ID code: '4M2Z' 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' --------------------------------------------------------------------------------- 3674 C1' A C 2 beta 3669 3675 3672 3696 C1' A C 3 beta 3691 3697 3694 3718 C1' G C 4 beta 3713 3719 3716 3741 C1' G C 5 beta 3736 3742 3739 3764 C1' U C 6 beta 3759 3765 3762 3784 C1' C C 7 beta 3779 3785 3782 3804 C1' A C 8 beta 3799 3805 3802 3826 C1' U C 9 beta 3821 3827 3824 3846 C1' U C 10 beta 3841 3847 3844 3866 C1' C C 11 beta 3861 3867 3864 3886 C1' G C 12 beta 3881 3887 3884 3909 C1' C C 13 beta 3904 3910 3907 3929 C1' A C 14 beta 3924 3930 3927 3951 C1' A C 15 beta 3946 3952 3949 3973 C1' G C 16 beta 3968 3974 3971 3996 C1' A C 17 beta 3991 3997 3994 4018 C1' G C 18 beta 4013 4019 4016 4041 C1' U C 19 beta 4036 4042 4039 4061 C1' G C 20 beta 4056 4062 4059 4084 C1' G C 21 beta 4079 4085 4082 4107 C1' C C 22 beta 4102 4108 4105 4127 C1' C C 23 beta 4122 4128 4125 4147 C1' U C 24 beta 4142 4148 4145 4167 C1' U C 25 beta 4162 4168 4165 4187 C1' G C 26 beta 4182 4188 4185 4210 C1' C C 27 beta 4205 4211 4208 4230 C1' G C 28 beta 4225 4231 4228 4255 C1' A D 2 beta 4250 4256 4253 4277 C1' A D 3 beta 4272 4278 4275 4299 C1' G D 4 beta 4294 4300 4297 4322 C1' G D 5 beta 4317 4323 4320 4345 C1' U D 6 beta 4340 4346 4343 4365 C1' C D 7 beta 4360 4366 4363 4385 C1' A D 8 beta 4380 4386 4383 4407 C1' U D 9 beta 4402 4408 4405 4427 C1' U D 10 beta 4422 4428 4425 4447 C1' C D 11 beta 4442 4448 4445 4467 C1' G D 12 beta 4462 4468 4465 4490 C1' C D 13 beta 4485 4491 4488 4510 C1' A D 14 beta 4505 4511 4508 4532 C1' A D 15 beta 4527 4533 4530 4554 C1' G D 16 beta 4549 4555 4552 4577 C1' A D 17 beta 4572 4578 4575 4599 C1' G D 18 beta 4594 4600 4597 4622 C1' U D 19 beta 4617 4623 4620 4642 C1' G D 20 beta 4637 4643 4640 4665 C1' G D 21 beta 4660 4666 4663 4688 C1' C D 22 beta 4683 4689 4686 4708 C1' C D 23 beta 4703 4709 4706 4728 C1' U D 24 beta 4723 4729 4726 4748 C1' U D 25 beta 4743 4749 4746 4768 C1' G D 26 beta 4763 4769 4766 4791 C1' C D 27 beta 4786 4792 4789 4811 C1' G D 28 beta 4806 4812 4809 4840 C1' C C 103 beta 4835 4841 4838 4863 C1' C D 103 beta 4858 4864 4861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3672 C2' A C 2 OK 3674 3670 3673 3694 C2' A C 3 OK 3696 3692 3695 3716 C2' G C 4 OK 3718 3714 3717 3739 C2' G C 5 OK 3741 3737 3740 3762 C2' U C 6 OK 3764 3760 3763 3782 C2' C C 7 OK 3784 3780 3783 3802 C2' A C 8 OK 3804 3800 3803 3824 C2' U C 9 OK 3826 3822 3825 3844 C2' U C 10 OK 3846 3842 3845 3864 C2' C C 11 OK 3866 3862 3865 3884 C2' G C 12 OK 3886 3882 3885 3907 C2' C C 13 OK 3909 3905 3908 3927 C2' A C 14 OK 3929 3925 3928 3949 C2' A C 15 OK 3951 3947 3950 3971 C2' G C 16 OK 3973 3969 3972 3994 C2' A C 17 OK 3996 3992 3995 4016 C2' G C 18 OK 4018 4014 4017 4039 C2' U C 19 OK 4041 4037 4040 4059 C2' G C 20 OK 4061 4057 4060 4082 C2' G C 21 OK 4084 4080 4083 4105 C2' C C 22 OK 4107 4103 4106 4125 C2' C C 23 OK 4127 4123 4126 4145 C2' U C 24 OK 4147 4143 4146 4165 C2' U C 25 OK 4167 4163 4166 4185 C2' G C 26 OK 4187 4183 4186 4208 C2' C C 27 OK 4210 4206 4209 4228 C2' G C 28 OK 4230 4226 4229 4253 C2' A D 2 OK 4255 4251 4254 4275 C2' A D 3 OK 4277 4273 4276 4297 C2' G D 4 OK 4299 4295 4298 4320 C2' G D 5 OK 4322 4318 4321 4343 C2' U D 6 OK 4345 4341 4344 4363 C2' C D 7 OK 4365 4361 4364 4383 C2' A D 8 OK 4385 4381 4384 4405 C2' U D 9 OK 4407 4403 4406 4425 C2' U D 10 OK 4427 4423 4426 4445 C2' C D 11 OK 4447 4443 4446 4465 C2' G D 12 OK 4467 4463 4466 4488 C2' C D 13 OK 4490 4486 4489 4508 C2' A D 14 OK 4510 4506 4509 4530 C2' A D 15 OK 4532 4528 4531 4552 C2' G D 16 OK 4554 4550 4553 4575 C2' A D 17 OK 4577 4573 4576 4597 C2' G D 18 OK 4599 4595 4598 4620 C2' U D 19 OK 4622 4618 4621 4640 C2' G D 20 OK 4642 4638 4641 4663 C2' G D 21 OK 4665 4661 4664 4686 C2' C D 22 OK 4688 4684 4687 4706 C2' C D 23 OK 4708 4704 4707 4726 C2' U D 24 OK 4728 4724 4727 4746 C2' U D 25 OK 4748 4744 4747 4766 C2' G D 26 OK 4768 4764 4767 4789 C2' C D 27 OK 4791 4787 4790 4809 C2' G D 28 OK 4811 4807 4810 4838 C2' C C 103 OK 4840 4836 4839 4861 C2' C D 103 OK 4863 4859 4862 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3670 C3' A C 2 OK 3668 3671 3672 3692 C3' A C 3 OK 3690 3693 3694 3714 C3' G C 4 OK 3712 3715 3716 3737 C3' G C 5 OK 3735 3738 3739 3760 C3' U C 6 OK 3758 3761 3762 3780 C3' C C 7 OK 3778 3781 3782 3800 C3' A C 8 OK 3798 3801 3802 3822 C3' U C 9 OK 3820 3823 3824 3842 C3' U C 10 OK 3840 3843 3844 3862 C3' C C 11 OK 3860 3863 3864 3882 C3' G C 12 OK 3880 3883 3884 3905 C3' C C 13 OK 3903 3906 3907 3925 C3' A C 14 OK 3923 3926 3927 3947 C3' A C 15 OK 3945 3948 3949 3969 C3' G C 16 OK 3967 3970 3971 3992 C3' A C 17 OK 3990 3993 3994 4014 C3' G C 18 OK 4012 4015 4016 4037 C3' U C 19 OK 4035 4038 4039 4057 C3' G C 20 OK 4055 4058 4059 4080 C3' G C 21 OK 4078 4081 4082 4103 C3' C C 22 OK 4101 4104 4105 4123 C3' C C 23 OK 4121 4124 4125 4143 C3' U C 24 OK 4141 4144 4145 4163 C3' U C 25 OK 4161 4164 4165 4183 C3' G C 26 OK 4181 4184 4185 4206 C3' C C 27 OK 4204 4207 4208 4226 C3' G C 28 OK 4224 4227 4228 4251 C3' A D 2 OK 4249 4252 4253 4273 C3' A D 3 OK 4271 4274 4275 4295 C3' G D 4 OK 4293 4296 4297 4318 C3' G D 5 OK 4316 4319 4320 4341 C3' U D 6 OK 4339 4342 4343 4361 C3' C D 7 OK 4359 4362 4363 4381 C3' A D 8 OK 4379 4382 4383 4403 C3' U D 9 OK 4401 4404 4405 4423 C3' U D 10 OK 4421 4424 4425 4443 C3' C D 11 OK 4441 4444 4445 4463 C3' G D 12 OK 4461 4464 4465 4486 C3' C D 13 OK 4484 4487 4488 4506 C3' A D 14 OK 4504 4507 4508 4528 C3' A D 15 OK 4526 4529 4530 4550 C3' G D 16 OK 4548 4551 4552 4573 C3' A D 17 OK 4571 4574 4575 4595 C3' G D 18 OK 4593 4596 4597 4618 C3' U D 19 OK 4616 4619 4620 4638 C3' G D 20 OK 4636 4639 4640 4661 C3' G D 21 OK 4659 4662 4663 4684 C3' C D 22 OK 4682 4685 4686 4704 C3' C D 23 OK 4702 4705 4706 4724 C3' U D 24 OK 4722 4725 4726 4744 C3' U D 25 OK 4742 4745 4746 4764 C3' G D 26 OK 4762 4765 4766 4787 C3' C D 27 OK 4785 4788 4789 4807 C3' G D 28 OK 4805 4808 4809 4836 C3' C C 103 OK 4834 4837 4838 4859 C3' C D 103 OK 4857 4860 4861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3668 C4' A C 2 OK 3670 3667 3669 3690 C4' A C 3 OK 3692 3689 3691 3712 C4' G C 4 OK 3714 3711 3713 3735 C4' G C 5 OK 3737 3734 3736 3758 C4' U C 6 OK 3760 3757 3759 3778 C4' C C 7 OK 3780 3777 3779 3798 C4' A C 8 OK 3800 3797 3799 3820 C4' U C 9 OK 3822 3819 3821 3840 C4' U C 10 OK 3842 3839 3841 3860 C4' C C 11 OK 3862 3859 3861 3880 C4' G C 12 OK 3882 3879 3881 3903 C4' C C 13 OK 3905 3902 3904 3923 C4' A C 14 OK 3925 3922 3924 3945 C4' A C 15 OK 3947 3944 3946 3967 C4' G C 16 OK 3969 3966 3968 3990 C4' A C 17 OK 3992 3989 3991 4012 C4' G C 18 OK 4014 4011 4013 4035 C4' U C 19 OK 4037 4034 4036 4055 C4' G C 20 OK 4057 4054 4056 4078 C4' G C 21 OK 4080 4077 4079 4101 C4' C C 22 OK 4103 4100 4102 4121 C4' C C 23 OK 4123 4120 4122 4141 C4' U C 24 OK 4143 4140 4142 4161 C4' U C 25 OK 4163 4160 4162 4181 C4' G C 26 OK 4183 4180 4182 4204 C4' C C 27 OK 4206 4203 4205 4224 C4' G C 28 OK 4226 4223 4225 4249 C4' A D 2 OK 4251 4248 4250 4271 C4' A D 3 OK 4273 4270 4272 4293 C4' G D 4 OK 4295 4292 4294 4316 C4' G D 5 OK 4318 4315 4317 4339 C4' U D 6 OK 4341 4338 4340 4359 C4' C D 7 OK 4361 4358 4360 4379 C4' A D 8 OK 4381 4378 4380 4401 C4' U D 9 OK 4403 4400 4402 4421 C4' U D 10 OK 4423 4420 4422 4441 C4' C D 11 OK 4443 4440 4442 4461 C4' G D 12 OK 4463 4460 4462 4484 C4' C D 13 OK 4486 4483 4485 4504 C4' A D 14 OK 4506 4503 4505 4526 C4' A D 15 OK 4528 4525 4527 4548 C4' G D 16 OK 4550 4547 4549 4571 C4' A D 17 OK 4573 4570 4572 4593 C4' G D 18 OK 4595 4592 4594 4616 C4' U D 19 OK 4618 4615 4617 4636 C4' G D 20 OK 4638 4635 4637 4659 C4' G D 21 OK 4661 4658 4660 4682 C4' C D 22 OK 4684 4681 4683 4702 C4' C D 23 OK 4704 4701 4703 4722 C4' U D 24 OK 4724 4721 4723 4742 C4' U D 25 OK 4744 4741 4743 4762 C4' G D 26 OK 4764 4761 4763 4785 C4' C D 27 OK 4787 4784 4786 4805 C4' G D 28 OK 4807 4804 4806 4834 C4' C C 103 OK 4836 4833 4835 4857 C4' C D 103 OK 4859 4856 4858 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3667 C5' A C 2 3666 3668 3689 C5' A C 3 3688 3690 3711 C5' G C 4 3710 3712 3734 C5' G C 5 3733 3735 3757 C5' U C 6 3756 3758 3777 C5' C C 7 3776 3778 3797 C5' A C 8 3796 3798 3819 C5' U C 9 3818 3820 3839 C5' U C 10 3838 3840 3859 C5' C C 11 3858 3860 3879 C5' G C 12 3878 3880 3902 C5' C C 13 3901 3903 3922 C5' A C 14 3921 3923 3944 C5' A C 15 3943 3945 3966 C5' G C 16 3965 3967 3989 C5' A C 17 3988 3990 4011 C5' G C 18 4010 4012 4034 C5' U C 19 4033 4035 4054 C5' G C 20 4053 4055 4077 C5' G C 21 4076 4078 4100 C5' C C 22 4099 4101 4120 C5' C C 23 4119 4121 4140 C5' U C 24 4139 4141 4160 C5' U C 25 4159 4161 4180 C5' G C 26 4179 4181 4203 C5' C C 27 4202 4204 4223 C5' G C 28 4222 4224 4248 C5' A D 2 4247 4249 4270 C5' A D 3 4269 4271 4292 C5' G D 4 4291 4293 4315 C5' G D 5 4314 4316 4338 C5' U D 6 4337 4339 4358 C5' C D 7 4357 4359 4378 C5' A D 8 4377 4379 4400 C5' U D 9 4399 4401 4420 C5' U D 10 4419 4421 4440 C5' C D 11 4439 4441 4460 C5' G D 12 4459 4461 4483 C5' C D 13 4482 4484 4503 C5' A D 14 4502 4504 4525 C5' A D 15 4524 4526 4547 C5' G D 16 4546 4548 4570 C5' A D 17 4569 4571 4592 C5' G D 18 4591 4593 4615 C5' U D 19 4614 4616 4635 C5' G D 20 4634 4636 4658 C5' G D 21 4657 4659 4681 C5' C D 22 4680 4682 4701 C5' C D 23 4700 4702 4721 C5' U D 24 4720 4722 4741 C5' U D 25 4740 4742 4761 C5' G D 26 4760 4762 4784 C5' C D 27 4783 4785 4804 C5' G D 28 4803 4805 4833 C5' C C 103 4832 4834 4856 C5' C D 103 4855 4857 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3663 P A C 2 distorted distorted 3664 3665 3666 3685 P A C 3 distorted distorted 3671 3686 3687 3688 3707 P G C 4 distorted distorted 3693 3708 3709 3710 3730 P G C 5 distorted distorted 3715 3731 3732 3733 3753 P U C 6 distorted distorted 3738 3754 3755 3756 3773 P C C 7 distorted distorted 3761 3774 3775 3776 3793 P A C 8 distorted distorted 3781 3794 3795 3796 3815 P U C 9 distorted distorted 3801 3816 3817 3818 3835 P U C 10 distorted distorted 3823 3836 3837 3838 3855 P C C 11 distorted distorted 3843 3856 3857 3858 3875 P G C 12 distorted distorted 3863 3876 3877 3878 3898 P C C 13 distorted distorted 3883 3899 3900 3901 3918 P A C 14 distorted distorted 3906 3919 3920 3921 3940 P A C 15 distorted distorted 3926 3941 3942 3943 3962 P G C 16 distorted distorted 3948 3963 3964 3965 3985 P A C 17 distorted distorted 3970 3986 3987 3988 4007 P G C 18 distorted distorted 3993 4008 4009 4010 4030 P U C 19 distorted distorted 4015 4031 4032 4033 4050 P G C 20 distorted distorted 4038 4051 4052 4053 4073 P G C 21 distorted distorted 4058 4074 4075 4076 4096 P C C 22 distorted distorted 4081 4097 4098 4099 4116 P C C 23 distorted distorted 4104 4117 4118 4119 4136 P U C 24 distorted distorted 4124 4137 4138 4139 4156 P U C 25 distorted distorted 4144 4157 4158 4159 4176 P G C 26 distorted distorted 4164 4177 4178 4179 4199 P C C 27 distorted distorted 4184 4200 4201 4202 4219 P G C 28 distorted distorted 4207 4220 4221 4222 4244 P A D 2 distorted distorted 4245 4246 4247 4266 P A D 3 distorted distorted 4252 4267 4268 4269 4288 P G D 4 distorted distorted 4274 4289 4290 4291 4311 P G D 5 distorted distorted 4296 4312 4313 4314 4334 P U D 6 distorted distorted 4319 4335 4336 4337 4354 P C D 7 distorted distorted 4342 4355 4356 4357 4374 P A D 8 distorted distorted 4362 4375 4376 4377 4396 P U D 9 distorted distorted 4382 4397 4398 4399 4416 P U D 10 distorted distorted 4404 4417 4418 4419 4436 P C D 11 distorted distorted 4424 4437 4438 4439 4456 P G D 12 distorted distorted 4444 4457 4458 4459 4479 P C D 13 distorted distorted 4464 4480 4481 4482 4499 P A D 14 distorted distorted 4487 4500 4501 4502 4521 P A D 15 distorted distorted 4507 4522 4523 4524 4543 P G D 16 distorted distorted 4529 4544 4545 4546 4566 P A D 17 distorted distorted 4551 4567 4568 4569 4588 P G D 18 distorted distorted 4574 4589 4590 4591 4611 P U D 19 distorted distorted 4596 4612 4613 4614 4631 P G D 20 distorted distorted 4619 4632 4633 4634 4654 P G D 21 distorted distorted 4639 4655 4656 4657 4677 P C D 22 distorted distorted 4662 4678 4679 4680 4697 P C D 23 distorted distorted 4685 4698 4699 4700 4717 P U D 24 distorted distorted 4705 4718 4719 4720 4737 P U D 25 distorted distorted 4725 4738 4739 4740 4757 P G D 26 distorted distorted 4745 4758 4759 4760 4780 P C D 27 distorted distorted 4765 4781 4782 4783 4800 P G D 28 distorted distorted 4788 4801 4802 4803 4829 P C C 103 distorted distorted 4830 4831 4832 4852 P C D 103 distorted distorted 4853 4854 4855 ---------------------------------------------------------------------------------