ID code: '4LGT' 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' --------------------------------------------------------------------------------- 4061 C1' A E2587 alpha beta 4056 4078 4062 4059 4094 C1' G E2588 alpha beta 4089 4112 4095 4092 4128 C1' A E2589 alpha beta 4123 4145 4129 4126 4161 C1' A E2590 alpha beta 4156 4178 4162 4159 4194 C1' C E2591 alpha beta 4189 4209 4195 4192 4225 C1' G E2592 alpha beta 4220 4243 4226 4223 4259 C1' U E2593 alpha beta 4254 4274 4260 4257 4289 C1' C E2594 alpha beta 4284 4304 4290 4287 4320 C1' G E2595 alpha beta 4315 4338 4321 4318 4354 C1' U E2596 alpha beta 4349 4369 4355 4352 4384 C1' G E2597 alpha beta 4379 4402 4385 4382 4418 C1' A E2598 alpha beta 4413 4435 4419 4416 4451 C1' G E2599 alpha beta 4446 4469 4452 4449 4485 C1' A E2600 alpha beta 4480 4502 4486 4483 4518 C1' C E2601 alpha beta 4513 4533 4519 4516 4549 C1' A E2602 alpha beta 4544 4566 4550 4547 4582 C1' G E2603 alpha beta 4577 4600 4583 4580 4616 C1' U E2604 alpha beta 4611 4631 4617 4614 4643 C1' FHU E2605 alpha beta 4649 4659 4639 4644 4677 C1' C E2606 alpha beta 4672 4692 4678 4675 4708 C1' G E2607 alpha beta 4703 4727 4709 4706 8675 C1' G F2588 alpha beta 8670 8693 8676 8673 8709 C1' A F2589 alpha beta 8704 8726 8710 8707 8742 C1' A F2590 alpha beta 8737 8759 8743 8740 8775 C1' C F2591 alpha beta 8770 8790 8776 8773 8806 C1' G F2592 alpha beta 8801 8824 8807 8804 8840 C1' U F2593 alpha beta 8835 8855 8841 8838 8870 C1' C F2594 alpha beta 8865 8885 8871 8868 8901 C1' G F2595 alpha beta 8896 8919 8902 8899 8935 C1' U F2596 alpha beta 8930 8950 8936 8933 8965 C1' G F2597 alpha beta 8960 8983 8966 8963 8999 C1' A F2598 alpha beta 8994 9016 9000 8997 9032 C1' G F2599 alpha beta 9027 9050 9033 9030 9066 C1' A F2600 alpha beta 9061 9083 9067 9064 9099 C1' C F2601 alpha beta 9094 9114 9100 9097 9130 C1' A F2602 alpha beta 9125 9147 9131 9128 9163 C1' G F2603 alpha beta 9158 9181 9164 9161 9197 C1' U F2604 alpha beta 9192 9212 9198 9195 9224 C1' FHU F2605 alpha beta 9230 9241 9220 9225 9260 C1' C F2606 alpha beta 9255 9275 9261 9258 9291 C1' G F2607 alpha beta 9286 9310 9292 9289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4059 C2' A E2587 OK OK 4061 4057 4076 4060 4092 C2' G E2588 OK OK 4094 4090 4110 4093 4126 C2' A E2589 OK OK 4128 4124 4143 4127 4159 C2' A E2590 OK OK 4161 4157 4176 4160 4192 C2' C E2591 OK OK 4194 4190 4207 4193 4223 C2' G E2592 OK OK 4225 4221 4241 4224 4257 C2' U E2593 OK OK 4259 4255 4272 4258 4287 C2' C E2594 OK OK 4289 4285 4302 4288 4318 C2' G E2595 OK OK 4320 4316 4336 4319 4352 C2' U E2596 OK OK 4354 4350 4367 4353 4382 C2' G E2597 OK OK 4384 4380 4400 4383 4416 C2' A E2598 OK OK 4418 4414 4433 4417 4449 C2' G E2599 OK OK 4451 4447 4467 4450 4483 C2' A E2600 OK OK 4485 4481 4500 4484 4516 C2' C E2601 OK OK 4518 4514 4531 4517 4547 C2' A E2602 OK OK 4549 4545 4564 4548 4580 C2' G E2603 OK OK 4582 4578 4598 4581 4614 C2' U E2604 OK OK 4616 4612 4629 4615 4644 C2' FHU E2605 OK OK 4643 4646 4660 4645 4675 C2' C E2606 OK OK 4677 4673 4690 4676 4706 C2' G E2607 OK OK 4708 4704 4725 4707 8673 C2' G F2588 OK OK 8675 8671 8691 8674 8707 C2' A F2589 OK OK 8709 8705 8724 8708 8740 C2' A F2590 OK OK 8742 8738 8757 8741 8773 C2' C F2591 OK OK 8775 8771 8788 8774 8804 C2' G F2592 OK OK 8806 8802 8822 8805 8838 C2' U F2593 OK OK 8840 8836 8853 8839 8868 C2' C F2594 OK OK 8870 8866 8883 8869 8899 C2' G F2595 OK OK 8901 8897 8917 8900 8933 C2' U F2596 OK OK 8935 8931 8948 8934 8963 C2' G F2597 OK OK 8965 8961 8981 8964 8997 C2' A F2598 OK OK 8999 8995 9014 8998 9030 C2' G F2599 OK OK 9032 9028 9048 9031 9064 C2' A F2600 OK OK 9066 9062 9081 9065 9097 C2' C F2601 OK OK 9099 9095 9112 9098 9128 C2' A F2602 OK OK 9130 9126 9145 9129 9161 C2' G F2603 OK OK 9163 9159 9179 9162 9195 C2' U F2604 OK OK 9197 9193 9210 9196 9225 C2' FHU F2605 OK OK 9224 9227 9242 9226 9258 C2' C F2606 OK OK 9260 9256 9273 9259 9289 C2' G F2607 OK OK 9291 9287 9308 9290 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4057 C3' A E2587 OK OK 4055 4075 4058 4059 4090 C3' G E2588 OK OK 4088 4109 4091 4092 4124 C3' A E2589 OK OK 4122 4142 4125 4126 4157 C3' A E2590 OK OK 4155 4175 4158 4159 4190 C3' C E2591 OK OK 4188 4206 4191 4192 4221 C3' G E2592 OK OK 4219 4240 4222 4223 4255 C3' U E2593 OK OK 4253 4271 4256 4257 4285 C3' C E2594 OK OK 4283 4301 4286 4287 4316 C3' G E2595 OK OK 4314 4335 4317 4318 4350 C3' U E2596 OK OK 4348 4366 4351 4352 4380 C3' G E2597 OK OK 4378 4399 4381 4382 4414 C3' A E2598 OK OK 4412 4432 4415 4416 4447 C3' G E2599 OK OK 4445 4466 4448 4449 4481 C3' A E2600 OK OK 4479 4499 4482 4483 4514 C3' C E2601 OK OK 4512 4530 4515 4516 4545 C3' A E2602 OK OK 4543 4563 4546 4547 4578 C3' G E2603 OK OK 4576 4597 4579 4580 4612 C3' U E2604 OK OK 4610 4628 4613 4614 4646 C3' FHU E2605 OK OK 4647 4662 4648 4644 4673 C3' C E2606 OK OK 4671 4689 4674 4675 4704 C3' G E2607 OK OK 4702 4723 4705 4706 8671 C3' G F2588 OK OK 8669 8690 8672 8673 8705 C3' A F2589 OK OK 8703 8723 8706 8707 8738 C3' A F2590 OK OK 8736 8756 8739 8740 8771 C3' C F2591 OK OK 8769 8787 8772 8773 8802 C3' G F2592 OK OK 8800 8821 8803 8804 8836 C3' U F2593 OK OK 8834 8852 8837 8838 8866 C3' C F2594 OK OK 8864 8882 8867 8868 8897 C3' G F2595 OK OK 8895 8916 8898 8899 8931 C3' U F2596 OK OK 8929 8947 8932 8933 8961 C3' G F2597 OK OK 8959 8980 8962 8963 8995 C3' A F2598 OK OK 8993 9013 8996 8997 9028 C3' G F2599 OK OK 9026 9047 9029 9030 9062 C3' A F2600 OK OK 9060 9080 9063 9064 9095 C3' C F2601 OK OK 9093 9111 9096 9097 9126 C3' A F2602 OK OK 9124 9144 9127 9128 9159 C3' G F2603 OK OK 9157 9178 9160 9161 9193 C3' U F2604 OK OK 9191 9209 9194 9195 9227 C3' FHU F2605 OK OK 9228 9244 9229 9225 9256 C3' C F2606 OK OK 9254 9272 9257 9258 9287 C3' G F2607 OK OK 9285 9306 9288 9289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4055 C4' A E2587 OK OK 4057 4074 4054 4056 4088 C4' G E2588 OK OK 4090 4108 4087 4089 4122 C4' A E2589 OK OK 4124 4141 4121 4123 4155 C4' A E2590 OK OK 4157 4174 4154 4156 4188 C4' C E2591 OK OK 4190 4205 4187 4189 4219 C4' G E2592 OK OK 4221 4239 4218 4220 4253 C4' U E2593 OK OK 4255 4270 4252 4254 4283 C4' C E2594 OK OK 4285 4300 4282 4284 4314 C4' G E2595 OK OK 4316 4334 4313 4315 4348 C4' U E2596 OK OK 4350 4365 4347 4349 4378 C4' G E2597 OK OK 4380 4398 4377 4379 4412 C4' A E2598 OK OK 4414 4431 4411 4413 4445 C4' G E2599 OK OK 4447 4465 4444 4446 4479 C4' A E2600 OK OK 4481 4498 4478 4480 4512 C4' C E2601 OK OK 4514 4529 4511 4513 4543 C4' A E2602 OK OK 4545 4562 4542 4544 4576 C4' G E2603 OK OK 4578 4596 4575 4577 4610 C4' U E2604 OK OK 4612 4627 4609 4611 4647 C4' FHU E2605 OK OK 4646 4663 4650 4649 4671 C4' C E2606 OK OK 4673 4688 4670 4672 4702 C4' G E2607 OK OK 4704 4722 4701 4703 8669 C4' G F2588 OK OK 8671 8689 8668 8670 8703 C4' A F2589 OK OK 8705 8722 8702 8704 8736 C4' A F2590 OK OK 8738 8755 8735 8737 8769 C4' C F2591 OK OK 8771 8786 8768 8770 8800 C4' G F2592 OK OK 8802 8820 8799 8801 8834 C4' U F2593 OK OK 8836 8851 8833 8835 8864 C4' C F2594 OK OK 8866 8881 8863 8865 8895 C4' G F2595 OK OK 8897 8915 8894 8896 8929 C4' U F2596 OK OK 8931 8946 8928 8930 8959 C4' G F2597 OK OK 8961 8979 8958 8960 8993 C4' A F2598 OK OK 8995 9012 8992 8994 9026 C4' G F2599 OK OK 9028 9046 9025 9027 9060 C4' A F2600 OK OK 9062 9079 9059 9061 9093 C4' C F2601 OK OK 9095 9110 9092 9094 9124 C4' A F2602 OK OK 9126 9143 9123 9125 9157 C4' G F2603 OK OK 9159 9177 9156 9158 9191 C4' U F2604 OK OK 9193 9208 9190 9192 9228 C4' FHU F2605 OK OK 9227 9245 9231 9230 9254 C4' C F2606 OK OK 9256 9271 9253 9255 9285 C4' G F2607 OK OK 9287 9305 9284 9286 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4054 C5' A E2587 OK OK 4053 4072 4073 4055 4087 C5' G E2588 OK OK 4086 4106 4107 4088 4121 C5' A E2589 OK OK 4120 4139 4140 4122 4154 C5' A E2590 OK OK 4153 4172 4173 4155 4187 C5' C E2591 OK OK 4186 4203 4204 4188 4218 C5' G E2592 OK OK 4217 4237 4238 4219 4252 C5' U E2593 OK OK 4251 4268 4269 4253 4282 C5' C E2594 OK OK 4281 4298 4299 4283 4313 C5' G E2595 OK OK 4312 4332 4333 4314 4347 C5' U E2596 OK OK 4346 4363 4364 4348 4377 C5' G E2597 OK OK 4376 4396 4397 4378 4411 C5' A E2598 OK OK 4410 4429 4430 4412 4444 C5' G E2599 OK OK 4443 4463 4464 4445 4478 C5' A E2600 OK OK 4477 4496 4497 4479 4511 C5' C E2601 OK OK 4510 4527 4528 4512 4542 C5' A E2602 OK OK 4541 4560 4561 4543 4575 C5' G E2603 OK OK 4574 4594 4595 4576 4609 C5' U E2604 OK OK 4608 4625 4626 4610 4650 C5' FHU E2605 OK OK 4651 4664 4665 4647 4670 C5' C E2606 OK OK 4669 4686 4687 4671 4701 C5' G E2607 OK OK 4700 4720 4721 4702 8668 C5' G F2588 OK OK 8667 8687 8688 8669 8702 C5' A F2589 OK OK 8701 8720 8721 8703 8735 C5' A F2590 OK OK 8734 8753 8754 8736 8768 C5' C F2591 OK OK 8767 8784 8785 8769 8799 C5' G F2592 OK OK 8798 8818 8819 8800 8833 C5' U F2593 OK OK 8832 8849 8850 8834 8863 C5' C F2594 OK OK 8862 8879 8880 8864 8894 C5' G F2595 OK OK 8893 8913 8914 8895 8928 C5' U F2596 OK OK 8927 8944 8945 8929 8958 C5' G F2597 OK OK 8957 8977 8978 8959 8992 C5' A F2598 OK OK 8991 9010 9011 8993 9025 C5' G F2599 OK OK 9024 9044 9045 9026 9059 C5' A F2600 OK OK 9058 9077 9078 9060 9092 C5' C F2601 OK OK 9091 9108 9109 9093 9123 C5' A F2602 OK OK 9122 9141 9142 9124 9156 C5' G F2603 OK OK 9155 9175 9176 9157 9190 C5' U F2604 OK OK 9189 9206 9207 9191 9231 C5' FHU F2605 distorted distorted 9232 9246 9247 9228 9253 C5' C F2606 OK OK 9252 9269 9270 9254 9284 C5' G F2607 OK OK 9283 9303 9304 9285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4050 P A E2587 distorted distorted 4051 4052 4053 4083 P G E2588 distorted distorted 4058 4084 4085 4086 4117 P A E2589 distorted distorted 4091 4118 4119 4120 4150 P A E2590 distorted distorted 4125 4151 4152 4153 4183 P C E2591 distorted distorted 4158 4184 4185 4186 4214 P G E2592 distorted distorted 4191 4215 4216 4217 4248 P U E2593 distorted distorted 4222 4249 4250 4251 4278 P C E2594 distorted distorted 4256 4279 4280 4281 4309 P G E2595 distorted distorted 4286 4310 4311 4312 4343 P U E2596 distorted distorted 4317 4344 4345 4346 4373 P G E2597 distorted distorted 4351 4374 4375 4376 4407 P A E2598 distorted distorted 4381 4408 4409 4410 4440 P G E2599 distorted distorted 4415 4441 4442 4443 4474 P A E2600 distorted distorted 4448 4475 4476 4477 4507 P C E2601 distorted distorted 4482 4508 4509 4510 4538 P A E2602 distorted distorted 4515 4539 4540 4541 4571 P G E2603 distorted distorted 4546 4572 4573 4574 4605 P U E2604 distorted distorted 4579 4606 4607 4608 4652 P FHU E2605 distorted distorted 4613 4653 4654 4651 4666 P C E2606 distorted distorted 4648 4667 4668 4669 4697 P G E2607 distorted distorted 4674 4698 4699 4700 8664 P G F2588 OK OK 8665 8666 8667 8698 P A F2589 distorted distorted 8672 8699 8700 8701 8731 P A F2590 distorted distorted 8706 8732 8733 8734 8764 P C F2591 distorted distorted 8739 8765 8766 8767 8795 P G F2592 distorted distorted 8772 8796 8797 8798 8829 P U F2593 distorted distorted 8803 8830 8831 8832 8859 P C F2594 distorted distorted 8837 8860 8861 8862 8890 P G F2595 distorted distorted 8867 8891 8892 8893 8924 P U F2596 distorted distorted 8898 8925 8926 8927 8954 P G F2597 distorted distorted 8932 8955 8956 8957 8988 P A F2598 distorted distorted 8962 8989 8990 8991 9021 P G F2599 distorted distorted 8996 9022 9023 9024 9055 P A F2600 distorted distorted 9029 9056 9057 9058 9088 P C F2601 distorted distorted 9063 9089 9090 9091 9119 P A F2602 distorted distorted 9096 9120 9121 9122 9152 P G F2603 distorted distorted 9127 9153 9154 9155 9186 P U F2604 distorted distorted 9160 9187 9188 9189 9233 P FHU F2605 distorted distorted 9194 9234 9235 9232 9249 P C F2606 distorted distorted 9229 9250 9251 9252 9280 P G F2607 distorted distorted 9257 9281 9282 9283 ---------------------------------------------------------------------------------