ID code: '5C9H' 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' --------------------------------------------------------------------------------- 3899 C1' A D 1 beta 3894 3900 3897 3921 C1' G D 2 beta 3916 3922 3919 3944 C1' A D 3 beta 3939 3945 3942 3966 C1' A D 4 beta 3961 3967 3964 3988 C1' C D 5 beta 3983 3989 3986 4008 C1' U D 6 beta 4003 4009 4006 4028 C1' G D 7 beta 4023 4029 4026 4051 C1' U D 8 beta 4046 4052 4049 4071 C1' C D 9 beta 4066 4072 4069 4096 C1' U C 1 beta 4091 4097 4094 4116 C1' C C 2 beta 4111 4117 4114 4136 C1' A C 3 beta 4131 4137 4134 4158 C1' U C 4 beta 4153 4159 4156 4178 C1' U C 5 beta 4173 4179 4176 4198 C1' C C 6 beta 4193 4199 4196 4218 C1' A C 7 beta 4213 4219 4216 4240 C1' G C 8 beta 4235 4241 4238 4263 C1' U C 9 beta 4258 4264 4261 4283 C1' U C 10 beta 4278 4284 4281 4303 C1' C C 11 beta 4298 4304 4301 4323 C1' U C 12 beta 4318 4324 4321 4344 C1' G E -1 beta 4339 4345 4342 4367 C1' A E 0 beta 4362 4368 4365 4389 C1' A E 1 beta 4384 4390 4387 4411 C1' C E 2 beta 4406 4412 4409 4431 C1' U E 3 beta 4426 4432 4429 4451 C1' G E 4 beta 4446 4452 4449 4474 C1' U E 5 beta 4469 4475 4472 4494 C1' C E 6 beta 4489 4495 4492 4514 C1' A E 7 beta 4509 4515 4512 4536 C1' U E 8 beta 4531 4537 4534 4557 C1' C G -3 beta 4552 4558 4555 4577 C1' A G -2 beta 4572 4578 4575 4599 C1' U G -1 beta 4594 4600 4597 4619 C1' U G 0 beta 4614 4620 4617 4639 C1' C G 1 beta 4634 4640 4637 4659 C1' A G 2 beta 4654 4660 4657 4681 C1' G G 3 beta 4676 4682 4679 4704 C1' U G 4 beta 4699 4705 4702 4724 C1' U G 5 beta 4719 4725 4722 4744 C1' C G 6 beta 4739 4745 4742 4764 C1' U G 7 beta 4759 4765 4762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3897 C2' A D 1 OK 3899 3895 3898 3919 C2' G D 2 OK 3921 3917 3920 3942 C2' A D 3 OK 3944 3940 3943 3964 C2' A D 4 OK 3966 3962 3965 3986 C2' C D 5 OK 3988 3984 3987 4006 C2' U D 6 OK 4008 4004 4007 4026 C2' G D 7 OK 4028 4024 4027 4049 C2' U D 8 OK 4051 4047 4050 4069 C2' C D 9 OK 4071 4067 4070 4094 C2' U C 1 OK 4096 4092 4095 4114 C2' C C 2 OK 4116 4112 4115 4134 C2' A C 3 OK 4136 4132 4135 4156 C2' U C 4 OK 4158 4154 4157 4176 C2' U C 5 OK 4178 4174 4177 4196 C2' C C 6 OK 4198 4194 4197 4216 C2' A C 7 OK 4218 4214 4217 4238 C2' G C 8 OK 4240 4236 4239 4261 C2' U C 9 OK 4263 4259 4262 4281 C2' U C 10 OK 4283 4279 4282 4301 C2' C C 11 OK 4303 4299 4302 4321 C2' U C 12 OK 4323 4319 4322 4342 C2' G E -1 OK 4344 4340 4343 4365 C2' A E 0 OK 4367 4363 4366 4387 C2' A E 1 OK 4389 4385 4388 4409 C2' C E 2 OK 4411 4407 4410 4429 C2' U E 3 OK 4431 4427 4430 4449 C2' G E 4 OK 4451 4447 4450 4472 C2' U E 5 OK 4474 4470 4473 4492 C2' C E 6 OK 4494 4490 4493 4512 C2' A E 7 OK 4514 4510 4513 4534 C2' U E 8 OK 4536 4532 4535 4555 C2' C G -3 OK 4557 4553 4556 4575 C2' A G -2 OK 4577 4573 4576 4597 C2' U G -1 OK 4599 4595 4598 4617 C2' U G 0 OK 4619 4615 4618 4637 C2' C G 1 OK 4639 4635 4638 4657 C2' A G 2 OK 4659 4655 4658 4679 C2' G G 3 OK 4681 4677 4680 4702 C2' U G 4 OK 4704 4700 4703 4722 C2' U G 5 OK 4724 4720 4723 4742 C2' C G 6 OK 4744 4740 4743 4762 C2' U G 7 OK 4764 4760 4763 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3895 C3' A D 1 OK 3893 3896 3897 3917 C3' G D 2 OK 3915 3918 3919 3940 C3' A D 3 OK 3938 3941 3942 3962 C3' A D 4 OK 3960 3963 3964 3984 C3' C D 5 OK 3982 3985 3986 4004 C3' U D 6 OK 4002 4005 4006 4024 C3' G D 7 OK 4022 4025 4026 4047 C3' U D 8 OK 4045 4048 4049 4067 C3' C D 9 OK 4065 4068 4069 4092 C3' U C 1 OK 4090 4093 4094 4112 C3' C C 2 OK 4110 4113 4114 4132 C3' A C 3 OK 4130 4133 4134 4154 C3' U C 4 OK 4152 4155 4156 4174 C3' U C 5 OK 4172 4175 4176 4194 C3' C C 6 OK 4192 4195 4196 4214 C3' A C 7 OK 4212 4215 4216 4236 C3' G C 8 OK 4234 4237 4238 4259 C3' U C 9 OK 4257 4260 4261 4279 C3' U C 10 OK 4277 4280 4281 4299 C3' C C 11 OK 4297 4300 4301 4319 C3' U C 12 OK 4317 4320 4321 4340 C3' G E -1 OK 4338 4341 4342 4363 C3' A E 0 OK 4361 4364 4365 4385 C3' A E 1 OK 4383 4386 4387 4407 C3' C E 2 OK 4405 4408 4409 4427 C3' U E 3 OK 4425 4428 4429 4447 C3' G E 4 OK 4445 4448 4449 4470 C3' U E 5 OK 4468 4471 4472 4490 C3' C E 6 OK 4488 4491 4492 4510 C3' A E 7 OK 4508 4511 4512 4532 C3' U E 8 OK 4530 4533 4534 4553 C3' C G -3 OK 4551 4554 4555 4573 C3' A G -2 OK 4571 4574 4575 4595 C3' U G -1 OK 4593 4596 4597 4615 C3' U G 0 OK 4613 4616 4617 4635 C3' C G 1 OK 4633 4636 4637 4655 C3' A G 2 OK 4653 4656 4657 4677 C3' G G 3 OK 4675 4678 4679 4700 C3' U G 4 OK 4698 4701 4702 4720 C3' U G 5 OK 4718 4721 4722 4740 C3' C G 6 OK 4738 4741 4742 4760 C3' U G 7 OK 4758 4761 4762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3893 C4' A D 1 OK 3895 3892 3894 3915 C4' G D 2 OK 3917 3914 3916 3938 C4' A D 3 OK 3940 3937 3939 3960 C4' A D 4 OK 3962 3959 3961 3982 C4' C D 5 OK 3984 3981 3983 4002 C4' U D 6 OK 4004 4001 4003 4022 C4' G D 7 OK 4024 4021 4023 4045 C4' U D 8 OK 4047 4044 4046 4065 C4' C D 9 OK 4067 4064 4066 4090 C4' U C 1 OK 4092 4089 4091 4110 C4' C C 2 OK 4112 4109 4111 4130 C4' A C 3 OK 4132 4129 4131 4152 C4' U C 4 OK 4154 4151 4153 4172 C4' U C 5 OK 4174 4171 4173 4192 C4' C C 6 OK 4194 4191 4193 4212 C4' A C 7 OK 4214 4211 4213 4234 C4' G C 8 OK 4236 4233 4235 4257 C4' U C 9 OK 4259 4256 4258 4277 C4' U C 10 OK 4279 4276 4278 4297 C4' C C 11 OK 4299 4296 4298 4317 C4' U C 12 OK 4319 4316 4318 4338 C4' G E -1 OK 4340 4337 4339 4361 C4' A E 0 OK 4363 4360 4362 4383 C4' A E 1 OK 4385 4382 4384 4405 C4' C E 2 OK 4407 4404 4406 4425 C4' U E 3 OK 4427 4424 4426 4445 C4' G E 4 OK 4447 4444 4446 4468 C4' U E 5 OK 4470 4467 4469 4488 C4' C E 6 OK 4490 4487 4489 4508 C4' A E 7 OK 4510 4507 4509 4530 C4' U E 8 OK 4532 4529 4531 4551 C4' C G -3 OK 4553 4550 4552 4571 C4' A G -2 OK 4573 4570 4572 4593 C4' U G -1 OK 4595 4592 4594 4613 C4' U G 0 OK 4615 4612 4614 4633 C4' C G 1 OK 4635 4632 4634 4653 C4' A G 2 OK 4655 4652 4654 4675 C4' G G 3 OK 4677 4674 4676 4698 C4' U G 4 OK 4700 4697 4699 4718 C4' U G 5 OK 4720 4717 4719 4738 C4' C G 6 OK 4740 4737 4739 4758 C4' U G 7 OK 4760 4757 4759 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3892 C5' A D 1 3891 3893 3914 C5' G D 2 3913 3915 3937 C5' A D 3 3936 3938 3959 C5' A D 4 3958 3960 3981 C5' C D 5 3980 3982 4001 C5' U D 6 4000 4002 4021 C5' G D 7 4020 4022 4044 C5' U D 8 4043 4045 4064 C5' C D 9 4063 4065 4089 C5' U C 1 4088 4090 4109 C5' C C 2 4108 4110 4129 C5' A C 3 4128 4130 4151 C5' U C 4 4150 4152 4171 C5' U C 5 4170 4172 4191 C5' C C 6 4190 4192 4211 C5' A C 7 4210 4212 4233 C5' G C 8 4232 4234 4256 C5' U C 9 4255 4257 4276 C5' U C 10 4275 4277 4296 C5' C C 11 4295 4297 4316 C5' U C 12 4315 4317 4337 C5' G E -1 4336 4338 4360 C5' A E 0 4359 4361 4382 C5' A E 1 4381 4383 4404 C5' C E 2 4403 4405 4424 C5' U E 3 4423 4425 4444 C5' G E 4 4443 4445 4467 C5' U E 5 4466 4468 4487 C5' C E 6 4486 4488 4507 C5' A E 7 4506 4508 4529 C5' U E 8 4528 4530 4550 C5' C G -3 4549 4551 4570 C5' A G -2 4569 4571 4592 C5' U G -1 4591 4593 4612 C5' U G 0 4611 4613 4632 C5' C G 1 4631 4633 4652 C5' A G 2 4651 4653 4674 C5' G G 3 4673 4675 4697 C5' U G 4 4696 4698 4717 C5' U G 5 4716 4718 4737 C5' C G 6 4736 4738 4757 C5' U G 7 4756 4758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3888 P A D 1 OK OK 3889 3890 3891 3910 P G D 2 distorted distorted 3896 3911 3912 3913 3933 P A D 3 distorted distorted 3918 3934 3935 3936 3955 P A D 4 distorted distorted 3941 3956 3957 3958 3977 P C D 5 distorted distorted 3963 3978 3979 3980 3997 P U D 6 distorted distorted 3985 3998 3999 4000 4017 P G D 7 distorted distorted 4005 4018 4019 4020 4040 P U D 8 distorted distorted 4025 4041 4042 4043 4060 P C D 9 distorted distorted 4048 4061 4062 4063 4080 P A D 10 distorted distorted 4068 4081 4082 4083 4085 P U C 1 OK OK 4086 4087 4088 4105 P C C 2 distorted distorted 4093 4106 4107 4108 4125 P A C 3 distorted distorted 4113 4126 4127 4128 4147 P U C 4 distorted distorted 4133 4148 4149 4150 4167 P U C 5 distorted distorted 4155 4168 4169 4170 4187 P C C 6 distorted distorted 4175 4188 4189 4190 4207 P A C 7 distorted distorted 4195 4208 4209 4210 4229 P G C 8 distorted distorted 4215 4230 4231 4232 4252 P U C 9 distorted distorted 4237 4253 4254 4255 4272 P U C 10 distorted distorted 4260 4273 4274 4275 4292 P C C 11 distorted distorted 4280 4293 4294 4295 4312 P U C 12 distorted distorted 4300 4313 4314 4315 4333 P G E -1 OK OK 4334 4335 4336 4356 P A E 0 distorted distorted 4341 4357 4358 4359 4378 P A E 1 distorted distorted 4364 4379 4380 4381 4400 P C E 2 distorted distorted 4386 4401 4402 4403 4420 P U E 3 distorted distorted 4408 4421 4422 4423 4440 P G E 4 distorted distorted 4428 4441 4442 4443 4463 P U E 5 distorted distorted 4448 4464 4465 4466 4483 P C E 6 distorted distorted 4471 4484 4485 4486 4503 P A E 7 distorted distorted 4491 4504 4505 4506 4525 P U E 8 distorted distorted 4511 4526 4527 4528 4546 P C G -3 distorted distorted 4547 4548 4549 4566 P A G -2 distorted distorted 4554 4567 4568 4569 4588 P U G -1 distorted distorted 4574 4589 4590 4591 4608 P U G 0 distorted distorted 4596 4609 4610 4611 4628 P C G 1 distorted distorted 4616 4629 4630 4631 4648 P A G 2 distorted distorted 4636 4649 4650 4651 4670 P G G 3 distorted distorted 4656 4671 4672 4673 4693 P U G 4 distorted distorted 4678 4694 4695 4696 4713 P U G 5 distorted distorted 4701 4714 4715 4716 4733 P C G 6 distorted distorted 4721 4734 4735 4736 4753 P U G 7 distorted distorted 4741 4754 4755 4756 ---------------------------------------------------------------------------------