ID code: '4A2X' 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' --------------------------------------------------------------------------------- 3977 C1' G L 1 beta 3972 3978 3975 4000 C1' G L 2 beta 3995 4001 3998 4023 C1' G L 3 beta 4018 4024 4021 4046 C1' A L 4 beta 4041 4047 4044 4068 C1' G L 5 beta 4063 4069 4066 4091 C1' A L 6 beta 4086 4092 4089 4113 C1' A L 7 beta 4108 4114 4111 4135 C1' C L 8 beta 4130 4136 4133 4155 C1' A L 9 beta 4150 4156 4153 4177 C1' A L 10 beta 4172 4178 4175 4199 C1' C L 11 beta 4194 4200 4197 4219 C1' G L 12 beta 4214 4220 4217 4242 C1' C L 13 beta 4237 4243 4240 4262 C1' G L 14 beta 4257 4263 4260 4283 C1' C M 1 beta 4278 4284 4281 4303 C1' G M 2 beta 4298 4304 4301 4326 C1' C M 3 beta 4321 4327 4324 4346 C1' G M 4 beta 4341 4347 4344 4369 C1' U M 5 beta 4364 4370 4367 4389 C1' U M 6 beta 4384 4390 4387 4409 C1' G M 7 beta 4404 4410 4407 4432 C1' U M 8 beta 4427 4433 4430 4452 C1' U M 9 beta 4447 4453 4450 4472 C1' C M 10 beta 4467 4473 4470 4492 C1' U M 11 beta 4487 4493 4490 4512 C1' C M 12 beta 4507 4513 4510 4532 C1' C M 13 beta 4527 4533 4530 4552 C1' C M 14 beta 4547 4553 4550 4570 C1' G N 1 beta 4565 4571 4568 4593 C1' G N 2 beta 4588 4594 4591 4616 C1' G N 3 beta 4611 4617 4614 4639 C1' A N 4 beta 4634 4640 4637 4661 C1' G N 5 beta 4656 4662 4659 4684 C1' A N 6 beta 4679 4685 4682 4706 C1' A N 7 beta 4701 4707 4704 4728 C1' C N 8 beta 4723 4729 4726 4748 C1' A N 9 beta 4743 4749 4746 4770 C1' A N 10 beta 4765 4771 4768 4792 C1' C N 11 beta 4787 4793 4790 4812 C1' G N 12 beta 4807 4813 4810 4835 C1' C N 13 beta 4830 4836 4833 4855 C1' G N 14 beta 4850 4856 4853 4876 C1' C O 1 beta 4871 4877 4874 4896 C1' G O 2 beta 4891 4897 4894 4919 C1' C O 3 beta 4914 4920 4917 4939 C1' G O 4 beta 4934 4940 4937 4962 C1' U O 5 beta 4957 4963 4960 4982 C1' U O 6 beta 4977 4983 4980 5002 C1' G O 7 beta 4997 5003 5000 5025 C1' U O 8 beta 5020 5026 5023 5045 C1' U O 9 beta 5040 5046 5043 5065 C1' C O 10 beta 5060 5066 5063 5085 C1' U O 11 beta 5080 5086 5083 5105 C1' C O 12 beta 5100 5106 5103 5125 C1' C O 13 beta 5120 5126 5123 5145 C1' C O 14 beta 5140 5146 5143 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3975 C2' G L 1 OK 3977 3973 3976 3998 C2' G L 2 OK 4000 3996 3999 4021 C2' G L 3 OK 4023 4019 4022 4044 C2' A L 4 OK 4046 4042 4045 4066 C2' G L 5 OK 4068 4064 4067 4089 C2' A L 6 OK 4091 4087 4090 4111 C2' A L 7 OK 4113 4109 4112 4133 C2' C L 8 OK 4135 4131 4134 4153 C2' A L 9 OK 4155 4151 4154 4175 C2' A L 10 OK 4177 4173 4176 4197 C2' C L 11 OK 4199 4195 4198 4217 C2' G L 12 OK 4219 4215 4218 4240 C2' C L 13 OK 4242 4238 4241 4260 C2' G L 14 OK 4262 4258 4261 4281 C2' C M 1 OK 4283 4279 4282 4301 C2' G M 2 OK 4303 4299 4302 4324 C2' C M 3 OK 4326 4322 4325 4344 C2' G M 4 OK 4346 4342 4345 4367 C2' U M 5 OK 4369 4365 4368 4387 C2' U M 6 OK 4389 4385 4388 4407 C2' G M 7 OK 4409 4405 4408 4430 C2' U M 8 OK 4432 4428 4431 4450 C2' U M 9 OK 4452 4448 4451 4470 C2' C M 10 OK 4472 4468 4471 4490 C2' U M 11 OK 4492 4488 4491 4510 C2' C M 12 OK 4512 4508 4511 4530 C2' C M 13 OK 4532 4528 4531 4550 C2' C M 14 OK 4552 4548 4551 4568 C2' G N 1 OK 4570 4566 4569 4591 C2' G N 2 OK 4593 4589 4592 4614 C2' G N 3 OK 4616 4612 4615 4637 C2' A N 4 OK 4639 4635 4638 4659 C2' G N 5 OK 4661 4657 4660 4682 C2' A N 6 OK 4684 4680 4683 4704 C2' A N 7 OK 4706 4702 4705 4726 C2' C N 8 OK 4728 4724 4727 4746 C2' A N 9 OK 4748 4744 4747 4768 C2' A N 10 OK 4770 4766 4769 4790 C2' C N 11 OK 4792 4788 4791 4810 C2' G N 12 OK 4812 4808 4811 4833 C2' C N 13 OK 4835 4831 4834 4853 C2' G N 14 OK 4855 4851 4854 4874 C2' C O 1 OK 4876 4872 4875 4894 C2' G O 2 OK 4896 4892 4895 4917 C2' C O 3 OK 4919 4915 4918 4937 C2' G O 4 OK 4939 4935 4938 4960 C2' U O 5 OK 4962 4958 4961 4980 C2' U O 6 OK 4982 4978 4981 5000 C2' G O 7 OK 5002 4998 5001 5023 C2' U O 8 OK 5025 5021 5024 5043 C2' U O 9 OK 5045 5041 5044 5063 C2' C O 10 OK 5065 5061 5064 5083 C2' U O 11 OK 5085 5081 5084 5103 C2' C O 12 OK 5105 5101 5104 5123 C2' C O 13 OK 5125 5121 5124 5143 C2' C O 14 OK 5145 5141 5144 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3973 C3' G L 1 OK 3971 3974 3975 3996 C3' G L 2 OK 3994 3997 3998 4019 C3' G L 3 OK 4017 4020 4021 4042 C3' A L 4 OK 4040 4043 4044 4064 C3' G L 5 OK 4062 4065 4066 4087 C3' A L 6 OK 4085 4088 4089 4109 C3' A L 7 OK 4107 4110 4111 4131 C3' C L 8 OK 4129 4132 4133 4151 C3' A L 9 OK 4149 4152 4153 4173 C3' A L 10 OK 4171 4174 4175 4195 C3' C L 11 OK 4193 4196 4197 4215 C3' G L 12 OK 4213 4216 4217 4238 C3' C L 13 OK 4236 4239 4240 4258 C3' G L 14 OK 4256 4259 4260 4279 C3' C M 1 OK 4277 4280 4281 4299 C3' G M 2 OK 4297 4300 4301 4322 C3' C M 3 OK 4320 4323 4324 4342 C3' G M 4 OK 4340 4343 4344 4365 C3' U M 5 OK 4363 4366 4367 4385 C3' U M 6 OK 4383 4386 4387 4405 C3' G M 7 OK 4403 4406 4407 4428 C3' U M 8 OK 4426 4429 4430 4448 C3' U M 9 OK 4446 4449 4450 4468 C3' C M 10 OK 4466 4469 4470 4488 C3' U M 11 OK 4486 4489 4490 4508 C3' C M 12 OK 4506 4509 4510 4528 C3' C M 13 OK 4526 4529 4530 4548 C3' C M 14 OK 4546 4549 4550 4566 C3' G N 1 OK 4564 4567 4568 4589 C3' G N 2 OK 4587 4590 4591 4612 C3' G N 3 OK 4610 4613 4614 4635 C3' A N 4 OK 4633 4636 4637 4657 C3' G N 5 OK 4655 4658 4659 4680 C3' A N 6 OK 4678 4681 4682 4702 C3' A N 7 OK 4700 4703 4704 4724 C3' C N 8 OK 4722 4725 4726 4744 C3' A N 9 OK 4742 4745 4746 4766 C3' A N 10 OK 4764 4767 4768 4788 C3' C N 11 OK 4786 4789 4790 4808 C3' G N 12 OK 4806 4809 4810 4831 C3' C N 13 OK 4829 4832 4833 4851 C3' G N 14 OK 4849 4852 4853 4872 C3' C O 1 OK 4870 4873 4874 4892 C3' G O 2 OK 4890 4893 4894 4915 C3' C O 3 OK 4913 4916 4917 4935 C3' G O 4 OK 4933 4936 4937 4958 C3' U O 5 OK 4956 4959 4960 4978 C3' U O 6 OK 4976 4979 4980 4998 C3' G O 7 OK 4996 4999 5000 5021 C3' U O 8 OK 5019 5022 5023 5041 C3' U O 9 OK 5039 5042 5043 5061 C3' C O 10 OK 5059 5062 5063 5081 C3' U O 11 OK 5079 5082 5083 5101 C3' C O 12 OK 5099 5102 5103 5121 C3' C O 13 OK 5119 5122 5123 5141 C3' C O 14 OK 5139 5142 5143 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3971 C4' G L 1 OK 3973 3970 3972 3994 C4' G L 2 OK 3996 3993 3995 4017 C4' G L 3 OK 4019 4016 4018 4040 C4' A L 4 OK 4042 4039 4041 4062 C4' G L 5 OK 4064 4061 4063 4085 C4' A L 6 OK 4087 4084 4086 4107 C4' A L 7 OK 4109 4106 4108 4129 C4' C L 8 OK 4131 4128 4130 4149 C4' A L 9 OK 4151 4148 4150 4171 C4' A L 10 OK 4173 4170 4172 4193 C4' C L 11 OK 4195 4192 4194 4213 C4' G L 12 OK 4215 4212 4214 4236 C4' C L 13 OK 4238 4235 4237 4256 C4' G L 14 OK 4258 4255 4257 4277 C4' C M 1 OK 4279 4276 4278 4297 C4' G M 2 OK 4299 4296 4298 4320 C4' C M 3 OK 4322 4319 4321 4340 C4' G M 4 OK 4342 4339 4341 4363 C4' U M 5 OK 4365 4362 4364 4383 C4' U M 6 OK 4385 4382 4384 4403 C4' G M 7 OK 4405 4402 4404 4426 C4' U M 8 OK 4428 4425 4427 4446 C4' U M 9 OK 4448 4445 4447 4466 C4' C M 10 OK 4468 4465 4467 4486 C4' U M 11 OK 4488 4485 4487 4506 C4' C M 12 OK 4508 4505 4507 4526 C4' C M 13 OK 4528 4525 4527 4546 C4' C M 14 OK 4548 4545 4547 4564 C4' G N 1 OK 4566 4563 4565 4587 C4' G N 2 OK 4589 4586 4588 4610 C4' G N 3 OK 4612 4609 4611 4633 C4' A N 4 OK 4635 4632 4634 4655 C4' G N 5 OK 4657 4654 4656 4678 C4' A N 6 OK 4680 4677 4679 4700 C4' A N 7 OK 4702 4699 4701 4722 C4' C N 8 OK 4724 4721 4723 4742 C4' A N 9 OK 4744 4741 4743 4764 C4' A N 10 OK 4766 4763 4765 4786 C4' C N 11 OK 4788 4785 4787 4806 C4' G N 12 OK 4808 4805 4807 4829 C4' C N 13 OK 4831 4828 4830 4849 C4' G N 14 OK 4851 4848 4850 4870 C4' C O 1 OK 4872 4869 4871 4890 C4' G O 2 OK 4892 4889 4891 4913 C4' C O 3 OK 4915 4912 4914 4933 C4' G O 4 OK 4935 4932 4934 4956 C4' U O 5 OK 4958 4955 4957 4976 C4' U O 6 OK 4978 4975 4977 4996 C4' G O 7 OK 4998 4995 4997 5019 C4' U O 8 OK 5021 5018 5020 5039 C4' U O 9 OK 5041 5038 5040 5059 C4' C O 10 OK 5061 5058 5060 5079 C4' U O 11 OK 5081 5078 5080 5099 C4' C O 12 OK 5101 5098 5100 5119 C4' C O 13 OK 5121 5118 5120 5139 C4' C O 14 OK 5141 5138 5140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3970 C5' G L 1 3969 3971 3993 C5' G L 2 3992 3994 4016 C5' G L 3 4015 4017 4039 C5' A L 4 4038 4040 4061 C5' G L 5 4060 4062 4084 C5' A L 6 4083 4085 4106 C5' A L 7 4105 4107 4128 C5' C L 8 4127 4129 4148 C5' A L 9 4147 4149 4170 C5' A L 10 4169 4171 4192 C5' C L 11 4191 4193 4212 C5' G L 12 4211 4213 4235 C5' C L 13 4234 4236 4255 C5' G L 14 4254 4256 4276 C5' C M 1 4275 4277 4296 C5' G M 2 4295 4297 4319 C5' C M 3 4318 4320 4339 C5' G M 4 4338 4340 4362 C5' U M 5 4361 4363 4382 C5' U M 6 4381 4383 4402 C5' G M 7 4401 4403 4425 C5' U M 8 4424 4426 4445 C5' U M 9 4444 4446 4465 C5' C M 10 4464 4466 4485 C5' U M 11 4484 4486 4505 C5' C M 12 4504 4506 4525 C5' C M 13 4524 4526 4545 C5' C M 14 4544 4546 4563 C5' G N 1 4562 4564 4586 C5' G N 2 4585 4587 4609 C5' G N 3 4608 4610 4632 C5' A N 4 4631 4633 4654 C5' G N 5 4653 4655 4677 C5' A N 6 4676 4678 4699 C5' A N 7 4698 4700 4721 C5' C N 8 4720 4722 4741 C5' A N 9 4740 4742 4763 C5' A N 10 4762 4764 4785 C5' C N 11 4784 4786 4805 C5' G N 12 4804 4806 4828 C5' C N 13 4827 4829 4848 C5' G N 14 4847 4849 4869 C5' C O 1 4868 4870 4889 C5' G O 2 4888 4890 4912 C5' C O 3 4911 4913 4932 C5' G O 4 4931 4933 4955 C5' U O 5 4954 4956 4975 C5' U O 6 4974 4976 4995 C5' G O 7 4994 4996 5018 C5' U O 8 5017 5019 5038 C5' U O 9 5037 5039 5058 C5' C O 10 5057 5059 5078 C5' U O 11 5077 5079 5098 C5' C O 12 5097 5099 5118 C5' C O 13 5117 5119 5138 C5' C O 14 5137 5139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3989 P G L 2 distorted distorted 3974 3990 3991 3992 4012 P G L 3 distorted distorted 3997 4013 4014 4015 4035 P A L 4 distorted distorted 4020 4036 4037 4038 4057 P G L 5 distorted distorted 4043 4058 4059 4060 4080 P A L 6 distorted distorted 4065 4081 4082 4083 4102 P A L 7 distorted distorted 4088 4103 4104 4105 4124 P C L 8 distorted distorted 4110 4125 4126 4127 4144 P A L 9 distorted distorted 4132 4145 4146 4147 4166 P A L 10 distorted distorted 4152 4167 4168 4169 4188 P C L 11 distorted distorted 4174 4189 4190 4191 4208 P G L 12 distorted distorted 4196 4209 4210 4211 4231 P C L 13 distorted distorted 4216 4232 4233 4234 4251 P G L 14 distorted distorted 4239 4252 4253 4254 4292 P G M 2 distorted distorted 4280 4293 4294 4295 4315 P C M 3 distorted distorted 4300 4316 4317 4318 4335 P G M 4 distorted distorted 4323 4336 4337 4338 4358 P U M 5 distorted distorted 4343 4359 4360 4361 4378 P U M 6 distorted distorted 4366 4379 4380 4381 4398 P G M 7 distorted distorted 4386 4399 4400 4401 4421 P U M 8 distorted distorted 4406 4422 4423 4424 4441 P U M 9 distorted distorted 4429 4442 4443 4444 4461 P C M 10 distorted distorted 4449 4462 4463 4464 4481 P U M 11 distorted distorted 4469 4482 4483 4484 4501 P C M 12 distorted distorted 4489 4502 4503 4504 4521 P C M 13 distorted distorted 4509 4522 4523 4524 4541 P C M 14 distorted distorted 4529 4542 4543 4544 4582 P G N 2 distorted distorted 4567 4583 4584 4585 4605 P G N 3 distorted distorted 4590 4606 4607 4608 4628 P A N 4 distorted distorted 4613 4629 4630 4631 4650 P G N 5 distorted distorted 4636 4651 4652 4653 4673 P A N 6 distorted distorted 4658 4674 4675 4676 4695 P A N 7 distorted distorted 4681 4696 4697 4698 4717 P C N 8 distorted distorted 4703 4718 4719 4720 4737 P A N 9 distorted distorted 4725 4738 4739 4740 4759 P A N 10 distorted distorted 4745 4760 4761 4762 4781 P C N 11 distorted distorted 4767 4782 4783 4784 4801 P G N 12 distorted distorted 4789 4802 4803 4804 4824 P C N 13 distorted distorted 4809 4825 4826 4827 4844 P G N 14 distorted distorted 4832 4845 4846 4847 4885 P G O 2 distorted distorted 4873 4886 4887 4888 4908 P C O 3 distorted distorted 4893 4909 4910 4911 4928 P G O 4 distorted distorted 4916 4929 4930 4931 4951 P U O 5 distorted distorted 4936 4952 4953 4954 4971 P U O 6 distorted distorted 4959 4972 4973 4974 4991 P G O 7 distorted distorted 4979 4992 4993 4994 5014 P U O 8 distorted distorted 4999 5015 5016 5017 5034 P U O 9 distorted distorted 5022 5035 5036 5037 5054 P C O 10 distorted distorted 5042 5055 5056 5057 5074 P U O 11 distorted distorted 5062 5075 5076 5077 5094 P C O 12 distorted distorted 5082 5095 5096 5097 5114 P C O 13 distorted distorted 5102 5115 5116 5117 5134 P C O 14 distorted distorted 5122 5135 5136 5137 ---------------------------------------------------------------------------------