ID code: '2ZH7' 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' --------------------------------------------------------------------------------- 3635 C1' G B 1 beta 3630 3636 3633 3658 C1' G B 2 beta 3653 3659 3656 3681 C1' C B 3 beta 3676 3682 3679 3701 C1' C B 4 beta 3696 3702 3699 3721 C1' C B 5 beta 3716 3722 3719 3741 C1' G B 6 beta 3736 3742 3739 3764 C1' G B 7 beta 3759 3765 3762 3787 C1' G B 8 beta 3782 3788 3785 3810 C1' G B 9 beta 3805 3811 3808 3833 C1' C B 10 beta 3828 3834 3831 3853 C1' G B 11 beta 3848 3854 3851 3876 C1' G B 12 beta 3871 3877 3874 3899 C1' U B 13 beta 3894 3900 3897 3919 C1' U B 14 beta 3914 3920 3917 3939 C1' C B 15 beta 3934 3940 3937 3959 C1' G B 16 beta 3954 3960 3957 3982 C1' A B 17 beta 3977 3983 3980 4004 C1' U B 18 beta 3999 4005 4002 4024 C1' U B 19 beta 4019 4025 4022 4044 C1' C B 20 beta 4039 4045 4042 4064 C1' C B 21 beta 4059 4065 4062 4084 C1' G B 22 beta 4079 4085 4082 4107 C1' C B 23 beta 4102 4108 4105 4127 C1' C B 24 beta 4122 4128 4125 4147 C1' C B 25 beta 4142 4148 4145 4167 C1' U B 26 beta 4162 4168 4165 4187 C1' G B 27 beta 4182 4188 4185 4210 C1' G B 28 beta 4205 4211 4208 4233 C1' G B 29 beta 4228 4234 4231 4256 C1' C B 30 beta 4251 4257 4254 4276 C1' C B 31 beta 4271 4277 4274 4296 C1' A B 32 beta 4291 4297 4294 4318 C1' G B 33 beta 4313 4319 4316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3633 C2' G B 1 OK 3635 3631 3634 3656 C2' G B 2 OK 3658 3654 3657 3679 C2' C B 3 OK 3681 3677 3680 3699 C2' C B 4 OK 3701 3697 3700 3719 C2' C B 5 OK 3721 3717 3720 3739 C2' G B 6 OK 3741 3737 3740 3762 C2' G B 7 OK 3764 3760 3763 3785 C2' G B 8 OK 3787 3783 3786 3808 C2' G B 9 OK 3810 3806 3809 3831 C2' C B 10 OK 3833 3829 3832 3851 C2' G B 11 OK 3853 3849 3852 3874 C2' G B 12 OK 3876 3872 3875 3897 C2' U B 13 OK 3899 3895 3898 3917 C2' U B 14 OK 3919 3915 3918 3937 C2' C B 15 OK 3939 3935 3938 3957 C2' G B 16 OK 3959 3955 3958 3980 C2' A B 17 OK 3982 3978 3981 4002 C2' U B 18 OK 4004 4000 4003 4022 C2' U B 19 OK 4024 4020 4023 4042 C2' C B 20 OK 4044 4040 4043 4062 C2' C B 21 OK 4064 4060 4063 4082 C2' G B 22 OK 4084 4080 4083 4105 C2' C B 23 OK 4107 4103 4106 4125 C2' C B 24 OK 4127 4123 4126 4145 C2' C B 25 OK 4147 4143 4146 4165 C2' U B 26 OK 4167 4163 4166 4185 C2' G B 27 OK 4187 4183 4186 4208 C2' G B 28 OK 4210 4206 4209 4231 C2' G B 29 OK 4233 4229 4232 4254 C2' C B 30 OK 4256 4252 4255 4274 C2' C B 31 OK 4276 4272 4275 4294 C2' A B 32 OK 4296 4292 4295 4316 C2' G B 33 OK 4318 4314 4317 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3631 C3' G B 1 OK 3629 3632 3633 3654 C3' G B 2 OK 3652 3655 3656 3677 C3' C B 3 OK 3675 3678 3679 3697 C3' C B 4 OK 3695 3698 3699 3717 C3' C B 5 OK 3715 3718 3719 3737 C3' G B 6 OK 3735 3738 3739 3760 C3' G B 7 OK 3758 3761 3762 3783 C3' G B 8 OK 3781 3784 3785 3806 C3' G B 9 OK 3804 3807 3808 3829 C3' C B 10 OK 3827 3830 3831 3849 C3' G B 11 OK 3847 3850 3851 3872 C3' G B 12 OK 3870 3873 3874 3895 C3' U B 13 OK 3893 3896 3897 3915 C3' U B 14 OK 3913 3916 3917 3935 C3' C B 15 OK 3933 3936 3937 3955 C3' G B 16 OK 3953 3956 3957 3978 C3' A B 17 OK 3976 3979 3980 4000 C3' U B 18 OK 3998 4001 4002 4020 C3' U B 19 OK 4018 4021 4022 4040 C3' C B 20 OK 4038 4041 4042 4060 C3' C B 21 OK 4058 4061 4062 4080 C3' G B 22 OK 4078 4081 4082 4103 C3' C B 23 OK 4101 4104 4105 4123 C3' C B 24 OK 4121 4124 4125 4143 C3' C B 25 OK 4141 4144 4145 4163 C3' U B 26 OK 4161 4164 4165 4183 C3' G B 27 OK 4181 4184 4185 4206 C3' G B 28 OK 4204 4207 4208 4229 C3' G B 29 OK 4227 4230 4231 4252 C3' C B 30 OK 4250 4253 4254 4272 C3' C B 31 OK 4270 4273 4274 4292 C3' A B 32 OK 4290 4293 4294 4314 C3' G B 33 OK 4312 4315 4316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3629 C4' G B 1 OK 3631 3628 3630 3652 C4' G B 2 OK 3654 3651 3653 3675 C4' C B 3 OK 3677 3674 3676 3695 C4' C B 4 OK 3697 3694 3696 3715 C4' C B 5 OK 3717 3714 3716 3735 C4' G B 6 OK 3737 3734 3736 3758 C4' G B 7 OK 3760 3757 3759 3781 C4' G B 8 OK 3783 3780 3782 3804 C4' G B 9 OK 3806 3803 3805 3827 C4' C B 10 OK 3829 3826 3828 3847 C4' G B 11 OK 3849 3846 3848 3870 C4' G B 12 OK 3872 3869 3871 3893 C4' U B 13 OK 3895 3892 3894 3913 C4' U B 14 OK 3915 3912 3914 3933 C4' C B 15 OK 3935 3932 3934 3953 C4' G B 16 OK 3955 3952 3954 3976 C4' A B 17 OK 3978 3975 3977 3998 C4' U B 18 OK 4000 3997 3999 4018 C4' U B 19 OK 4020 4017 4019 4038 C4' C B 20 OK 4040 4037 4039 4058 C4' C B 21 OK 4060 4057 4059 4078 C4' G B 22 OK 4080 4077 4079 4101 C4' C B 23 OK 4103 4100 4102 4121 C4' C B 24 OK 4123 4120 4122 4141 C4' C B 25 OK 4143 4140 4142 4161 C4' U B 26 OK 4163 4160 4162 4181 C4' G B 27 OK 4183 4180 4182 4204 C4' G B 28 OK 4206 4203 4205 4227 C4' G B 29 OK 4229 4226 4228 4250 C4' C B 30 OK 4252 4249 4251 4270 C4' C B 31 OK 4272 4269 4271 4290 C4' A B 32 OK 4292 4289 4291 4312 C4' G B 33 OK 4314 4311 4313 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3628 C5' G B 1 3627 3629 3651 C5' G B 2 3650 3652 3674 C5' C B 3 3673 3675 3694 C5' C B 4 3693 3695 3714 C5' C B 5 3713 3715 3734 C5' G B 6 3733 3735 3757 C5' G B 7 3756 3758 3780 C5' G B 8 3779 3781 3803 C5' G B 9 3802 3804 3826 C5' C B 10 3825 3827 3846 C5' G B 11 3845 3847 3869 C5' G B 12 3868 3870 3892 C5' U B 13 3891 3893 3912 C5' U B 14 3911 3913 3932 C5' C B 15 3931 3933 3952 C5' G B 16 3951 3953 3975 C5' A B 17 3974 3976 3997 C5' U B 18 3996 3998 4017 C5' U B 19 4016 4018 4037 C5' C B 20 4036 4038 4057 C5' C B 21 4056 4058 4077 C5' G B 22 4076 4078 4100 C5' C B 23 4099 4101 4120 C5' C B 24 4119 4121 4140 C5' C B 25 4139 4141 4160 C5' U B 26 4159 4161 4180 C5' G B 27 4179 4181 4203 C5' G B 28 4202 4204 4226 C5' G B 29 4225 4227 4249 C5' C B 30 4248 4250 4269 C5' C B 31 4268 4270 4289 C5' A B 32 4288 4290 4311 C5' G B 33 4310 4312 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3624 P G B 1 distorted distorted 3625 3626 3627 3647 P G B 2 distorted distorted 3632 3648 3649 3650 3670 P C B 3 distorted distorted 3655 3671 3672 3673 3690 P C B 4 distorted distorted 3678 3691 3692 3693 3710 P C B 5 distorted distorted 3698 3711 3712 3713 3730 P G B 6 distorted distorted 3718 3731 3732 3733 3753 P G B 7 distorted distorted 3738 3754 3755 3756 3776 P G B 8 distorted distorted 3761 3777 3778 3779 3799 P G B 9 distorted distorted 3784 3800 3801 3802 3822 P C B 10 distorted distorted 3807 3823 3824 3825 3842 P G B 11 distorted distorted 3830 3843 3844 3845 3865 P G B 12 distorted distorted 3850 3866 3867 3868 3888 P U B 13 distorted distorted 3873 3889 3890 3891 3908 P U B 14 distorted distorted 3896 3909 3910 3911 3928 P C B 15 distorted distorted 3916 3929 3930 3931 3948 P G B 16 distorted distorted 3936 3949 3950 3951 3971 P A B 17 distorted distorted 3956 3972 3973 3974 3993 P U B 18 distorted distorted 3979 3994 3995 3996 4013 P U B 19 distorted distorted 4001 4014 4015 4016 4033 P C B 20 distorted distorted 4021 4034 4035 4036 4053 P C B 21 distorted distorted 4041 4054 4055 4056 4073 P G B 22 distorted distorted 4061 4074 4075 4076 4096 P C B 23 distorted distorted 4081 4097 4098 4099 4116 P C B 24 distorted distorted 4104 4117 4118 4119 4136 P C B 25 distorted distorted 4124 4137 4138 4139 4156 P U B 26 distorted distorted 4144 4157 4158 4159 4176 P G B 27 distorted distorted 4164 4177 4178 4179 4199 P G B 28 distorted distorted 4184 4200 4201 4202 4222 P G B 29 distorted distorted 4207 4223 4224 4225 4245 P C B 30 distorted distorted 4230 4246 4247 4248 4265 P C B 31 distorted distorted 4253 4266 4267 4268 4285 P A B 32 distorted distorted 4273 4286 4287 4288 4307 P G B 33 distorted distorted 4293 4308 4309 4310 ---------------------------------------------------------------------------------