ID code: '5AXN' 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' --------------------------------------------------------------------------------- 3780 C1' GTP P 2 beta 3775 3781 3778 3803 C1' G P 3 beta 3798 3804 3801 3826 C1' G P 4 beta 3821 3827 3824 3849 C1' A P 5 beta 3844 3850 3847 3871 C1' U P 6 beta 3866 3872 3869 3891 C1' U P 7 beta 3886 3892 3889 3911 C1' U P 8 beta 3906 3912 3909 3931 C1' A P 9 beta 3926 3932 3929 3953 C1' G P 10 beta 3948 3954 3951 3976 C1' C P 11 beta 3971 3977 3974 3996 C1' U P 12 beta 3991 3997 3994 4016 C1' C P 13 beta 4011 4017 4014 4036 C1' A P 14 beta 4031 4037 4034 4058 C1' G P 15 beta 4053 4059 4056 4081 C1' U P 16 beta 4076 4082 4079 4101 C1' U P 17 beta 4096 4102 4099 4121 C1' G P 18 beta 4116 4122 4119 4144 C1' G P 19 beta 4139 4145 4142 4167 C1' G P 20 beta 4162 4168 4165 4190 C1' A P 21 beta 4185 4191 4188 4212 C1' G P 22 beta 4207 4213 4210 4235 C1' A P 23 beta 4230 4236 4233 4257 C1' G P 24 beta 4252 4258 4255 4280 C1' C P 25 beta 4275 4281 4278 4300 C1' G P 26 beta 4295 4301 4298 4323 C1' C P 27 beta 4318 4324 4321 4343 C1' C P 28 beta 4338 4344 4341 4363 C1' A P 29 beta 4358 4364 4361 4385 C1' G P 30 beta 4380 4386 4383 4408 C1' A P 38 beta 4403 4409 4406 4430 C1' U P 39 beta 4425 4431 4428 4450 C1' C P 40 beta 4445 4451 4448 4470 C1' U P 41 beta 4465 4471 4468 4490 C1' G P 42 beta 4485 4491 4488 4513 C1' G P 43 beta 4508 4514 4511 4536 C1' A P 44 beta 4531 4537 4534 4558 C1' G P 45 beta 4553 4559 4556 4581 C1' G P 46 beta 4576 4582 4579 4604 C1' U P 47 beta 4599 4605 4602 4624 C1' C P 48 beta 4619 4625 4622 4644 C1' C P 49 beta 4639 4645 4642 4664 C1' U P 50 beta 4659 4665 4662 4684 C1' G P 51 beta 4679 4685 4682 4707 C1' U P 52 beta 4702 4708 4705 4727 C1' G P 53 beta 4722 4728 4725 4750 C1' U P 54 beta 4745 4751 4748 4770 C1' U P 55 beta 4765 4771 4768 4790 C1' C P 56 beta 4785 4791 4788 4810 C1' G P 57 beta 4805 4811 4808 4833 C1' A P 58 beta 4828 4834 4831 4855 C1' U P 59 beta 4850 4856 4853 4875 C1' C P 60 beta 4870 4876 4873 4895 C1' C P 61 beta 4890 4896 4893 4915 C1' A P 62 beta 4910 4916 4913 4937 C1' C P 63 beta 4932 4938 4935 4957 C1' A P 64 beta 4952 4958 4955 4979 C1' G P 65 beta 4974 4980 4977 5002 C1' A P 66 beta 4997 5003 5000 5024 C1' A P 67 beta 5019 5025 5022 5046 C1' U P 68 beta 5041 5047 5044 5066 C1' C P 69 beta 5061 5067 5064 5086 C1' C P 70 beta 5081 5087 5084 5106 C1' C P 71 beta 5101 5107 5104 5126 C1' C P 72 beta 5121 5127 5124 5146 C1' A P 73 beta 5141 5147 5144 5168 C1' C P 74 beta 5163 5169 5166 5201 C1' GNP A 304 beta 5196 5202 5199 5233 C1' GNP B 301 beta 5228 5234 5231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3778 C2' GTP P 2 OK 3780 3776 3779 3801 C2' G P 3 OK 3803 3799 3802 3824 C2' G P 4 OK 3826 3822 3825 3847 C2' A P 5 OK 3849 3845 3848 3869 C2' U P 6 OK 3871 3867 3870 3889 C2' U P 7 OK 3891 3887 3890 3909 C2' U P 8 OK 3911 3907 3910 3929 C2' A P 9 OK 3931 3927 3930 3951 C2' G P 10 OK 3953 3949 3952 3974 C2' C P 11 OK 3976 3972 3975 3994 C2' U P 12 OK 3996 3992 3995 4014 C2' C P 13 OK 4016 4012 4015 4034 C2' A P 14 OK 4036 4032 4035 4056 C2' G P 15 OK 4058 4054 4057 4079 C2' U P 16 OK 4081 4077 4080 4099 C2' U P 17 OK 4101 4097 4100 4119 C2' G P 18 OK 4121 4117 4120 4142 C2' G P 19 OK 4144 4140 4143 4165 C2' G P 20 OK 4167 4163 4166 4188 C2' A P 21 OK 4190 4186 4189 4210 C2' G P 22 OK 4212 4208 4211 4233 C2' A P 23 OK 4235 4231 4234 4255 C2' G P 24 OK 4257 4253 4256 4278 C2' C P 25 OK 4280 4276 4279 4298 C2' G P 26 OK 4300 4296 4299 4321 C2' C P 27 OK 4323 4319 4322 4341 C2' C P 28 OK 4343 4339 4342 4361 C2' A P 29 OK 4363 4359 4362 4383 C2' G P 30 OK 4385 4381 4384 4406 C2' A P 38 OK 4408 4404 4407 4428 C2' U P 39 OK 4430 4426 4429 4448 C2' C P 40 OK 4450 4446 4449 4468 C2' U P 41 OK 4470 4466 4469 4488 C2' G P 42 OK 4490 4486 4489 4511 C2' G P 43 OK 4513 4509 4512 4534 C2' A P 44 OK 4536 4532 4535 4556 C2' G P 45 OK 4558 4554 4557 4579 C2' G P 46 OK 4581 4577 4580 4602 C2' U P 47 OK 4604 4600 4603 4622 C2' C P 48 OK 4624 4620 4623 4642 C2' C P 49 OK 4644 4640 4643 4662 C2' U P 50 OK 4664 4660 4663 4682 C2' G P 51 OK 4684 4680 4683 4705 C2' U P 52 OK 4707 4703 4706 4725 C2' G P 53 OK 4727 4723 4726 4748 C2' U P 54 OK 4750 4746 4749 4768 C2' U P 55 OK 4770 4766 4769 4788 C2' C P 56 OK 4790 4786 4789 4808 C2' G P 57 OK 4810 4806 4809 4831 C2' A P 58 OK 4833 4829 4832 4853 C2' U P 59 OK 4855 4851 4854 4873 C2' C P 60 OK 4875 4871 4874 4893 C2' C P 61 OK 4895 4891 4894 4913 C2' A P 62 OK 4915 4911 4914 4935 C2' C P 63 OK 4937 4933 4936 4955 C2' A P 64 OK 4957 4953 4956 4977 C2' G P 65 OK 4979 4975 4978 5000 C2' A P 66 OK 5002 4998 5001 5022 C2' A P 67 OK 5024 5020 5023 5044 C2' U P 68 OK 5046 5042 5045 5064 C2' C P 69 OK 5066 5062 5065 5084 C2' C P 70 OK 5086 5082 5085 5104 C2' C P 71 OK 5106 5102 5105 5124 C2' C P 72 OK 5126 5122 5125 5144 C2' A P 73 OK 5146 5142 5145 5166 C2' C P 74 OK 5168 5164 5167 5199 C2' GNP A 304 OK 5201 5197 5200 5231 C2' GNP B 301 OK 5233 5229 5232 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3776 C3' GTP P 2 OK 3774 3777 3778 3799 C3' G P 3 OK 3797 3800 3801 3822 C3' G P 4 OK 3820 3823 3824 3845 C3' A P 5 OK 3843 3846 3847 3867 C3' U P 6 OK 3865 3868 3869 3887 C3' U P 7 OK 3885 3888 3889 3907 C3' U P 8 OK 3905 3908 3909 3927 C3' A P 9 OK 3925 3928 3929 3949 C3' G P 10 OK 3947 3950 3951 3972 C3' C P 11 OK 3970 3973 3974 3992 C3' U P 12 OK 3990 3993 3994 4012 C3' C P 13 OK 4010 4013 4014 4032 C3' A P 14 OK 4030 4033 4034 4054 C3' G P 15 OK 4052 4055 4056 4077 C3' U P 16 OK 4075 4078 4079 4097 C3' U P 17 OK 4095 4098 4099 4117 C3' G P 18 OK 4115 4118 4119 4140 C3' G P 19 OK 4138 4141 4142 4163 C3' G P 20 OK 4161 4164 4165 4186 C3' A P 21 OK 4184 4187 4188 4208 C3' G P 22 OK 4206 4209 4210 4231 C3' A P 23 OK 4229 4232 4233 4253 C3' G P 24 OK 4251 4254 4255 4276 C3' C P 25 OK 4274 4277 4278 4296 C3' G P 26 OK 4294 4297 4298 4319 C3' C P 27 OK 4317 4320 4321 4339 C3' C P 28 OK 4337 4340 4341 4359 C3' A P 29 OK 4357 4360 4361 4381 C3' G P 30 OK 4379 4382 4383 4404 C3' A P 38 OK 4402 4405 4406 4426 C3' U P 39 OK 4424 4427 4428 4446 C3' C P 40 OK 4444 4447 4448 4466 C3' U P 41 OK 4464 4467 4468 4486 C3' G P 42 OK 4484 4487 4488 4509 C3' G P 43 OK 4507 4510 4511 4532 C3' A P 44 OK 4530 4533 4534 4554 C3' G P 45 OK 4552 4555 4556 4577 C3' G P 46 OK 4575 4578 4579 4600 C3' U P 47 OK 4598 4601 4602 4620 C3' C P 48 OK 4618 4621 4622 4640 C3' C P 49 OK 4638 4641 4642 4660 C3' U P 50 OK 4658 4661 4662 4680 C3' G P 51 OK 4678 4681 4682 4703 C3' U P 52 OK 4701 4704 4705 4723 C3' G P 53 OK 4721 4724 4725 4746 C3' U P 54 OK 4744 4747 4748 4766 C3' U P 55 OK 4764 4767 4768 4786 C3' C P 56 OK 4784 4787 4788 4806 C3' G P 57 OK 4804 4807 4808 4829 C3' A P 58 OK 4827 4830 4831 4851 C3' U P 59 OK 4849 4852 4853 4871 C3' C P 60 OK 4869 4872 4873 4891 C3' C P 61 OK 4889 4892 4893 4911 C3' A P 62 OK 4909 4912 4913 4933 C3' C P 63 OK 4931 4934 4935 4953 C3' A P 64 OK 4951 4954 4955 4975 C3' G P 65 OK 4973 4976 4977 4998 C3' A P 66 OK 4996 4999 5000 5020 C3' A P 67 OK 5018 5021 5022 5042 C3' U P 68 OK 5040 5043 5044 5062 C3' C P 69 OK 5060 5063 5064 5082 C3' C P 70 OK 5080 5083 5084 5102 C3' C P 71 OK 5100 5103 5104 5122 C3' C P 72 OK 5120 5123 5124 5142 C3' A P 73 OK 5140 5143 5144 5164 C3' C P 74 OK 5162 5165 5166 5197 C3' GNP A 304 OK 5195 5198 5199 5229 C3' GNP B 301 OK 5227 5230 5231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3774 C4' GTP P 2 OK 3776 3773 3775 3797 C4' G P 3 OK 3799 3796 3798 3820 C4' G P 4 OK 3822 3819 3821 3843 C4' A P 5 OK 3845 3842 3844 3865 C4' U P 6 OK 3867 3864 3866 3885 C4' U P 7 OK 3887 3884 3886 3905 C4' U P 8 OK 3907 3904 3906 3925 C4' A P 9 OK 3927 3924 3926 3947 C4' G P 10 OK 3949 3946 3948 3970 C4' C P 11 OK 3972 3969 3971 3990 C4' U P 12 OK 3992 3989 3991 4010 C4' C P 13 OK 4012 4009 4011 4030 C4' A P 14 OK 4032 4029 4031 4052 C4' G P 15 OK 4054 4051 4053 4075 C4' U P 16 OK 4077 4074 4076 4095 C4' U P 17 OK 4097 4094 4096 4115 C4' G P 18 OK 4117 4114 4116 4138 C4' G P 19 OK 4140 4137 4139 4161 C4' G P 20 OK 4163 4160 4162 4184 C4' A P 21 OK 4186 4183 4185 4206 C4' G P 22 OK 4208 4205 4207 4229 C4' A P 23 OK 4231 4228 4230 4251 C4' G P 24 OK 4253 4250 4252 4274 C4' C P 25 OK 4276 4273 4275 4294 C4' G P 26 OK 4296 4293 4295 4317 C4' C P 27 OK 4319 4316 4318 4337 C4' C P 28 OK 4339 4336 4338 4357 C4' A P 29 OK 4359 4356 4358 4379 C4' G P 30 OK 4381 4378 4380 4402 C4' A P 38 OK 4404 4401 4403 4424 C4' U P 39 OK 4426 4423 4425 4444 C4' C P 40 OK 4446 4443 4445 4464 C4' U P 41 OK 4466 4463 4465 4484 C4' G P 42 OK 4486 4483 4485 4507 C4' G P 43 OK 4509 4506 4508 4530 C4' A P 44 OK 4532 4529 4531 4552 C4' G P 45 OK 4554 4551 4553 4575 C4' G P 46 OK 4577 4574 4576 4598 C4' U P 47 OK 4600 4597 4599 4618 C4' C P 48 OK 4620 4617 4619 4638 C4' C P 49 OK 4640 4637 4639 4658 C4' U P 50 OK 4660 4657 4659 4678 C4' G P 51 OK 4680 4677 4679 4701 C4' U P 52 OK 4703 4700 4702 4721 C4' G P 53 OK 4723 4720 4722 4744 C4' U P 54 OK 4746 4743 4745 4764 C4' U P 55 OK 4766 4763 4765 4784 C4' C P 56 OK 4786 4783 4785 4804 C4' G P 57 OK 4806 4803 4805 4827 C4' A P 58 OK 4829 4826 4828 4849 C4' U P 59 OK 4851 4848 4850 4869 C4' C P 60 OK 4871 4868 4870 4889 C4' C P 61 OK 4891 4888 4890 4909 C4' A P 62 OK 4911 4908 4910 4931 C4' C P 63 OK 4933 4930 4932 4951 C4' A P 64 OK 4953 4950 4952 4973 C4' G P 65 OK 4975 4972 4974 4996 C4' A P 66 OK 4998 4995 4997 5018 C4' A P 67 OK 5020 5017 5019 5040 C4' U P 68 OK 5042 5039 5041 5060 C4' C P 69 OK 5062 5059 5061 5080 C4' C P 70 OK 5082 5079 5081 5100 C4' C P 71 OK 5102 5099 5101 5120 C4' C P 72 OK 5122 5119 5121 5140 C4' A P 73 OK 5142 5139 5141 5162 C4' C P 74 OK 5164 5161 5163 5195 C4' GNP A 304 OK 5197 5194 5196 5227 C4' GNP B 301 OK 5229 5226 5228 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3773 C5' GTP P 2 3772 3774 3796 C5' G P 3 3795 3797 3819 C5' G P 4 3818 3820 3842 C5' A P 5 3841 3843 3864 C5' U P 6 3863 3865 3884 C5' U P 7 3883 3885 3904 C5' U P 8 3903 3905 3924 C5' A P 9 3923 3925 3946 C5' G P 10 3945 3947 3969 C5' C P 11 3968 3970 3989 C5' U P 12 3988 3990 4009 C5' C P 13 4008 4010 4029 C5' A P 14 4028 4030 4051 C5' G P 15 4050 4052 4074 C5' U P 16 4073 4075 4094 C5' U P 17 4093 4095 4114 C5' G P 18 4113 4115 4137 C5' G P 19 4136 4138 4160 C5' G P 20 4159 4161 4183 C5' A P 21 4182 4184 4205 C5' G P 22 4204 4206 4228 C5' A P 23 4227 4229 4250 C5' G P 24 4249 4251 4273 C5' C P 25 4272 4274 4293 C5' G P 26 4292 4294 4316 C5' C P 27 4315 4317 4336 C5' C P 28 4335 4337 4356 C5' A P 29 4355 4357 4378 C5' G P 30 4377 4379 4401 C5' A P 38 4400 4402 4423 C5' U P 39 4422 4424 4443 C5' C P 40 4442 4444 4463 C5' U P 41 4462 4464 4483 C5' G P 42 4482 4484 4506 C5' G P 43 4505 4507 4529 C5' A P 44 4528 4530 4551 C5' G P 45 4550 4552 4574 C5' G P 46 4573 4575 4597 C5' U P 47 4596 4598 4617 C5' C P 48 4616 4618 4637 C5' C P 49 4636 4638 4657 C5' U P 50 4656 4658 4677 C5' G P 51 4676 4678 4700 C5' U P 52 4699 4701 4720 C5' G P 53 4719 4721 4743 C5' U P 54 4742 4744 4763 C5' U P 55 4762 4764 4783 C5' C P 56 4782 4784 4803 C5' G P 57 4802 4804 4826 C5' A P 58 4825 4827 4848 C5' U P 59 4847 4849 4868 C5' C P 60 4867 4869 4888 C5' C P 61 4887 4889 4908 C5' A P 62 4907 4909 4930 C5' C P 63 4929 4931 4950 C5' A P 64 4949 4951 4972 C5' G P 65 4971 4973 4995 C5' A P 66 4994 4996 5017 C5' A P 67 5016 5018 5039 C5' U P 68 5038 5040 5059 C5' C P 69 5058 5060 5079 C5' C P 70 5078 5080 5099 C5' C P 71 5098 5100 5119 C5' C P 72 5118 5120 5139 C5' A P 73 5138 5140 5161 C5' C P 74 5160 5162 5194 C5' GNP A 304 5193 5195 5226 C5' GNP B 301 5225 5227 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3792 P G P 3 distorted distorted 3777 3793 3794 3795 3815 P G P 4 distorted distorted 3800 3816 3817 3818 3838 P A P 5 distorted distorted 3823 3839 3840 3841 3860 P U P 6 distorted distorted 3846 3861 3862 3863 3880 P U P 7 distorted distorted 3868 3881 3882 3883 3900 P U P 8 distorted distorted 3888 3901 3902 3903 3920 P A P 9 distorted distorted 3908 3921 3922 3923 3942 P G P 10 distorted distorted 3928 3943 3944 3945 3965 P C P 11 distorted distorted 3950 3966 3967 3968 3985 P U P 12 distorted distorted 3973 3986 3987 3988 4005 P C P 13 distorted distorted 3993 4006 4007 4008 4025 P A P 14 distorted distorted 4013 4026 4027 4028 4047 P G P 15 distorted distorted 4033 4048 4049 4050 4070 P U P 16 distorted distorted 4055 4071 4072 4073 4090 P U P 17 distorted distorted 4078 4091 4092 4093 4110 P G P 18 distorted distorted 4098 4111 4112 4113 4133 P G P 19 distorted distorted 4118 4134 4135 4136 4156 P G P 20 distorted distorted 4141 4157 4158 4159 4179 P A P 21 distorted distorted 4164 4180 4181 4182 4201 P G P 22 distorted distorted 4187 4202 4203 4204 4224 P A P 23 distorted distorted 4209 4225 4226 4227 4246 P G P 24 distorted distorted 4232 4247 4248 4249 4269 P C P 25 distorted distorted 4254 4270 4271 4272 4289 P G P 26 distorted distorted 4277 4290 4291 4292 4312 P C P 27 distorted distorted 4297 4313 4314 4315 4332 P C P 28 distorted distorted 4320 4333 4334 4335 4352 P A P 29 distorted distorted 4340 4353 4354 4355 4374 P G P 30 distorted distorted 4360 4375 4376 4377 4397 P A P 38 distorted distorted 4398 4399 4400 4419 P U P 39 distorted distorted 4405 4420 4421 4422 4439 P C P 40 distorted distorted 4427 4440 4441 4442 4459 P U P 41 distorted distorted 4447 4460 4461 4462 4479 P G P 42 distorted distorted 4467 4480 4481 4482 4502 P G P 43 distorted distorted 4487 4503 4504 4505 4525 P A P 44 distorted distorted 4510 4526 4527 4528 4547 P G P 45 distorted distorted 4533 4548 4549 4550 4570 P G P 46 distorted distorted 4555 4571 4572 4573 4593 P U P 47 distorted distorted 4578 4594 4595 4596 4613 P C P 48 distorted distorted 4601 4614 4615 4616 4633 P C P 49 distorted distorted 4621 4634 4635 4636 4653 P U P 50 distorted distorted 4641 4654 4655 4656 4673 P G P 51 distorted distorted 4661 4674 4675 4676 4696 P U P 52 distorted distorted 4681 4697 4698 4699 4716 P G P 53 distorted distorted 4704 4717 4718 4719 4739 P U P 54 distorted distorted 4724 4740 4741 4742 4759 P U P 55 distorted distorted 4747 4760 4761 4762 4779 P C P 56 distorted distorted 4767 4780 4781 4782 4799 P G P 57 distorted distorted 4787 4800 4801 4802 4822 P A P 58 distorted distorted 4807 4823 4824 4825 4844 P U P 59 distorted distorted 4830 4845 4846 4847 4864 P C P 60 distorted distorted 4852 4865 4866 4867 4884 P C P 61 distorted distorted 4872 4885 4886 4887 4904 P A P 62 distorted distorted 4892 4905 4906 4907 4926 P C P 63 distorted distorted 4912 4927 4928 4929 4946 P A P 64 distorted distorted 4934 4947 4948 4949 4968 P G P 65 distorted distorted 4954 4969 4970 4971 4991 P A P 66 distorted distorted 4976 4992 4993 4994 5013 P A P 67 distorted distorted 4999 5014 5015 5016 5035 P U P 68 distorted distorted 5021 5036 5037 5038 5055 P C P 69 distorted distorted 5043 5056 5057 5058 5075 P C P 70 distorted distorted 5063 5076 5077 5078 5095 P C P 71 distorted distorted 5083 5096 5097 5098 5115 P C P 72 distorted distorted 5103 5116 5117 5118 5135 P A P 73 distorted distorted 5123 5136 5137 5138 5157 P C P 74 distorted distorted 5143 5158 5159 5160 ---------------------------------------------------------------------------------