ID code: '4LG2' 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' --------------------------------------------------------------------------------- 3821 C1' C E 1 beta 3816 3822 3819 3841 C1' U E 2 beta 3836 3842 3839 3861 C1' A E 3 beta 3856 3862 3859 3883 C1' G E 4 beta 3878 3884 3881 3906 C1' A E 5 beta 3901 3907 3904 3928 C1' C E 6 beta 3923 3929 3926 3948 C1' G E 7 beta 3943 3949 3946 3971 C1' U E 8 beta 3966 3972 3969 3991 C1' C E 9 beta 3986 3992 3989 4012 C1' G F 4 beta 4007 4013 4010 4035 C1' A F 5 beta 4030 4036 4033 4057 C1' C F 6 beta 4052 4058 4055 4077 C1' G F 7 beta 4072 4078 4075 4100 C1' U F 8 beta 4095 4101 4098 4120 C1' C F 9 beta 4115 4121 4118 4140 C1' U F 10 beta 4135 4141 4138 4160 C1' A F 11 beta 4155 4161 4158 4182 C1' G F 12 beta 4177 4183 4180 4206 C1' C J 1 beta 4201 4207 4204 4226 C1' U J 2 beta 4221 4227 4224 4246 C1' A J 3 beta 4241 4247 4244 4268 C1' G J 4 beta 4263 4269 4266 4291 C1' A J 5 beta 4286 4292 4289 4313 C1' C J 6 beta 4308 4314 4311 4333 C1' G J 7 beta 4328 4334 4331 4356 C1' U J 8 beta 4351 4357 4354 4376 C1' C J 9 beta 4371 4377 4374 4396 C1' U J 10 beta 4391 4397 4394 4416 C1' A J 11 beta 4411 4417 4414 4438 C1' G J 12 beta 4433 4439 4436 4459 C1' C I 1 beta 4454 4460 4457 4479 C1' U I 2 beta 4474 4480 4477 4499 C1' A I 3 beta 4494 4500 4497 4521 C1' G I 4 beta 4516 4522 4519 4544 C1' A I 5 beta 4539 4545 4542 4566 C1' C I 6 beta 4561 4567 4564 4586 C1' G I 7 beta 4581 4587 4584 4609 C1' U I 8 beta 4604 4610 4607 4629 C1' C I 9 beta 4624 4630 4627 4649 C1' U I 10 beta 4644 4650 4647 4669 C1' A I 11 beta 4664 4670 4667 4691 C1' G I 12 beta 4686 4692 4689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3819 C2' C E 1 OK 3821 3817 3820 3839 C2' U E 2 OK 3841 3837 3840 3859 C2' A E 3 OK 3861 3857 3860 3881 C2' G E 4 OK 3883 3879 3882 3904 C2' A E 5 OK 3906 3902 3905 3926 C2' C E 6 OK 3928 3924 3927 3946 C2' G E 7 OK 3948 3944 3947 3969 C2' U E 8 OK 3971 3967 3970 3989 C2' C E 9 OK 3991 3987 3990 4010 C2' G F 4 OK 4012 4008 4011 4033 C2' A F 5 OK 4035 4031 4034 4055 C2' C F 6 OK 4057 4053 4056 4075 C2' G F 7 OK 4077 4073 4076 4098 C2' U F 8 OK 4100 4096 4099 4118 C2' C F 9 OK 4120 4116 4119 4138 C2' U F 10 OK 4140 4136 4139 4158 C2' A F 11 OK 4160 4156 4159 4180 C2' G F 12 OK 4182 4178 4181 4204 C2' C J 1 OK 4206 4202 4205 4224 C2' U J 2 OK 4226 4222 4225 4244 C2' A J 3 OK 4246 4242 4245 4266 C2' G J 4 OK 4268 4264 4267 4289 C2' A J 5 OK 4291 4287 4290 4311 C2' C J 6 OK 4313 4309 4312 4331 C2' G J 7 OK 4333 4329 4332 4354 C2' U J 8 OK 4356 4352 4355 4374 C2' C J 9 OK 4376 4372 4375 4394 C2' U J 10 OK 4396 4392 4395 4414 C2' A J 11 OK 4416 4412 4415 4436 C2' G J 12 OK 4438 4434 4437 4457 C2' C I 1 OK 4459 4455 4458 4477 C2' U I 2 OK 4479 4475 4478 4497 C2' A I 3 OK 4499 4495 4498 4519 C2' G I 4 OK 4521 4517 4520 4542 C2' A I 5 OK 4544 4540 4543 4564 C2' C I 6 OK 4566 4562 4565 4584 C2' G I 7 OK 4586 4582 4585 4607 C2' U I 8 OK 4609 4605 4608 4627 C2' C I 9 OK 4629 4625 4628 4647 C2' U I 10 OK 4649 4645 4648 4667 C2' A I 11 OK 4669 4665 4668 4689 C2' G I 12 OK 4691 4687 4690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3817 C3' C E 1 OK 3815 3818 3819 3837 C3' U E 2 OK 3835 3838 3839 3857 C3' A E 3 OK 3855 3858 3859 3879 C3' G E 4 OK 3877 3880 3881 3902 C3' A E 5 OK 3900 3903 3904 3924 C3' C E 6 OK 3922 3925 3926 3944 C3' G E 7 OK 3942 3945 3946 3967 C3' U E 8 OK 3965 3968 3969 3987 C3' C E 9 OK 3985 3988 3989 4008 C3' G F 4 OK 4006 4009 4010 4031 C3' A F 5 OK 4029 4032 4033 4053 C3' C F 6 OK 4051 4054 4055 4073 C3' G F 7 OK 4071 4074 4075 4096 C3' U F 8 OK 4094 4097 4098 4116 C3' C F 9 OK 4114 4117 4118 4136 C3' U F 10 OK 4134 4137 4138 4156 C3' A F 11 OK 4154 4157 4158 4178 C3' G F 12 OK 4176 4179 4180 4202 C3' C J 1 OK 4200 4203 4204 4222 C3' U J 2 OK 4220 4223 4224 4242 C3' A J 3 OK 4240 4243 4244 4264 C3' G J 4 OK 4262 4265 4266 4287 C3' A J 5 OK 4285 4288 4289 4309 C3' C J 6 OK 4307 4310 4311 4329 C3' G J 7 OK 4327 4330 4331 4352 C3' U J 8 OK 4350 4353 4354 4372 C3' C J 9 OK 4370 4373 4374 4392 C3' U J 10 OK 4390 4393 4394 4412 C3' A J 11 OK 4410 4413 4414 4434 C3' G J 12 OK 4432 4435 4436 4455 C3' C I 1 OK 4453 4456 4457 4475 C3' U I 2 OK 4473 4476 4477 4495 C3' A I 3 OK 4493 4496 4497 4517 C3' G I 4 OK 4515 4518 4519 4540 C3' A I 5 OK 4538 4541 4542 4562 C3' C I 6 OK 4560 4563 4564 4582 C3' G I 7 OK 4580 4583 4584 4605 C3' U I 8 OK 4603 4606 4607 4625 C3' C I 9 OK 4623 4626 4627 4645 C3' U I 10 OK 4643 4646 4647 4665 C3' A I 11 OK 4663 4666 4667 4687 C3' G I 12 OK 4685 4688 4689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3815 C4' C E 1 OK 3817 3814 3816 3835 C4' U E 2 OK 3837 3834 3836 3855 C4' A E 3 OK 3857 3854 3856 3877 C4' G E 4 OK 3879 3876 3878 3900 C4' A E 5 OK 3902 3899 3901 3922 C4' C E 6 OK 3924 3921 3923 3942 C4' G E 7 OK 3944 3941 3943 3965 C4' U E 8 OK 3967 3964 3966 3985 C4' C E 9 OK 3987 3984 3986 4006 C4' G F 4 OK 4008 4005 4007 4029 C4' A F 5 OK 4031 4028 4030 4051 C4' C F 6 OK 4053 4050 4052 4071 C4' G F 7 OK 4073 4070 4072 4094 C4' U F 8 OK 4096 4093 4095 4114 C4' C F 9 OK 4116 4113 4115 4134 C4' U F 10 OK 4136 4133 4135 4154 C4' A F 11 OK 4156 4153 4155 4176 C4' G F 12 OK 4178 4175 4177 4200 C4' C J 1 OK 4202 4199 4201 4220 C4' U J 2 OK 4222 4219 4221 4240 C4' A J 3 OK 4242 4239 4241 4262 C4' G J 4 OK 4264 4261 4263 4285 C4' A J 5 OK 4287 4284 4286 4307 C4' C J 6 OK 4309 4306 4308 4327 C4' G J 7 OK 4329 4326 4328 4350 C4' U J 8 OK 4352 4349 4351 4370 C4' C J 9 OK 4372 4369 4371 4390 C4' U J 10 OK 4392 4389 4391 4410 C4' A J 11 OK 4412 4409 4411 4432 C4' G J 12 OK 4434 4431 4433 4453 C4' C I 1 OK 4455 4452 4454 4473 C4' U I 2 OK 4475 4472 4474 4493 C4' A I 3 OK 4495 4492 4494 4515 C4' G I 4 OK 4517 4514 4516 4538 C4' A I 5 OK 4540 4537 4539 4560 C4' C I 6 OK 4562 4559 4561 4580 C4' G I 7 OK 4582 4579 4581 4603 C4' U I 8 OK 4605 4602 4604 4623 C4' C I 9 OK 4625 4622 4624 4643 C4' U I 10 OK 4645 4642 4644 4663 C4' A I 11 OK 4665 4662 4664 4685 C4' G I 12 OK 4687 4684 4686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3814 C5' C E 1 3813 3815 3834 C5' U E 2 3833 3835 3854 C5' A E 3 3853 3855 3876 C5' G E 4 3875 3877 3899 C5' A E 5 3898 3900 3921 C5' C E 6 3920 3922 3941 C5' G E 7 3940 3942 3964 C5' U E 8 3963 3965 3984 C5' C E 9 3983 3985 4005 C5' G F 4 4004 4006 4028 C5' A F 5 4027 4029 4050 C5' C F 6 4049 4051 4070 C5' G F 7 4069 4071 4093 C5' U F 8 4092 4094 4113 C5' C F 9 4112 4114 4133 C5' U F 10 4132 4134 4153 C5' A F 11 4152 4154 4175 C5' G F 12 4174 4176 4199 C5' C J 1 4198 4200 4219 C5' U J 2 4218 4220 4239 C5' A J 3 4238 4240 4261 C5' G J 4 4260 4262 4284 C5' A J 5 4283 4285 4306 C5' C J 6 4305 4307 4326 C5' G J 7 4325 4327 4349 C5' U J 8 4348 4350 4369 C5' C J 9 4368 4370 4389 C5' U J 10 4388 4390 4409 C5' A J 11 4408 4410 4431 C5' G J 12 4430 4432 4452 C5' C I 1 4451 4453 4472 C5' U I 2 4471 4473 4492 C5' A I 3 4491 4493 4514 C5' G I 4 4513 4515 4537 C5' A I 5 4536 4538 4559 C5' C I 6 4558 4560 4579 C5' G I 7 4578 4580 4602 C5' U I 8 4601 4603 4622 C5' C I 9 4621 4623 4642 C5' U I 10 4641 4643 4662 C5' A I 11 4661 4663 4684 C5' G I 12 4683 4685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3830 P U E 2 distorted distorted 3818 3831 3832 3833 3850 P A E 3 distorted distorted 3838 3851 3852 3853 3872 P G E 4 distorted distorted 3858 3873 3874 3875 3895 P A E 5 distorted distorted 3880 3896 3897 3898 3917 P C E 6 distorted distorted 3903 3918 3919 3920 3937 P G E 7 distorted distorted 3925 3938 3939 3940 3960 P U E 8 distorted distorted 3945 3961 3962 3963 3980 P C E 9 distorted distorted 3968 3981 3982 3983 4001 P G F 4 distorted distorted 4002 4003 4004 4024 P A F 5 distorted distorted 4009 4025 4026 4027 4046 P C F 6 distorted distorted 4032 4047 4048 4049 4066 P G F 7 distorted distorted 4054 4067 4068 4069 4089 P U F 8 distorted distorted 4074 4090 4091 4092 4109 P C F 9 distorted distorted 4097 4110 4111 4112 4129 P U F 10 distorted distorted 4117 4130 4131 4132 4149 P A F 11 distorted distorted 4137 4150 4151 4152 4171 P G F 12 distorted distorted 4157 4172 4173 4174 4195 P C J 1 distorted distorted 4196 4197 4198 4215 P U J 2 distorted distorted 4203 4216 4217 4218 4235 P A J 3 distorted distorted 4223 4236 4237 4238 4257 P G J 4 distorted distorted 4243 4258 4259 4260 4280 P A J 5 distorted distorted 4265 4281 4282 4283 4302 P C J 6 distorted distorted 4288 4303 4304 4305 4322 P G J 7 distorted distorted 4310 4323 4324 4325 4345 P U J 8 distorted distorted 4330 4346 4347 4348 4365 P C J 9 distorted distorted 4353 4366 4367 4368 4385 P U J 10 distorted distorted 4373 4386 4387 4388 4405 P A J 11 distorted distorted 4393 4406 4407 4408 4427 P G J 12 distorted distorted 4413 4428 4429 4430 4468 P U I 2 distorted distorted 4456 4469 4470 4471 4488 P A I 3 distorted distorted 4476 4489 4490 4491 4510 P G I 4 distorted distorted 4496 4511 4512 4513 4533 P A I 5 distorted distorted 4518 4534 4535 4536 4555 P C I 6 distorted distorted 4541 4556 4557 4558 4575 P G I 7 distorted distorted 4563 4576 4577 4578 4598 P U I 8 distorted distorted 4583 4599 4600 4601 4618 P C I 9 distorted distorted 4606 4619 4620 4621 4638 P U I 10 distorted distorted 4626 4639 4640 4641 4658 P A I 11 distorted distorted 4646 4659 4660 4661 4680 P G I 12 distorted distorted 4666 4681 4682 4683 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