ID code: '1A35' 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' --------------------------------------------------------------------------------- 3787 C1' A C 1 beta 3783 3788 3786 3808 C1' A C 2 beta 3804 3809 3807 3829 C1' A C 3 beta 3825 3830 3828 3850 C1' A C 4 beta 3846 3851 3849 3871 C1' A C 5 beta 3867 3872 3870 3892 C1' G C 6 beta 3888 3893 3891 3914 C1' A C 7 beta 3910 3915 3913 3935 C1' C C 8 beta 3931 3936 3934 3954 C1' T C 9 beta 3950 3955 3953 3974 C1' T C 10 beta 3970 3975 3973 3994 C1' A C 11 beta 3990 3995 3993 4015 C1' G C 12 beta 4011 4016 4014 4037 C1' A C 13 beta 4033 4038 4036 4058 C1' A C 14 beta 4054 4059 4057 4079 C1' A C 15 beta 4075 4080 4078 4100 C1' A C 16 beta 4096 4101 4099 4121 C1' A C 17 beta 4117 4122 4120 4141 C1' BRU C 18 beta 4146 4132 4142 4161 C1' BRU C 19 beta 4166 4152 4162 4182 C1' T C 20 beta 4178 4183 4181 4202 C1' T C 21 beta 4198 4203 4201 4222 C1' T C 22 beta 4218 4223 4221 4240 C1' A D 101 beta 4236 4241 4239 4261 C1' A D 102 beta 4257 4262 4260 4282 C1' A D 103 beta 4278 4283 4281 4303 C1' A D 104 beta 4299 4304 4302 4324 C1' A D 105 beta 4320 4325 4323 4345 C1' T D 106 beta 4341 4346 4344 4364 C1' BRU D 107 beta 4369 4355 4365 4384 C1' BRU D 108 beta 4389 4375 4385 4404 C1' BRU D 109 beta 4409 4395 4405 4424 C1' BRU D 110 beta 4429 4415 4425 4445 C1' C D 111 beta 4441 4446 4444 4463 C1' BRU D 112 beta 4468 4454 4464 4484 C1' A D 113 beta 4480 4485 4483 4505 C1' A D 114 beta 4501 4506 4504 4526 C1' G D 115 beta 4522 4527 4525 4548 C1' T D 116 beta 4544 4549 4547 4568 C1' C D 117 beta 4564 4569 4567 4587 C1' T D 118 beta 4583 4588 4586 4607 C1' T D 119 beta 4603 4608 4606 4627 C1' T D 120 beta 4623 4628 4626 4646 C1' BRU D 121 beta 4651 4637 4647 4667 C1' T D 122 beta 4663 4668 4666 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3786 C2' A C 1 3787 3784 3807 C2' A C 2 3808 3805 3828 C2' A C 3 3829 3826 3849 C2' A C 4 3850 3847 3870 C2' A C 5 3871 3868 3891 C2' G C 6 3892 3889 3913 C2' A C 7 3914 3911 3934 C2' C C 8 3935 3932 3953 C2' T C 9 3954 3951 3973 C2' T C 10 3974 3971 3993 C2' A C 11 3994 3991 4014 C2' G C 12 4015 4012 4036 C2' A C 13 4037 4034 4057 C2' A C 14 4058 4055 4078 C2' A C 15 4079 4076 4099 C2' A C 16 4100 4097 4120 C2' A C 17 4121 4118 4142 C2' BRU C 18 4141 4143 4162 C2' BRU C 19 4161 4163 4181 C2' T C 20 4182 4179 4201 C2' T C 21 4202 4199 4221 C2' T C 22 4222 4219 4239 C2' A D 101 4240 4237 4260 C2' A D 102 4261 4258 4281 C2' A D 103 4282 4279 4302 C2' A D 104 4303 4300 4323 C2' A D 105 4324 4321 4344 C2' T D 106 4345 4342 4365 C2' BRU D 107 4364 4366 4385 C2' BRU D 108 4384 4386 4405 C2' BRU D 109 4404 4406 4425 C2' BRU D 110 4424 4426 4444 C2' C D 111 4445 4442 4464 C2' BRU D 112 4463 4465 4483 C2' A D 113 4484 4481 4504 C2' A D 114 4505 4502 4525 C2' G D 115 4526 4523 4547 C2' T D 116 4548 4545 4567 C2' C D 117 4568 4565 4586 C2' T D 118 4587 4584 4606 C2' T D 119 4607 4604 4626 C2' T D 120 4627 4624 4647 C2' BRU D 121 4646 4648 4666 C2' T D 122 4667 4664 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3784 C3' A C 1 OK 3782 3785 3786 3805 C3' A C 2 OK 3803 3806 3807 3826 C3' A C 3 OK 3824 3827 3828 3847 C3' A C 4 OK 3845 3848 3849 3868 C3' A C 5 OK 3866 3869 3870 3889 C3' G C 6 OK 3887 3890 3891 3911 C3' A C 7 OK 3909 3912 3913 3932 C3' C C 8 OK 3930 3933 3934 3951 C3' T C 9 OK 3949 3952 3953 3971 C3' T C 10 OK 3969 3972 3973 3991 C3' A C 11 OK 3989 3992 3993 4012 C3' G C 12 OK 4010 4013 4014 4034 C3' A C 13 OK 4032 4035 4036 4055 C3' A C 14 OK 4053 4056 4057 4076 C3' A C 15 OK 4074 4077 4078 4097 C3' A C 16 OK 4095 4098 4099 4118 C3' A C 17 OK 4116 4119 4120 4143 C3' BRU C 18 OK 4144 4145 4142 4163 C3' BRU C 19 OK 4164 4165 4162 4179 C3' T C 20 OK 4177 4180 4181 4199 C3' T C 21 OK 4197 4200 4201 4219 C3' T C 22 OK 4217 4220 4221 4237 C3' A D 101 OK 4235 4238 4239 4258 C3' A D 102 OK 4256 4259 4260 4279 C3' A D 103 OK 4277 4280 4281 4300 C3' A D 104 OK 4298 4301 4302 4321 C3' A D 105 OK 4319 4322 4323 4342 C3' T D 106 OK 4340 4343 4344 4366 C3' BRU D 107 OK 4367 4368 4365 4386 C3' BRU D 108 OK 4387 4388 4385 4406 C3' BRU D 109 OK 4407 4408 4405 4426 C3' BRU D 110 OK 4427 4428 4425 4442 C3' C D 111 OK 4440 4443 4444 4465 C3' BRU D 112 OK 4466 4467 4464 4481 C3' A D 113 OK 4479 4482 4483 4502 C3' A D 114 OK 4500 4503 4504 4523 C3' G D 115 OK 4521 4524 4525 4545 C3' T D 116 OK 4543 4546 4547 4565 C3' C D 117 OK 4563 4566 4567 4584 C3' T D 118 OK 4582 4585 4586 4604 C3' T D 119 OK 4602 4605 4606 4624 C3' T D 120 OK 4622 4625 4626 4648 C3' BRU D 121 OK 4649 4650 4647 4664 C3' T D 122 OK 4662 4665 4666 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3782 C4' A C 1 OK 3784 3781 3783 3803 C4' A C 2 OK 3805 3802 3804 3824 C4' A C 3 OK 3826 3823 3825 3845 C4' A C 4 OK 3847 3844 3846 3866 C4' A C 5 OK 3868 3865 3867 3887 C4' G C 6 OK 3889 3886 3888 3909 C4' A C 7 OK 3911 3908 3910 3930 C4' C C 8 OK 3932 3929 3931 3949 C4' T C 9 OK 3951 3948 3950 3969 C4' T C 10 OK 3971 3968 3970 3989 C4' A C 11 OK 3991 3988 3990 4010 C4' G C 12 OK 4012 4009 4011 4032 C4' A C 13 OK 4034 4031 4033 4053 C4' A C 14 OK 4055 4052 4054 4074 C4' A C 15 OK 4076 4073 4075 4095 C4' A C 16 OK 4097 4094 4096 4116 C4' A C 17 OK 4118 4115 4117 4144 C4' BRU C 18 OK 4143 4147 4146 4164 C4' BRU C 19 OK 4163 4167 4166 4177 C4' T C 20 OK 4179 4176 4178 4197 C4' T C 21 OK 4199 4196 4198 4217 C4' T C 22 OK 4219 4216 4218 4235 C4' A D 101 OK 4237 4234 4236 4256 C4' A D 102 OK 4258 4255 4257 4277 C4' A D 103 OK 4279 4276 4278 4298 C4' A D 104 OK 4300 4297 4299 4319 C4' A D 105 OK 4321 4318 4320 4340 C4' T D 106 OK 4342 4339 4341 4367 C4' BRU D 107 OK 4366 4370 4369 4387 C4' BRU D 108 OK 4386 4390 4389 4407 C4' BRU D 109 OK 4406 4410 4409 4427 C4' BRU D 110 OK 4426 4430 4429 4440 C4' C D 111 OK 4442 4439 4441 4466 C4' BRU D 112 OK 4465 4469 4468 4479 C4' A D 113 OK 4481 4478 4480 4500 C4' A D 114 OK 4502 4499 4501 4521 C4' G D 115 OK 4523 4520 4522 4543 C4' T D 116 OK 4545 4542 4544 4563 C4' C D 117 OK 4565 4562 4564 4582 C4' T D 118 OK 4584 4581 4583 4602 C4' T D 119 OK 4604 4601 4603 4622 C4' T D 120 OK 4624 4621 4623 4649 C4' BRU D 121 OK 4648 4652 4651 4662 C4' T D 122 OK 4664 4661 4663 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3781 C5' A C 1 3780 3782 3802 C5' A C 2 3801 3803 3823 C5' A C 3 3822 3824 3844 C5' A C 4 3843 3845 3865 C5' A C 5 3864 3866 3886 C5' G C 6 3885 3887 3908 C5' A C 7 3907 3909 3929 C5' C C 8 3928 3930 3948 C5' T C 9 3947 3949 3968 C5' T C 10 3967 3969 3988 C5' A C 11 3987 3989 4009 C5' G C 12 4008 4010 4031 C5' A C 13 4030 4032 4052 C5' A C 14 4051 4053 4073 C5' A C 15 4072 4074 4094 C5' A C 16 4093 4095 4115 C5' A C 17 4114 4116 4147 C5' BRU C 18 4148 4144 4167 C5' BRU C 19 4168 4164 4176 C5' T C 20 4175 4177 4196 C5' T C 21 4195 4197 4216 C5' T C 22 4215 4217 4234 C5' A D 101 4233 4235 4255 C5' A D 102 4254 4256 4276 C5' A D 103 4275 4277 4297 C5' A D 104 4296 4298 4318 C5' A D 105 4317 4319 4339 C5' T D 106 4338 4340 4370 C5' BRU D 107 4371 4367 4390 C5' BRU D 108 4391 4387 4410 C5' BRU D 109 4411 4407 4430 C5' BRU D 110 4431 4427 4439 C5' C D 111 4438 4440 4469 C5' BRU D 112 4470 4466 4478 C5' A D 113 4477 4479 4499 C5' A D 114 4498 4500 4520 C5' G D 115 4519 4521 4542 C5' T D 116 4541 4543 4562 C5' C D 117 4561 4563 4581 C5' T D 118 4580 4582 4601 C5' T D 119 4600 4602 4621 C5' T D 120 4620 4622 4652 C5' BRU D 121 4653 4649 4661 C5' T D 122 4660 4662 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3798 P A C 2 distorted distorted 3785 3799 3800 3801 3819 P A C 3 distorted distorted 3806 3820 3821 3822 3840 P A C 4 distorted distorted 3827 3841 3842 3843 3861 P A C 5 distorted distorted 3848 3862 3863 3864 3882 P G C 6 OK OK 3869 3883 3884 3885 3904 P A C 7 distorted distorted 3890 3905 3906 3907 3925 P C C 8 distorted distorted 3912 3926 3927 3928 3944 P T C 9 distorted distorted 3933 3945 3946 3947 3964 P T C 10 distorted distorted 3952 3965 3966 3967 3984 P A C 11 distorted distorted 3972 3985 3986 3987 4005 P G C 12 distorted distorted 3992 4006 4007 4008 4027 P A C 13 distorted distorted 4013 4028 4029 4030 4048 P A C 14 distorted distorted 4035 4049 4050 4051 4069 P A C 15 distorted distorted 4056 4070 4071 4072 4090 P A C 16 distorted distorted 4077 4091 4092 4093 4111 P A C 17 distorted distorted 4098 4112 4113 4114 4149 P BRU C 18 distorted distorted 4119 4150 4151 4148 4169 P BRU C 19 distorted distorted 4145 4170 4171 4168 4172 P T C 20 distorted distorted 4165 4173 4174 4175 4192 P T C 21 distorted distorted 4180 4193 4194 4195 4212 P T C 22 distorted distorted 4200 4213 4214 4215 4251 P A D 102 distorted distorted 4238 4252 4253 4254 4272 P A D 103 distorted distorted 4259 4273 4274 4275 4293 P A D 104 distorted distorted 4280 4294 4295 4296 4314 P A D 105 distorted distorted 4301 4315 4316 4317 4335 P T D 106 distorted distorted 4322 4336 4337 4338 4372 P BRU D 107 distorted distorted 4343 4373 4374 4371 4392 P BRU D 108 distorted distorted 4368 4393 4394 4391 4412 P BRU D 109 distorted distorted 4388 4413 4414 4411 4432 P BRU D 110 distorted distorted 4408 4433 4434 4431 4435 P C D 111 distorted distorted 4428 4436 4437 4438 4471 P BRU D 112 distorted distorted 4443 4472 4473 4470 4474 P A D 113 distorted distorted 4467 4475 4476 4477 4495 P A D 114 distorted distorted 4482 4496 4497 4498 4516 P G D 115 distorted distorted 4503 4517 4518 4519 4538 P T D 116 distorted distorted 4524 4539 4540 4541 4558 P C D 117 distorted distorted 4546 4559 4560 4561 4577 P T D 118 distorted distorted 4566 4578 4579 4580 4597 P T D 119 distorted distorted 4585 4598 4599 4600 4617 P T D 120 distorted distorted 4605 4618 4619 4620 4654 P BRU D 121 distorted distorted 4625 4655 4656 4653 4657 P T D 122 distorted distorted 4650 4658 4659 4660 ---------------------------------------------------------------------------------