ID code: '1A31' 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' --------------------------------------------------------------------------------- 3699 C1' A C 1 beta 3695 3700 3698 3720 C1' A C 2 beta 3716 3721 3719 3741 C1' A C 3 beta 3737 3742 3740 3762 C1' A C 4 beta 3758 3763 3761 3783 C1' A C 5 beta 3779 3784 3782 3804 C1' G C 6 beta 3800 3805 3803 3826 C1' A C 7 beta 3822 3827 3825 3847 C1' C C 8 beta 3843 3848 3846 3865 C1' 5IU C 9 beta 3870 3856 3866 3885 C1' 5IU C 10 beta 3889 3876 3886 3902 C1' T C 11 beta 3898 3903 3901 3922 C1' G C 12 beta 3918 3923 3921 3944 C1' A C 13 beta 3940 3945 3943 3965 C1' A C 14 beta 3961 3966 3964 3986 C1' A C 15 beta 3982 3987 3985 4007 C1' A C 16 beta 4003 4008 4006 4028 C1' A C 17 beta 4024 4029 4027 4048 C1' 5IU C 18 beta 4053 4039 4049 4068 C1' 5IU C 19 beta 4073 4059 4069 4088 C1' 5IU C 20 beta 4093 4079 4089 4108 C1' 5IU C 21 beta 4113 4099 4109 4129 C1' T C 22 beta 4125 4130 4128 4147 C1' A D 101 beta 4143 4148 4146 4168 C1' A D 102 beta 4164 4169 4167 4189 C1' A D 103 beta 4185 4190 4188 4210 C1' A D 104 beta 4206 4211 4209 4231 C1' A D 105 beta 4227 4232 4230 4252 C1' T D 106 beta 4248 4253 4251 4271 C1' 5IU D 107 beta 4276 4262 4272 4291 C1' 5IU D 108 beta 4296 4282 4292 4311 C1' 5IU D 109 beta 4316 4302 4312 4331 C1' 5IU D 110 beta 4336 4322 4332 4352 C1' C D 111 beta 4348 4353 4351 4371 C1' A D 112 beta 4367 4372 4370 4392 C1' A D 113 beta 4388 4393 4391 4413 C1' A D 114 beta 4409 4414 4412 4434 C1' G D 115 beta 4430 4435 4433 4456 C1' T D 116 beta 4452 4457 4455 4476 C1' C D 117 beta 4472 4477 4475 4495 C1' T D 118 beta 4491 4496 4494 4515 C1' T D 119 beta 4511 4516 4514 4535 C1' T D 120 beta 4531 4536 4534 4555 C1' T D 121 beta 4551 4556 4554 4575 C1' T D 122 beta 4571 4576 4574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3698 C2' A C 1 3699 3696 3719 C2' A C 2 3720 3717 3740 C2' A C 3 3741 3738 3761 C2' A C 4 3762 3759 3782 C2' A C 5 3783 3780 3803 C2' G C 6 3804 3801 3825 C2' A C 7 3826 3823 3846 C2' C C 8 3847 3844 3866 C2' 5IU C 9 3865 3867 3886 C2' 5IU C 10 3885 3887 3901 C2' T C 11 3902 3899 3921 C2' G C 12 3922 3919 3943 C2' A C 13 3944 3941 3964 C2' A C 14 3965 3962 3985 C2' A C 15 3986 3983 4006 C2' A C 16 4007 4004 4027 C2' A C 17 4028 4025 4049 C2' 5IU C 18 4048 4050 4069 C2' 5IU C 19 4068 4070 4089 C2' 5IU C 20 4088 4090 4109 C2' 5IU C 21 4108 4110 4128 C2' T C 22 4129 4126 4146 C2' A D 101 4147 4144 4167 C2' A D 102 4168 4165 4188 C2' A D 103 4189 4186 4209 C2' A D 104 4210 4207 4230 C2' A D 105 4231 4228 4251 C2' T D 106 4252 4249 4272 C2' 5IU D 107 4271 4273 4292 C2' 5IU D 108 4291 4293 4312 C2' 5IU D 109 4311 4313 4332 C2' 5IU D 110 4331 4333 4351 C2' C D 111 4352 4349 4370 C2' A D 112 4371 4368 4391 C2' A D 113 4392 4389 4412 C2' A D 114 4413 4410 4433 C2' G D 115 4434 4431 4455 C2' T D 116 4456 4453 4475 C2' C D 117 4476 4473 4494 C2' T D 118 4495 4492 4514 C2' T D 119 4515 4512 4534 C2' T D 120 4535 4532 4554 C2' T D 121 4555 4552 4574 C2' T D 122 4575 4572 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3696 C3' A C 1 OK 3694 3697 3698 3717 C3' A C 2 OK 3715 3718 3719 3738 C3' A C 3 OK 3736 3739 3740 3759 C3' A C 4 OK 3757 3760 3761 3780 C3' A C 5 OK 3778 3781 3782 3801 C3' G C 6 OK 3799 3802 3803 3823 C3' A C 7 OK 3821 3824 3825 3844 C3' C C 8 OK 3842 3845 3846 3867 C3' 5IU C 9 OK 3868 3869 3866 3887 C3' 5IU C 10 3888 3886 3899 C3' T C 11 OK 3897 3900 3901 3919 C3' G C 12 OK 3917 3920 3921 3941 C3' A C 13 OK 3939 3942 3943 3962 C3' A C 14 OK 3960 3963 3964 3983 C3' A C 15 OK 3981 3984 3985 4004 C3' A C 16 OK 4002 4005 4006 4025 C3' A C 17 OK 4023 4026 4027 4050 C3' 5IU C 18 OK 4051 4052 4049 4070 C3' 5IU C 19 OK 4071 4072 4069 4090 C3' 5IU C 20 OK 4091 4092 4089 4110 C3' 5IU C 21 OK 4111 4112 4109 4126 C3' T C 22 OK 4124 4127 4128 4144 C3' A D 101 OK 4142 4145 4146 4165 C3' A D 102 OK 4163 4166 4167 4186 C3' A D 103 OK 4184 4187 4188 4207 C3' A D 104 OK 4205 4208 4209 4228 C3' A D 105 OK 4226 4229 4230 4249 C3' T D 106 OK 4247 4250 4251 4273 C3' 5IU D 107 OK 4274 4275 4272 4293 C3' 5IU D 108 OK 4294 4295 4292 4313 C3' 5IU D 109 OK 4314 4315 4312 4333 C3' 5IU D 110 OK 4334 4335 4332 4349 C3' C D 111 OK 4347 4350 4351 4368 C3' A D 112 OK 4366 4369 4370 4389 C3' A D 113 OK 4387 4390 4391 4410 C3' A D 114 OK 4408 4411 4412 4431 C3' G D 115 OK 4429 4432 4433 4453 C3' T D 116 OK 4451 4454 4455 4473 C3' C D 117 OK 4471 4474 4475 4492 C3' T D 118 OK 4490 4493 4494 4512 C3' T D 119 OK 4510 4513 4514 4532 C3' T D 120 OK 4530 4533 4534 4552 C3' T D 121 OK 4550 4553 4554 4572 C3' T D 122 OK 4570 4573 4574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3694 C4' A C 1 OK 3696 3693 3695 3715 C4' A C 2 OK 3717 3714 3716 3736 C4' A C 3 OK 3738 3735 3737 3757 C4' A C 4 OK 3759 3756 3758 3778 C4' A C 5 OK 3780 3777 3779 3799 C4' G C 6 OK 3801 3798 3800 3821 C4' A C 7 OK 3823 3820 3822 3842 C4' C C 8 OK 3844 3841 3843 3868 C4' 5IU C 9 OK 3867 3871 3870 3888 C4' 5IU C 10 OK 3887 3890 3889 3897 C4' T C 11 OK 3899 3896 3898 3917 C4' G C 12 OK 3919 3916 3918 3939 C4' A C 13 OK 3941 3938 3940 3960 C4' A C 14 OK 3962 3959 3961 3981 C4' A C 15 OK 3983 3980 3982 4002 C4' A C 16 OK 4004 4001 4003 4023 C4' A C 17 OK 4025 4022 4024 4051 C4' 5IU C 18 OK 4050 4054 4053 4071 C4' 5IU C 19 OK 4070 4074 4073 4091 C4' 5IU C 20 OK 4090 4094 4093 4111 C4' 5IU C 21 OK 4110 4114 4113 4124 C4' T C 22 OK 4126 4123 4125 4142 C4' A D 101 OK 4144 4141 4143 4163 C4' A D 102 OK 4165 4162 4164 4184 C4' A D 103 OK 4186 4183 4185 4205 C4' A D 104 OK 4207 4204 4206 4226 C4' A D 105 OK 4228 4225 4227 4247 C4' T D 106 OK 4249 4246 4248 4274 C4' 5IU D 107 OK 4273 4277 4276 4294 C4' 5IU D 108 OK 4293 4297 4296 4314 C4' 5IU D 109 OK 4313 4317 4316 4334 C4' 5IU D 110 OK 4333 4337 4336 4347 C4' C D 111 OK 4349 4346 4348 4366 C4' A D 112 OK 4368 4365 4367 4387 C4' A D 113 OK 4389 4386 4388 4408 C4' A D 114 OK 4410 4407 4409 4429 C4' G D 115 OK 4431 4428 4430 4451 C4' T D 116 OK 4453 4450 4452 4471 C4' C D 117 OK 4473 4470 4472 4490 C4' T D 118 OK 4492 4489 4491 4510 C4' T D 119 OK 4512 4509 4511 4530 C4' T D 120 OK 4532 4529 4531 4550 C4' T D 121 OK 4552 4549 4551 4570 C4' T D 122 OK 4572 4569 4571 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3693 C5' A C 1 3692 3694 3714 C5' A C 2 3713 3715 3735 C5' A C 3 3734 3736 3756 C5' A C 4 3755 3757 3777 C5' A C 5 3776 3778 3798 C5' G C 6 3797 3799 3820 C5' A C 7 3819 3821 3841 C5' C C 8 3840 3842 3871 C5' 5IU C 9 3872 3868 3890 C5' 5IU C 10 3891 3888 3896 C5' T C 11 3895 3897 3916 C5' G C 12 3915 3917 3938 C5' A C 13 3937 3939 3959 C5' A C 14 3958 3960 3980 C5' A C 15 3979 3981 4001 C5' A C 16 4000 4002 4022 C5' A C 17 4021 4023 4054 C5' 5IU C 18 4055 4051 4074 C5' 5IU C 19 4075 4071 4094 C5' 5IU C 20 4095 4091 4114 C5' 5IU C 21 4115 4111 4123 C5' T C 22 4122 4124 4141 C5' A D 101 4140 4142 4162 C5' A D 102 4161 4163 4183 C5' A D 103 4182 4184 4204 C5' A D 104 4203 4205 4225 C5' A D 105 4224 4226 4246 C5' T D 106 4245 4247 4277 C5' 5IU D 107 4278 4274 4297 C5' 5IU D 108 4298 4294 4317 C5' 5IU D 109 4318 4314 4337 C5' 5IU D 110 4338 4334 4346 C5' C D 111 4345 4347 4365 C5' A D 112 4364 4366 4386 C5' A D 113 4385 4387 4407 C5' A D 114 4406 4408 4428 C5' G D 115 4427 4429 4450 C5' T D 116 4449 4451 4470 C5' C D 117 4469 4471 4489 C5' T D 118 4488 4490 4509 C5' T D 119 4508 4510 4529 C5' T D 120 4528 4530 4549 C5' T D 121 4548 4550 4569 C5' T D 122 4568 4570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3710 P A C 2 distorted distorted 3697 3711 3712 3713 3731 P A C 3 distorted distorted 3718 3732 3733 3734 3752 P A C 4 distorted distorted 3739 3753 3754 3755 3773 P A C 5 distorted distorted 3760 3774 3775 3776 3794 P G C 6 OK OK 3781 3795 3796 3797 3816 P A C 7 distorted distorted 3802 3817 3818 3819 3837 P C C 8 distorted distorted 3824 3838 3839 3840 3873 P 5IU C 9 distorted distorted 3845 3874 3875 3872 3892 P 5IU C 10 distorted distorted 3869 3893 3894 3891 3912 P G C 12 distorted distorted 3900 3913 3914 3915 3934 P A C 13 distorted distorted 3920 3935 3936 3937 3955 P A C 14 distorted distorted 3942 3956 3957 3958 3976 P A C 15 distorted distorted 3963 3977 3978 3979 3997 P A C 16 distorted distorted 3984 3998 3999 4000 4018 P A C 17 distorted distorted 4005 4019 4020 4021 4056 P 5IU C 18 distorted distorted 4026 4057 4058 4055 4076 P 5IU C 19 distorted distorted 4052 4077 4078 4075 4096 P 5IU C 20 distorted distorted 4072 4097 4098 4095 4116 P 5IU C 21 distorted distorted 4092 4117 4118 4115 4119 P T C 22 distorted distorted 4112 4120 4121 4122 4158 P A D 102 distorted distorted 4145 4159 4160 4161 4179 P A D 103 distorted distorted 4166 4180 4181 4182 4200 P A D 104 distorted distorted 4187 4201 4202 4203 4221 P A D 105 distorted distorted 4208 4222 4223 4224 4242 P T D 106 distorted distorted 4229 4243 4244 4245 4279 P 5IU D 107 distorted distorted 4250 4280 4281 4278 4299 P 5IU D 108 distorted distorted 4275 4300 4301 4298 4319 P 5IU D 109 distorted distorted 4295 4320 4321 4318 4339 P 5IU D 110 distorted distorted 4315 4340 4341 4338 4342 P C D 111 distorted distorted 4335 4343 4344 4345 4361 P A D 112 distorted distorted 4350 4362 4363 4364 4382 P A D 113 distorted distorted 4369 4383 4384 4385 4403 P A D 114 distorted distorted 4390 4404 4405 4406 4424 P G D 115 distorted distorted 4411 4425 4426 4427 4446 P T D 116 distorted distorted 4432 4447 4448 4449 4466 P C D 117 distorted distorted 4454 4467 4468 4469 4485 P T D 118 distorted distorted 4474 4486 4487 4488 4505 P T D 119 distorted distorted 4493 4506 4507 4508 4525 P T D 120 distorted distorted 4513 4526 4527 4528 4545 P T D 121 distorted distorted 4533 4546 4547 4548 4565 P T D 122 distorted distorted 4553 4566 4567 4568 ---------------------------------------------------------------------------------