ID code: '1QTM' 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' --------------------------------------------------------------------------------- 4195 C1' G B 101 beta 4191 4196 4194 4217 C1' A B 102 beta 4213 4218 4216 4238 C1' C B 103 beta 4234 4239 4237 4257 C1' C B 104 beta 4253 4258 4256 4276 C1' A B 105 beta 4272 4277 4275 4297 C1' C B 106 beta 4293 4298 4296 4316 C1' G B 107 beta 4312 4317 4315 4338 C1' G B 108 beta 4334 4339 4337 4360 C1' C B 109 beta 4356 4361 4359 4379 C1' G B 110 beta 4375 4380 4378 4401 C1' C B 111 beta 4397 4402 4400 4427 C1' T2D B 112 beta 4426 4414 4423 4479 C1' A C 205 beta 4475 4480 4478 4500 C1' G C 206 beta 4496 4501 4499 4522 C1' C C 207 beta 4518 4523 4521 4541 C1' G C 208 beta 4537 4542 4540 4563 C1' C C 209 beta 4559 4564 4562 4582 C1' C C 210 beta 4578 4583 4581 4601 C1' G C 211 beta 4597 4602 4600 4623 C1' T C 212 beta 4619 4624 4622 4643 C1' G C 213 beta 4639 4644 4642 4665 C1' G C 214 beta 4661 4666 4664 4687 C1' T C 215 beta 4683 4688 4686 4707 C1' C C 216 beta 4703 4708 4706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4194 C2' G B 101 4195 4192 4216 C2' A B 102 4217 4214 4237 C2' C B 103 4238 4235 4256 C2' C B 104 4257 4254 4275 C2' A B 105 4276 4273 4296 C2' C B 106 4297 4294 4315 C2' G B 107 4316 4313 4337 C2' G B 108 4338 4335 4359 C2' C B 109 4360 4357 4378 C2' G B 110 4379 4376 4400 C2' C B 111 4401 4398 4423 C2' T2D B 112 4427 4428 4478 C2' A C 205 4479 4476 4499 C2' G C 206 4500 4497 4521 C2' C C 207 4522 4519 4540 C2' G C 208 4541 4538 4562 C2' C C 209 4563 4560 4581 C2' C C 210 4582 4579 4600 C2' G C 211 4601 4598 4622 C2' T C 212 4623 4620 4642 C2' G C 213 4643 4640 4664 C2' G C 214 4665 4662 4686 C2' T C 215 4687 4684 4706 C2' C C 216 4707 4704 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4192 C3' G B 101 OK 4190 4193 4194 4214 C3' A B 102 OK 4212 4215 4216 4235 C3' C B 103 OK 4233 4236 4237 4254 C3' C B 104 OK 4252 4255 4256 4273 C3' A B 105 OK 4271 4274 4275 4294 C3' C B 106 OK 4292 4295 4296 4313 C3' G B 107 OK 4311 4314 4315 4335 C3' G B 108 OK 4333 4336 4337 4357 C3' C B 109 OK 4355 4358 4359 4376 C3' G B 110 OK 4374 4377 4378 4398 C3' C B 111 OK 4396 4399 4400 4428 C3' T2D B 112 4425 4423 4476 C3' A C 205 OK 4474 4477 4478 4497 C3' G C 206 OK 4495 4498 4499 4519 C3' C C 207 OK 4517 4520 4521 4538 C3' G C 208 OK 4536 4539 4540 4560 C3' C C 209 OK 4558 4561 4562 4579 C3' C C 210 OK 4577 4580 4581 4598 C3' G C 211 OK 4596 4599 4600 4620 C3' T C 212 OK 4618 4621 4622 4640 C3' G C 213 OK 4638 4641 4642 4662 C3' G C 214 OK 4660 4663 4664 4684 C3' T C 215 OK 4682 4685 4686 4704 C3' C C 216 OK 4702 4705 4706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4190 C4' G B 101 OK 4192 4189 4191 4212 C4' A B 102 OK 4214 4211 4213 4233 C4' C B 103 OK 4235 4232 4234 4252 C4' C B 104 OK 4254 4251 4253 4271 C4' A B 105 OK 4273 4270 4272 4292 C4' C B 106 OK 4294 4291 4293 4311 C4' G B 107 OK 4313 4310 4312 4333 C4' G B 108 OK 4335 4332 4334 4355 C4' C B 109 OK 4357 4354 4356 4374 C4' G B 110 OK 4376 4373 4375 4396 C4' C B 111 OK 4398 4395 4397 4425 C4' T2D B 112 OK 4428 4424 4426 4474 C4' A C 205 OK 4476 4473 4475 4495 C4' G C 206 OK 4497 4494 4496 4517 C4' C C 207 OK 4519 4516 4518 4536 C4' G C 208 OK 4538 4535 4537 4558 C4' C C 209 OK 4560 4557 4559 4577 C4' C C 210 OK 4579 4576 4578 4596 C4' G C 211 OK 4598 4595 4597 4618 C4' T C 212 OK 4620 4617 4619 4638 C4' G C 213 OK 4640 4637 4639 4660 C4' G C 214 OK 4662 4659 4661 4682 C4' T C 215 OK 4684 4681 4683 4702 C4' C C 216 OK 4704 4701 4703 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4189 C5' G B 101 4188 4190 4211 C5' A B 102 4210 4212 4232 C5' C B 103 4231 4233 4251 C5' C B 104 4250 4252 4270 C5' A B 105 4269 4271 4291 C5' C B 106 4290 4292 4310 C5' G B 107 4309 4311 4332 C5' G B 108 4331 4333 4354 C5' C B 109 4353 4355 4373 C5' G B 110 4372 4374 4395 C5' C B 111 4394 4396 4424 C5' T2D B 112 4413 4425 4473 C5' A C 205 4472 4474 4494 C5' G C 206 4493 4495 4516 C5' C C 207 4515 4517 4535 C5' G C 208 4534 4536 4557 C5' C C 209 4556 4558 4576 C5' C C 210 4575 4577 4595 C5' G C 211 4594 4596 4617 C5' T C 212 4616 4618 4637 C5' G C 213 4636 4638 4659 C5' G C 214 4658 4660 4681 C5' T C 215 4680 4682 4701 C5' C C 216 4700 4702 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4207 P A B 102 distorted distorted 4193 4208 4209 4210 4228 P C B 103 distorted distorted 4215 4229 4230 4231 4247 P C B 104 distorted distorted 4236 4248 4249 4250 4266 P A B 105 distorted distorted 4255 4267 4268 4269 4287 P C B 106 distorted distorted 4274 4288 4289 4290 4306 P G B 107 distorted distorted 4295 4307 4308 4309 4328 P G B 108 distorted distorted 4314 4329 4330 4331 4350 P C B 109 distorted distorted 4336 4351 4352 4353 4369 P G B 110 distorted distorted 4358 4370 4371 4372 4391 P C B 111 distorted distorted 4377 4392 4393 4394 4410 P T2D B 112 OK OK 4399 4411 4412 4413 4490 P G C 206 distorted distorted 4477 4491 4492 4493 4512 P C C 207 distorted distorted 4498 4513 4514 4515 4531 P G C 208 distorted distorted 4520 4532 4533 4534 4553 P C C 209 distorted distorted 4539 4554 4555 4556 4572 P C C 210 distorted distorted 4561 4573 4574 4575 4591 P G C 211 distorted distorted 4580 4592 4593 4594 4613 P T C 212 distorted distorted 4599 4614 4615 4616 4633 P G C 213 distorted distorted 4621 4634 4635 4636 4655 P G C 214 distorted distorted 4641 4656 4657 4658 4677 P T C 215 distorted distorted 4663 4678 4679 4680 4697 P C C 216 distorted distorted 4685 4698 4699 4700 ---------------------------------------------------------------------------------