ID code: '2ZH4' 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' --------------------------------------------------------------------------------- 3643 C1' G B 1 beta 3638 3644 3641 3666 C1' G B 2 beta 3661 3667 3664 3689 C1' C B 3 beta 3684 3690 3687 3709 C1' C B 4 beta 3704 3710 3707 3729 C1' C B 5 beta 3724 3730 3727 3749 C1' G B 6 beta 3744 3750 3747 3772 C1' G B 7 beta 3767 3773 3770 3795 C1' G B 8 beta 3790 3796 3793 3818 C1' G B 9 beta 3813 3819 3816 3841 C1' C B 10 beta 3836 3842 3839 3861 C1' G B 11 beta 3856 3862 3859 3884 C1' G B 12 beta 3879 3885 3882 3907 C1' U B 13 beta 3902 3908 3905 3927 C1' U B 14 beta 3922 3928 3925 3947 C1' C B 15 beta 3942 3948 3945 3967 C1' G B 16 beta 3962 3968 3965 3990 C1' A B 17 beta 3985 3991 3988 4012 C1' U B 18 beta 4007 4013 4010 4032 C1' U B 19 beta 4027 4033 4030 4052 C1' C B 20 beta 4047 4053 4050 4072 C1' C B 21 beta 4067 4073 4070 4092 C1' G B 22 beta 4087 4093 4090 4115 C1' C B 23 beta 4110 4116 4113 4135 C1' C B 24 beta 4130 4136 4133 4155 C1' C B 25 beta 4150 4156 4153 4175 C1' U B 26 beta 4170 4176 4173 4195 C1' G B 27 beta 4190 4196 4193 4218 C1' G B 28 beta 4213 4219 4216 4241 C1' G B 29 beta 4236 4242 4239 4264 C1' C B 30 beta 4259 4265 4262 4284 C1' C B 31 beta 4279 4285 4282 4304 C1' A B 32 beta 4299 4305 4302 4326 C1' C B 33 beta 4321 4327 4324 4346 C1' G B 34 beta 4341 4347 4344 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3641 C2' G B 1 OK 3643 3639 3642 3664 C2' G B 2 OK 3666 3662 3665 3687 C2' C B 3 OK 3689 3685 3688 3707 C2' C B 4 OK 3709 3705 3708 3727 C2' C B 5 OK 3729 3725 3728 3747 C2' G B 6 OK 3749 3745 3748 3770 C2' G B 7 OK 3772 3768 3771 3793 C2' G B 8 OK 3795 3791 3794 3816 C2' G B 9 OK 3818 3814 3817 3839 C2' C B 10 OK 3841 3837 3840 3859 C2' G B 11 OK 3861 3857 3860 3882 C2' G B 12 OK 3884 3880 3883 3905 C2' U B 13 OK 3907 3903 3906 3925 C2' U B 14 OK 3927 3923 3926 3945 C2' C B 15 OK 3947 3943 3946 3965 C2' G B 16 OK 3967 3963 3966 3988 C2' A B 17 OK 3990 3986 3989 4010 C2' U B 18 OK 4012 4008 4011 4030 C2' U B 19 OK 4032 4028 4031 4050 C2' C B 20 OK 4052 4048 4051 4070 C2' C B 21 OK 4072 4068 4071 4090 C2' G B 22 OK 4092 4088 4091 4113 C2' C B 23 OK 4115 4111 4114 4133 C2' C B 24 OK 4135 4131 4134 4153 C2' C B 25 OK 4155 4151 4154 4173 C2' U B 26 OK 4175 4171 4174 4193 C2' G B 27 OK 4195 4191 4194 4216 C2' G B 28 OK 4218 4214 4217 4239 C2' G B 29 OK 4241 4237 4240 4262 C2' C B 30 OK 4264 4260 4263 4282 C2' C B 31 OK 4284 4280 4283 4302 C2' A B 32 OK 4304 4300 4303 4324 C2' C B 33 OK 4326 4322 4325 4344 C2' G B 34 OK 4346 4342 4345 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3639 C3' G B 1 OK 3637 3640 3641 3662 C3' G B 2 OK 3660 3663 3664 3685 C3' C B 3 OK 3683 3686 3687 3705 C3' C B 4 OK 3703 3706 3707 3725 C3' C B 5 OK 3723 3726 3727 3745 C3' G B 6 OK 3743 3746 3747 3768 C3' G B 7 OK 3766 3769 3770 3791 C3' G B 8 OK 3789 3792 3793 3814 C3' G B 9 OK 3812 3815 3816 3837 C3' C B 10 OK 3835 3838 3839 3857 C3' G B 11 OK 3855 3858 3859 3880 C3' G B 12 OK 3878 3881 3882 3903 C3' U B 13 OK 3901 3904 3905 3923 C3' U B 14 OK 3921 3924 3925 3943 C3' C B 15 OK 3941 3944 3945 3963 C3' G B 16 OK 3961 3964 3965 3986 C3' A B 17 OK 3984 3987 3988 4008 C3' U B 18 OK 4006 4009 4010 4028 C3' U B 19 OK 4026 4029 4030 4048 C3' C B 20 OK 4046 4049 4050 4068 C3' C B 21 OK 4066 4069 4070 4088 C3' G B 22 OK 4086 4089 4090 4111 C3' C B 23 OK 4109 4112 4113 4131 C3' C B 24 OK 4129 4132 4133 4151 C3' C B 25 OK 4149 4152 4153 4171 C3' U B 26 OK 4169 4172 4173 4191 C3' G B 27 OK 4189 4192 4193 4214 C3' G B 28 OK 4212 4215 4216 4237 C3' G B 29 OK 4235 4238 4239 4260 C3' C B 30 OK 4258 4261 4262 4280 C3' C B 31 OK 4278 4281 4282 4300 C3' A B 32 OK 4298 4301 4302 4322 C3' C B 33 OK 4320 4323 4324 4342 C3' G B 34 OK 4340 4343 4344 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3637 C4' G B 1 OK 3639 3636 3638 3660 C4' G B 2 OK 3662 3659 3661 3683 C4' C B 3 OK 3685 3682 3684 3703 C4' C B 4 OK 3705 3702 3704 3723 C4' C B 5 OK 3725 3722 3724 3743 C4' G B 6 OK 3745 3742 3744 3766 C4' G B 7 OK 3768 3765 3767 3789 C4' G B 8 OK 3791 3788 3790 3812 C4' G B 9 OK 3814 3811 3813 3835 C4' C B 10 OK 3837 3834 3836 3855 C4' G B 11 OK 3857 3854 3856 3878 C4' G B 12 OK 3880 3877 3879 3901 C4' U B 13 OK 3903 3900 3902 3921 C4' U B 14 OK 3923 3920 3922 3941 C4' C B 15 OK 3943 3940 3942 3961 C4' G B 16 OK 3963 3960 3962 3984 C4' A B 17 OK 3986 3983 3985 4006 C4' U B 18 OK 4008 4005 4007 4026 C4' U B 19 OK 4028 4025 4027 4046 C4' C B 20 OK 4048 4045 4047 4066 C4' C B 21 OK 4068 4065 4067 4086 C4' G B 22 OK 4088 4085 4087 4109 C4' C B 23 OK 4111 4108 4110 4129 C4' C B 24 OK 4131 4128 4130 4149 C4' C B 25 OK 4151 4148 4150 4169 C4' U B 26 OK 4171 4168 4170 4189 C4' G B 27 OK 4191 4188 4190 4212 C4' G B 28 OK 4214 4211 4213 4235 C4' G B 29 OK 4237 4234 4236 4258 C4' C B 30 OK 4260 4257 4259 4278 C4' C B 31 OK 4280 4277 4279 4298 C4' A B 32 OK 4300 4297 4299 4320 C4' C B 33 OK 4322 4319 4321 4340 C4' G B 34 OK 4342 4339 4341 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3636 C5' G B 1 3635 3637 3659 C5' G B 2 3658 3660 3682 C5' C B 3 3681 3683 3702 C5' C B 4 3701 3703 3722 C5' C B 5 3721 3723 3742 C5' G B 6 3741 3743 3765 C5' G B 7 3764 3766 3788 C5' G B 8 3787 3789 3811 C5' G B 9 3810 3812 3834 C5' C B 10 3833 3835 3854 C5' G B 11 3853 3855 3877 C5' G B 12 3876 3878 3900 C5' U B 13 3899 3901 3920 C5' U B 14 3919 3921 3940 C5' C B 15 3939 3941 3960 C5' G B 16 3959 3961 3983 C5' A B 17 3982 3984 4005 C5' U B 18 4004 4006 4025 C5' U B 19 4024 4026 4045 C5' C B 20 4044 4046 4065 C5' C B 21 4064 4066 4085 C5' G B 22 4084 4086 4108 C5' C B 23 4107 4109 4128 C5' C B 24 4127 4129 4148 C5' C B 25 4147 4149 4168 C5' U B 26 4167 4169 4188 C5' G B 27 4187 4189 4211 C5' G B 28 4210 4212 4234 C5' G B 29 4233 4235 4257 C5' C B 30 4256 4258 4277 C5' C B 31 4276 4278 4297 C5' A B 32 4296 4298 4319 C5' C B 33 4318 4320 4339 C5' G B 34 4338 4340 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3632 P G B 1 distorted distorted 3633 3634 3635 3655 P G B 2 distorted distorted 3640 3656 3657 3658 3678 P C B 3 distorted distorted 3663 3679 3680 3681 3698 P C B 4 distorted distorted 3686 3699 3700 3701 3718 P C B 5 distorted distorted 3706 3719 3720 3721 3738 P G B 6 distorted distorted 3726 3739 3740 3741 3761 P G B 7 distorted distorted 3746 3762 3763 3764 3784 P G B 8 distorted distorted 3769 3785 3786 3787 3807 P G B 9 distorted distorted 3792 3808 3809 3810 3830 P C B 10 distorted distorted 3815 3831 3832 3833 3850 P G B 11 distorted distorted 3838 3851 3852 3853 3873 P G B 12 distorted distorted 3858 3874 3875 3876 3896 P U B 13 distorted distorted 3881 3897 3898 3899 3916 P U B 14 distorted distorted 3904 3917 3918 3919 3936 P C B 15 distorted distorted 3924 3937 3938 3939 3956 P G B 16 distorted distorted 3944 3957 3958 3959 3979 P A B 17 distorted distorted 3964 3980 3981 3982 4001 P U B 18 distorted distorted 3987 4002 4003 4004 4021 P U B 19 distorted distorted 4009 4022 4023 4024 4041 P C B 20 distorted distorted 4029 4042 4043 4044 4061 P C B 21 distorted distorted 4049 4062 4063 4064 4081 P G B 22 distorted distorted 4069 4082 4083 4084 4104 P C B 23 distorted distorted 4089 4105 4106 4107 4124 P C B 24 distorted distorted 4112 4125 4126 4127 4144 P C B 25 distorted distorted 4132 4145 4146 4147 4164 P U B 26 distorted distorted 4152 4165 4166 4167 4184 P G B 27 distorted distorted 4172 4185 4186 4187 4207 P G B 28 distorted distorted 4192 4208 4209 4210 4230 P G B 29 distorted distorted 4215 4231 4232 4233 4253 P C B 30 distorted distorted 4238 4254 4255 4256 4273 P C B 31 distorted distorted 4261 4274 4275 4276 4293 P A B 32 distorted distorted 4281 4294 4295 4296 4315 P C B 33 distorted distorted 4301 4316 4317 4318 4335 P G B 34 distorted distorted 4323 4336 4337 4338 ---------------------------------------------------------------------------------