 4243 4244 4262 C3' C C 9 OK 4260 4263 4264 4281 C3' T C 10 OK 4279 4282 4283 4301 C3' T C 11 OK 4299 4302 4303 4340 C3' A D 2 OK 4338 4341 4342 4361 C3' A D 3 OK 4359 4362 4363 4382 C3' G D 4 OK 4380 4383 4384 4404 C3' A D 5 OK 4402 4405 4406 4425 C3' T D 6 OK 4423 4426 4427 4445 C3' A D 7 OK 4443 4446 4447 4466 C3' T D 8 OK 4464 4467 4468 4486 C3' C D 9 OK 4484 4487 4488 4505 C3' T D 10 OK 4503 4506 4507 4525 C3' T D 11 OK 4523 4526 4527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4114 C4' A C 2 OK 4116 4113 4115 4135 C4' A C 3 OK 4137 4134 4136 4156 C4' G C 4 OK 4158 4155 4157 4178 C4' A C 5 OK 4180 4177 4179 4199 C4' T C 6 OK 4201 4198 4200 4219 C4' A C 7 OK 4221 4218 4220 4240 C4' T C 8 OK 4242 4239 4241 4260 C4' C C 9 OK 4262 4259 4261 4279 C4' T C 10 OK 4281 4278 4280 4299 C4' T C 11 OK 4301 4298 4300 4338 C4' A D 2 OK 4340 4337 4339 4359 C4' A D 3 OK 4361 4358 4360 4380 C4' G D 4 OK 4382 4379 4381 4402 C4' A D 5 OK 4404 4401 4403 4423 C4' T D 6 OK 4425 4422 4424 4443 C4' A D 7 OK 4445 4442 4444 4464 C4' T D 8 OK 4466 4463 4465 4484 C4' C D 9 OK 4486 4483 4485 4503 C4' T D 10 OK 4505 4502 4504 4523 C4' T D 11 OK 4525 4522 4524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4113 C5' A C 2 4112 4114 4134 C5' A C 3 4133 4135 4155 C5' G C 4 4154 4156 4177 C5' A C 5 4176 4178 4198 C5' T C 6 4197 4199 4218 C5' A C 7 4217 4219 4239 C5' T C 8 4238 4240 4259 C5' C C 9 4258 4260 4278 C5' T C 10 4277 4279 4298 C5' T C 11 4297 4299 4337 C5' A D 2 4336 4338 4358 C5' A D 3 4357 4359 4379 C5' G D 4 4378 4380 4401 C5' A D 5 4400 4402 4422 C5' T D 6 4421 4423 4442 C5' A D 7 4441 4443 4463 C5' T D 8 4462 4464 4483 C5' C D 9 4482 4484 4502 C5' T D 10 4501 4503 4522 C5' T D 11 4521 4523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4130 P A C 3 distorted distorted 4117 4131 4132 4133 4151 P G C 4 distorted distorted 4138 4152 4153 4154 4173 P A C 5 distorted distorted 4159 4174 4175 4176 4194 P T C 6 distorted distorted 4181 4195 4196 4197 4214 P A C 7 distorted distorted 4202 4215 4216 4217 4235 P T C 8 distorted distorted 4222 4236 4237 4238 4255 P C C 9 distorted distorted 4243 4256 4257 4258 4274 P T C 10 distorted distorted 4263 4275 4276 4277 4294 P T C 11 distorted distorted 4282 4295 4296 4297 4354 P A D 3 distorted distorted 4341 4355 4356 4357 4375 P G D 4 distorted distorted 4362 4376 4377 4378 4397 P A D 5 distorted distorted 4383 4398 4399 4400 4418 P T D 6 distorted distorted 4405 4419 4420 4421 4438 P A D 7 distorted distorted 4426 4439 4440 4441 4459 P T D 8 distorted distorted 4446 4460 4461 4462 4479 P C D 9 distorted distorted 4467 4480 4481 4482 4498 P T D 10 distorted distorted 4487 4499 4500 4501 4518 P T D 11 distorted distorted 4506 4519 4520 4521 ---------------------------------------------------------------------------------