ID code: '1RVB' 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' --------------------------------------------------------------------------------- 4077 C1' A C 2 beta 4073 4078 4076 4098 C1' A C 3 beta 4094 4099 4097 4119 C1' G C 4 beta 4115 4120 4118 4141 C1' A C 5 beta 4137 4142 4140 4162 C1' T C 6 beta 4158 4163 4161 4182 C1' A C 7 beta 4178 4183 4181 4203 C1' T C 8 beta 4199 4204 4202 4223 C1' C C 9 beta 4219 4224 4222 4242 C1' T C 10 beta 4238 4243 4241 4262 C1' T C 11 beta 4258 4263 4261 4301 C1' A D 2 beta 4297 4302 4300 4322 C1' A D 3 beta 4318 4323 4321 4343 C1' G D 4 beta 4339 4344 4342 4365 C1' A D 5 beta 4361 4366 4364 4386 C1' T D 6 beta 4382 4387 4385 4406 C1' A D 7 beta 4402 4407 4405 4427 C1' T D 8 beta 4423 4428 4426 4447 C1' C D 9 beta 4443 4448 4446 4466 C1' T D 10 beta 4462 4467 4465 4486 C1' T D 11 beta 4482 4487 4485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4076 C2' A C 2 4077 4074 4097 C2' A C 3 4098 4095 4118 C2' G C 4 4119 4116 4140 C2' A C 5 4141 4138 4161 C2' T C 6 4162 4159 4181 C2' A C 7 4182 4179 4202 C2' T C 8 4203 4200 4222 C2' C C 9 4223 4220 4241 C2' T C 10 4242 4239 4261 C2' T C 11 4262 4259 4300 C2' A D 2 4301 4298 4321 C2' A D 3 4322 4319 4342 C2' G D 4 4343 4340 4364 C2' A D 5 4365 4362 4385 C2' T D 6 4386 4383 4405 C2' A D 7 4406 4403 4426 C2' T D 8 4427 4424 4446 C2' C D 9 4447 4444 4465 C2' T D 10 4466 4463 4485 C2' T D 11 4486 4483 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4074 C3' A C 2 OK 4072 4075 4076 4095 C3' A C 3 OK 4093 4096 4097 4116 C3' G C 4 OK 4114 4117 4118 4138 C3' A C 5 OK 4136 4139 4140 4159 C3' T C 6 OK 4157 4160 4161 4179 C3' A C 7 OK 4177 4180 4181 4200 C3' T C 8 OK 4198 4201 4202 4220 C3' C C 9 OK 4218 4221 4222 4239 C3' T C 10 OK 4237 4240 4241 4259 C3' T C 11 OK 4257 4260 4261 4298 C3' A D 2 OK 4296 4299 4300 4319 C3' A D 3 OK 4317 4320 4321 4340 C3' G D 4 OK 4338 4341 4342 4362 C3' A D 5 OK 4360 4363 4364 4383 C3' T D 6 OK 4381 4384 4385 4403 C3' A D 7 OK 4401 4404 4405 4424 C3' T D 8 OK 4422 4425 4426 4444 C3' C D 9 OK 4442 4445 4446 4463 C3' T D 10 OK 4461 4464 4465 4483 C3' T D 11 OK 4481 4484 4485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4072 C4' A C 2 OK 4074 4071 4073 4093 C4' A C 3 OK 4095 4092 4094 4114 C4' G C 4 OK 4116 4113 4115 4136 C4' A C 5 OK 4138 4135 4137 4157 C4' T C 6 OK 4159 4156 4158 4177 C4' A C 7 OK 4179 4176 4178 4198 C4' T C 8 OK 4200 4197 4199 4218 C4' C C 9 OK 4220 4217 4219 4237 C4' T C 10 OK 4239 4236 4238 4257 C4' T C 11 OK 4259 4256 4258 4296 C4' A D 2 OK 4298 4295 4297 4317 C4' A D 3 OK 4319 4316 4318 4338 C4' G D 4 OK 4340 4337 4339 4360 C4' A D 5 OK 4362 4359 4361 4381 C4' T D 6 OK 4383 4380 4382 4401 C4' A D 7 OK 4403 4400 4402 4422 C4' T D 8 OK 4424 4421 4423 4442 C4' C D 9 OK 4444 4441 4443 4461 C4' T D 10 OK 4463 4460 4462 4481 C4' T D 11 OK 4483 4480 4482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4071 C5' A C 2 4070 4072 4092 C5' A C 3 4091 4093 4113 C5' G C 4 4112 4114 4135 C5' A C 5 4134 4136 4156 C5' T C 6 4155 4157 4176 C5' A C 7 4175 4177 4197 C5' T C 8 4196 4198 4217 C5' C C 9 4216 4218 4236 C5' T C 10 4235 4237 4256 C5' T C 11 4255 4257 4295 C5' A D 2 4294 4296 4316 C5' A D 3 4315 4317 4337 C5' G D 4 4336 4338 4359 C5' A D 5 4358 4360 4380 C5' T D 6 4379 4381 4400 C5' A D 7 4399 4401 4421 C5' T D 8 4420 4422 4441 C5' C D 9 4440 4442 4460 C5' T D 10 4459 4461 4480 C5' T D 11 4479 4481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4088 P A C 3 distorted distorted 4075 4089 4090 4091 4109 P G C 4 distorted distorted 4096 4110 4111 4112 4131 P A C 5 distorted distorted 4117 4132 4133 4134 4152 P T C 6 distorted distorted 4139 4153 4154 4155 4172 P A C 7 distorted distorted 4160 4173 4174 4175 4193 P T C 8 distorted distorted 4180 4194 4195 4196 4213 P C C 9 distorted distorted 4201 4214 4215 4216 4232 P T C 10 distorted distorted 4221 4233 4234 4235 4252 P T C 11 distorted distorted 4240 4253 4254 4255 4312 P A D 3 distorted distorted 4299 4313 4314 4315 4333 P G D 4 distorted distorted 4320 4334 4335 4336 4355 P A D 5 distorted distorted 4341 4356 4357 4358 4376 P T D 6 distorted distorted 4363 4377 4378 4379 4396 P A D 7 distorted distorted 4384 4397 4398 4399 4417 P T D 8 distorted distorted 4404 4418 4419 4420 4437 P C D 9 distorted distorted 4425 4438 4439 4440 4456 P T D 10 distorted distorted 4445 4457 4458 4459 4476 P T D 11 distorted distorted 4464 4477 4478 4479 ---------------------------------------------------------------------------------