ID code: '3MFH' 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' --------------------------------------------------------------------------------- 4094 C1' DG P 1 beta 4090 4095 4093 4116 C1' DT P 2 beta 4112 4117 4115 4136 C1' DC P 3 beta 4132 4137 4135 4155 C1' DC P 4 beta 4151 4156 4154 4174 C1' DT P 5 beta 4170 4175 4173 4194 C1' DC P 6 beta 4190 4195 4193 4213 C1' DC P 7 beta 4209 4214 4212 4232 C1' DC P 8 beta 4228 4233 4231 4251 C1' DC P 9 beta 4247 4252 4250 4270 C1' DT P 10 beta 4266 4271 4269 4288 C1' DOC P 11 beta 4292 4280 4289 4306 C1' DT T 4 beta 4302 4307 4305 4326 C1' DT T 5 beta 4322 4327 4325 4346 C1' DG T 6 beta 4342 4347 4345 4368 C1' DA T 7 beta 4364 4369 4367 4389 C1' DG T 8 beta 4385 4390 4388 4411 C1' DG T 9 beta 4407 4412 4410 4433 C1' DG T 10 beta 4429 4434 4432 4455 C1' DG T 11 beta 4451 4456 4454 4477 C1' DA T 12 beta 4473 4478 4476 4498 C1' DG T 13 beta 4494 4499 4497 4520 C1' DG T 14 beta 4516 4521 4519 4542 C1' DA T 15 beta 4538 4543 4541 4563 C1' DC T 16 beta 4559 4564 4562 4592 C1' DTP A 514 beta 4588 4593 4591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4093 C2' DG P 1 4094 4091 4115 C2' DT P 2 4116 4113 4135 C2' DC P 3 4136 4133 4154 C2' DC P 4 4155 4152 4173 C2' DT P 5 4174 4171 4193 C2' DC P 6 4194 4191 4212 C2' DC P 7 4213 4210 4231 C2' DC P 8 4232 4229 4250 C2' DC P 9 4251 4248 4269 C2' DT P 10 4270 4267 4289 C2' DOC P 11 4288 4290 4305 C2' DT T 4 4306 4303 4325 C2' DT T 5 4326 4323 4345 C2' DG T 6 4346 4343 4367 C2' DA T 7 4368 4365 4388 C2' DG T 8 4389 4386 4410 C2' DG T 9 4411 4408 4432 C2' DG T 10 4433 4430 4454 C2' DG T 11 4455 4452 4476 C2' DA T 12 4477 4474 4497 C2' DG T 13 4498 4495 4519 C2' DG T 14 4520 4517 4541 C2' DA T 15 4542 4539 4562 C2' DC T 16 4563 4560 4591 C2' DTP A 514 4592 4589 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4091 C3' DG P 1 OK 4089 4092 4093 4113 C3' DT P 2 OK 4111 4114 4115 4133 C3' DC P 3 OK 4131 4134 4135 4152 C3' DC P 4 OK 4150 4153 4154 4171 C3' DT P 5 OK 4169 4172 4173 4191 C3' DC P 6 OK 4189 4192 4193 4210 C3' DC P 7 OK 4208 4211 4212 4229 C3' DC P 8 OK 4227 4230 4231 4248 C3' DC P 9 OK 4246 4249 4250 4267 C3' DT P 10 OK 4265 4268 4269 4290 C3' DOC P 11 4291 4289 4303 C3' DT T 4 OK 4301 4304 4305 4323 C3' DT T 5 OK 4321 4324 4325 4343 C3' DG T 6 OK 4341 4344 4345 4365 C3' DA T 7 OK 4363 4366 4367 4386 C3' DG T 8 OK 4384 4387 4388 4408 C3' DG T 9 OK 4406 4409 4410 4430 C3' DG T 10 OK 4428 4431 4432 4452 C3' DG T 11 OK 4450 4453 4454 4474 C3' DA T 12 OK 4472 4475 4476 4495 C3' DG T 13 OK 4493 4496 4497 4517 C3' DG T 14 OK 4515 4518 4519 4539 C3' DA T 15 OK 4537 4540 4541 4560 C3' DC T 16 OK 4558 4561 4562 4589 C3' DTP A 514 OK 4587 4590 4591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4089 C4' DG P 1 OK 4091 4088 4090 4111 C4' DT P 2 OK 4113 4110 4112 4131 C4' DC P 3 OK 4133 4130 4132 4150 C4' DC P 4 OK 4152 4149 4151 4169 C4' DT P 5 OK 4171 4168 4170 4189 C4' DC P 6 OK 4191 4188 4190 4208 C4' DC P 7 OK 4210 4207 4209 4227 C4' DC P 8 OK 4229 4226 4228 4246 C4' DC P 9 OK 4248 4245 4247 4265 C4' DT P 10 OK 4267 4264 4266 4291 C4' DOC P 11 OK 4290 4293 4292 4301 C4' DT T 4 OK 4303 4300 4302 4321 C4' DT T 5 OK 4323 4320 4322 4341 C4' DG T 6 OK 4343 4340 4342 4363 C4' DA T 7 OK 4365 4362 4364 4384 C4' DG T 8 OK 4386 4383 4385 4406 C4' DG T 9 OK 4408 4405 4407 4428 C4' DG T 10 OK 4430 4427 4429 4450 C4' DG T 11 OK 4452 4449 4451 4472 C4' DA T 12 OK 4474 4471 4473 4493 C4' DG T 13 OK 4495 4492 4494 4515 C4' DG T 14 OK 4517 4514 4516 4537 C4' DA T 15 OK 4539 4536 4538 4558 C4' DC T 16 OK 4560 4557 4559 4587 C4' DTP A 514 OK 4589 4586 4588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4088 C5' DG P 1 4087 4089 4110 C5' DT P 2 4109 4111 4130 C5' DC P 3 4129 4131 4149 C5' DC P 4 4148 4150 4168 C5' DT P 5 4167 4169 4188 C5' DC P 6 4187 4189 4207 C5' DC P 7 4206 4208 4226 C5' DC P 8 4225 4227 4245 C5' DC P 9 4244 4246 4264 C5' DT P 10 4263 4265 4293 C5' DOC P 11 4294 4291 4300 C5' DT T 4 4299 4301 4320 C5' DT T 5 4319 4321 4340 C5' DG T 6 4339 4341 4362 C5' DA T 7 4361 4363 4383 C5' DG T 8 4382 4384 4405 C5' DG T 9 4404 4406 4427 C5' DG T 10 4426 4428 4449 C5' DG T 11 4448 4450 4471 C5' DA T 12 4470 4472 4492 C5' DG T 13 4491 4493 4514 C5' DG T 14 4513 4515 4536 C5' DA T 15 4535 4537 4557 C5' DC T 16 4556 4558 4586 C5' DTP A 514 4585 4587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4106 P DT P 2 distorted distorted 4092 4107 4108 4109 4126 P DC P 3 distorted distorted 4114 4127 4128 4129 4145 P DC P 4 distorted distorted 4134 4146 4147 4148 4164 P DT P 5 distorted distorted 4153 4165 4166 4167 4184 P DC P 6 distorted distorted 4172 4185 4186 4187 4203 P DC P 7 distorted distorted 4192 4204 4205 4206 4222 P DC P 8 distorted distorted 4211 4223 4224 4225 4241 P DC P 9 distorted distorted 4230 4242 4243 4244 4260 P DT P 10 distorted distorted 4249 4261 4262 4263 4295 P DOC P 11 distorted distorted 4268 4296 4297 4294 4316 P DT T 5 distorted distorted 4304 4317 4318 4319 4336 P DG T 6 distorted distorted 4324 4337 4338 4339 4358 P DA T 7 distorted distorted 4344 4359 4360 4361 4379 P DG T 8 distorted distorted 4366 4380 4381 4382 4401 P DG T 9 distorted distorted 4387 4402 4403 4404 4423 P DG T 10 distorted distorted 4409 4424 4425 4426 4445 P DG T 11 distorted distorted 4431 4446 4447 4448 4467 P DA T 12 distorted distorted 4453 4468 4469 4470 4488 P DG T 13 distorted distorted 4475 4489 4490 4491 4510 P DG T 14 distorted distorted 4496 4511 4512 4513 4532 P DA T 15 distorted distorted 4518 4533 4534 4535 4553 P DC T 16 distorted distorted 4540 4554 4555 4556 ---------------------------------------------------------------------------------