ID code: '4K4V' 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' --------------------------------------------------------------------------------- 3716 C1' A B 599 beta 3711 3717 3714 3738 C1' G B 600 beta 3733 3739 3736 3761 C1' G B 601 beta 3756 3762 3759 3784 C1' U B 602 beta 3779 3785 3782 3804 C1' C B 603 beta 3799 3805 3802 3824 C1' U B 604 beta 3819 3825 3822 3844 C1' C B 605 beta 3839 3845 3842 3864 C1' U B 606 beta 3859 3865 3862 3884 C1' C B 607 beta 3879 3885 3882 3904 C1' U B 608 beta 3899 3905 3902 3924 C1' C B 609 beta 3919 3925 3922 3944 C1' G B 610 beta 3939 3945 3942 3967 C1' U B 611 beta 3962 3968 3965 3988 C1' C C 692 beta 3983 3989 3986 4008 C1' G C 693 beta 4003 4009 4006 4031 C1' A C 694 beta 4026 4032 4029 4053 C1' G C 695 beta 4048 4054 4051 4076 C1' A C 696 beta 4071 4077 4074 4098 C1' G C 697 beta 4093 4099 4096 4121 C1' A C 698 beta 4116 4122 4119 4143 C1' G C 699 beta 4138 4144 4141 4166 C1' A C 700 beta 4161 4167 4164 4187 C1' DC C 701 beta 4183 4188 4186 7912 C1' A F 599 beta 7907 7913 7910 7934 C1' G F 600 beta 7929 7935 7932 7957 C1' G F 601 beta 7952 7958 7955 7980 C1' U F 602 beta 7975 7981 7978 8000 C1' C F 603 beta 7995 8001 7998 8020 C1' U F 604 beta 8015 8021 8018 8040 C1' C F 605 beta 8035 8041 8038 8060 C1' U F 606 beta 8055 8061 8058 8080 C1' C F 607 beta 8075 8081 8078 8100 C1' U F 608 beta 8095 8101 8098 8120 C1' C F 609 beta 8115 8121 8118 8140 C1' G F 610 beta 8135 8141 8138 8163 C1' U F 611 beta 8158 8164 8161 8184 C1' C G 692 beta 8179 8185 8182 8204 C1' G G 693 beta 8199 8205 8202 8227 C1' A G 694 beta 8222 8228 8225 8249 C1' G G 695 beta 8244 8250 8247 8272 C1' A G 696 beta 8267 8273 8270 8294 C1' G G 697 beta 8289 8295 8292 8317 C1' A G 698 beta 8312 8318 8315 8339 C1' G G 699 beta 8334 8340 8337 8362 C1' A G 700 beta 8357 8363 8360 8383 C1' DC G 701 beta 8379 8384 8382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3714 C2' A B 599 OK 3716 3712 3715 3736 C2' G B 600 OK 3738 3734 3737 3759 C2' G B 601 OK 3761 3757 3760 3782 C2' U B 602 OK 3784 3780 3783 3802 C2' C B 603 OK 3804 3800 3803 3822 C2' U B 604 OK 3824 3820 3823 3842 C2' C B 605 OK 3844 3840 3843 3862 C2' U B 606 OK 3864 3860 3863 3882 C2' C B 607 OK 3884 3880 3883 3902 C2' U B 608 OK 3904 3900 3903 3922 C2' C B 609 OK 3924 3920 3923 3942 C2' G B 610 OK 3944 3940 3943 3965 C2' U B 611 OK 3967 3963 3966 3986 C2' C C 692 OK 3988 3984 3987 4006 C2' G C 693 OK 4008 4004 4007 4029 C2' A C 694 OK 4031 4027 4030 4051 C2' G C 695 OK 4053 4049 4052 4074 C2' A C 696 OK 4076 4072 4075 4096 C2' G C 697 OK 4098 4094 4097 4119 C2' A C 698 OK 4121 4117 4120 4141 C2' G C 699 OK 4143 4139 4142 4164 C2' A C 700 OK 4166 4162 4165 4186 C2' DC C 701 4187 4184 7910 C2' A F 599 OK 7912 7908 7911 7932 C2' G F 600 OK 7934 7930 7933 7955 C2' G F 601 OK 7957 7953 7956 7978 C2' U F 602 OK 7980 7976 7979 7998 C2' C F 603 OK 8000 7996 7999 8018 C2' U F 604 OK 8020 8016 8019 8038 C2' C F 605 OK 8040 8036 8039 8058 C2' U F 606 OK 8060 8056 8059 8078 C2' C F 607 OK 8080 8076 8079 8098 C2' U F 608 OK 8100 8096 8099 8118 C2' C F 609 OK 8120 8116 8119 8138 C2' G F 610 OK 8140 8136 8139 8161 C2' U F 611 OK 8163 8159 8162 8182 C2' C G 692 OK 8184 8180 8183 8202 C2' G G 693 OK 8204 8200 8203 8225 C2' A G 694 OK 8227 8223 8226 8247 C2' G G 695 OK 8249 8245 8248 8270 C2' A G 696 OK 8272 8268 8271 8292 C2' G G 697 OK 8294 8290 8293 8315 C2' A G 698 OK 8317 8313 8316 8337 C2' G G 699 OK 8339 8335 8338 8360 C2' A G 700 OK 8362 8358 8361 8382 C2' DC G 701 8383 8380 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3712 C3' A B 599 OK 3710 3713 3714 3734 C3' G B 600 OK 3732 3735 3736 3757 C3' G B 601 OK 3755 3758 3759 3780 C3' U B 602 OK 3778 3781 3782 3800 C3' C B 603 OK 3798 3801 3802 3820 C3' U B 604 OK 3818 3821 3822 3840 C3' C B 605 OK 3838 3841 3842 3860 C3' U B 606 OK 3858 3861 3862 3880 C3' C B 607 OK 3878 3881 3882 3900 C3' U B 608 OK 3898 3901 3902 3920 C3' C B 609 OK 3918 3921 3922 3940 C3' G B 610 OK 3938 3941 3942 3963 C3' U B 611 OK 3961 3964 3965 3984 C3' C C 692 OK 3982 3985 3986 4004 C3' G C 693 OK 4002 4005 4006 4027 C3' A C 694 OK 4025 4028 4029 4049 C3' G C 695 OK 4047 4050 4051 4072 C3' A C 696 OK 4070 4073 4074 4094 C3' G C 697 OK 4092 4095 4096 4117 C3' A C 698 OK 4115 4118 4119 4139 C3' G C 699 OK 4137 4140 4141 4162 C3' A C 700 OK 4160 4163 4164 4184 C3' DC C 701 OK 4182 4185 4186 7908 C3' A F 599 OK 7906 7909 7910 7930 C3' G F 600 OK 7928 7931 7932 7953 C3' G F 601 OK 7951 7954 7955 7976 C3' U F 602 OK 7974 7977 7978 7996 C3' C F 603 OK 7994 7997 7998 8016 C3' U F 604 OK 8014 8017 8018 8036 C3' C F 605 OK 8034 8037 8038 8056 C3' U F 606 OK 8054 8057 8058 8076 C3' C F 607 OK 8074 8077 8078 8096 C3' U F 608 OK 8094 8097 8098 8116 C3' C F 609 OK 8114 8117 8118 8136 C3' G F 610 OK 8134 8137 8138 8159 C3' U F 611 OK 8157 8160 8161 8180 C3' C G 692 OK 8178 8181 8182 8200 C3' G G 693 OK 8198 8201 8202 8223 C3' A G 694 OK 8221 8224 8225 8245 C3' G G 695 OK 8243 8246 8247 8268 C3' A G 696 OK 8266 8269 8270 8290 C3' G G 697 OK 8288 8291 8292 8313 C3' A G 698 OK 8311 8314 8315 8335 C3' G G 699 OK 8333 8336 8337 8358 C3' A G 700 OK 8356 8359 8360 8380 C3' DC G 701 OK 8378 8381 8382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3710 C4' A B 599 OK 3712 3709 3711 3732 C4' G B 600 OK 3734 3731 3733 3755 C4' G B 601 OK 3757 3754 3756 3778 C4' U B 602 OK 3780 3777 3779 3798 C4' C B 603 OK 3800 3797 3799 3818 C4' U B 604 OK 3820 3817 3819 3838 C4' C B 605 OK 3840 3837 3839 3858 C4' U B 606 OK 3860 3857 3859 3878 C4' C B 607 OK 3880 3877 3879 3898 C4' U B 608 OK 3900 3897 3899 3918 C4' C B 609 OK 3920 3917 3919 3938 C4' G B 610 OK 3940 3937 3939 3961 C4' U B 611 OK 3963 3960 3962 3982 C4' C C 692 OK 3984 3981 3983 4002 C4' G C 693 OK 4004 4001 4003 4025 C4' A C 694 OK 4027 4024 4026 4047 C4' G C 695 OK 4049 4046 4048 4070 C4' A C 696 OK 4072 4069 4071 4092 C4' G C 697 OK 4094 4091 4093 4115 C4' A C 698 OK 4117 4114 4116 4137 C4' G C 699 OK 4139 4136 4138 4160 C4' A C 700 OK 4162 4159 4161 4182 C4' DC C 701 OK 4184 4181 4183 7906 C4' A F 599 OK 7908 7905 7907 7928 C4' G F 600 OK 7930 7927 7929 7951 C4' G F 601 OK 7953 7950 7952 7974 C4' U F 602 OK 7976 7973 7975 7994 C4' C F 603 OK 7996 7993 7995 8014 C4' U F 604 OK 8016 8013 8015 8034 C4' C F 605 OK 8036 8033 8035 8054 C4' U F 606 OK 8056 8053 8055 8074 C4' C F 607 OK 8076 8073 8075 8094 C4' U F 608 OK 8096 8093 8095 8114 C4' C F 609 OK 8116 8113 8115 8134 C4' G F 610 OK 8136 8133 8135 8157 C4' U F 611 OK 8159 8156 8158 8178 C4' C G 692 OK 8180 8177 8179 8198 C4' G G 693 OK 8200 8197 8199 8221 C4' A G 694 OK 8223 8220 8222 8243 C4' G G 695 OK 8245 8242 8244 8266 C4' A G 696 OK 8268 8265 8267 8288 C4' G G 697 OK 8290 8287 8289 8311 C4' A G 698 OK 8313 8310 8312 8333 C4' G G 699 OK 8335 8332 8334 8356 C4' A G 700 OK 8358 8355 8357 8378 C4' DC G 701 OK 8380 8377 8379 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3709 C5' A B 599 3708 3710 3731 C5' G B 600 3730 3732 3754 C5' G B 601 3753 3755 3777 C5' U B 602 3776 3778 3797 C5' C B 603 3796 3798 3817 C5' U B 604 3816 3818 3837 C5' C B 605 3836 3838 3857 C5' U B 606 3856 3858 3877 C5' C B 607 3876 3878 3897 C5' U B 608 3896 3898 3917 C5' C B 609 3916 3918 3937 C5' G B 610 3936 3938 3960 C5' U B 611 3959 3961 3981 C5' C C 692 3980 3982 4001 C5' G C 693 4000 4002 4024 C5' A C 694 4023 4025 4046 C5' G C 695 4045 4047 4069 C5' A C 696 4068 4070 4091 C5' G C 697 4090 4092 4114 C5' A C 698 4113 4115 4136 C5' G C 699 4135 4137 4159 C5' A C 700 4158 4160 4181 C5' DC C 701 4180 4182 7905 C5' A F 599 7904 7906 7927 C5' G F 600 7926 7928 7950 C5' G F 601 7949 7951 7973 C5' U F 602 7972 7974 7993 C5' C F 603 7992 7994 8013 C5' U F 604 8012 8014 8033 C5' C F 605 8032 8034 8053 C5' U F 606 8052 8054 8073 C5' C F 607 8072 8074 8093 C5' U F 608 8092 8094 8113 C5' C F 609 8112 8114 8133 C5' G F 610 8132 8134 8156 C5' U F 611 8155 8157 8177 C5' C G 692 8176 8178 8197 C5' G G 693 8196 8198 8220 C5' A G 694 8219 8221 8242 C5' G G 695 8241 8243 8265 C5' A G 696 8264 8266 8287 C5' G G 697 8286 8288 8310 C5' A G 698 8309 8311 8332 C5' G G 699 8331 8333 8355 C5' A G 700 8354 8356 8377 C5' DC G 701 8376 8378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3705 P A B 599 distorted distorted 3706 3707 3708 3727 P G B 600 distorted distorted 3713 3728 3729 3730 3750 P G B 601 distorted distorted 3735 3751 3752 3753 3773 P U B 602 distorted distorted 3758 3774 3775 3776 3793 P C B 603 distorted distorted 3781 3794 3795 3796 3813 P U B 604 distorted distorted 3801 3814 3815 3816 3833 P C B 605 distorted distorted 3821 3834 3835 3836 3853 P U B 606 distorted distorted 3841 3854 3855 3856 3873 P C B 607 distorted distorted 3861 3874 3875 3876 3893 P U B 608 distorted distorted 3881 3894 3895 3896 3913 P C B 609 distorted distorted 3901 3914 3915 3916 3933 P G B 610 distorted distorted 3921 3934 3935 3936 3956 P U B 611 distorted distorted 3941 3957 3958 3959 3977 P C C 692 distorted distorted 3978 3979 3980 3997 P G C 693 distorted distorted 3985 3998 3999 4000 4020 P A C 694 distorted distorted 4005 4021 4022 4023 4042 P G C 695 distorted distorted 4028 4043 4044 4045 4065 P A C 696 distorted distorted 4050 4066 4067 4068 4087 P G C 697 distorted distorted 4073 4088 4089 4090 4110 P A C 698 distorted distorted 4095 4111 4112 4113 4132 P G C 699 distorted distorted 4118 4133 4134 4135 4155 P A C 700 distorted distorted 4140 4156 4157 4158 4177 P DC C 701 distorted distorted 4163 4178 4179 4180 7901 P A F 599 distorted distorted 7902 7903 7904 7923 P G F 600 distorted distorted 7909 7924 7925 7926 7946 P G F 601 distorted distorted 7931 7947 7948 7949 7969 P U F 602 distorted distorted 7954 7970 7971 7972 7989 P C F 603 distorted distorted 7977 7990 7991 7992 8009 P U F 604 distorted distorted 7997 8010 8011 8012 8029 P C F 605 distorted distorted 8017 8030 8031 8032 8049 P U F 606 distorted distorted 8037 8050 8051 8052 8069 P C F 607 distorted distorted 8057 8070 8071 8072 8089 P U F 608 distorted distorted 8077 8090 8091 8092 8109 P C F 609 distorted distorted 8097 8110 8111 8112 8129 P G F 610 distorted distorted 8117 8130 8131 8132 8152 P U F 611 distorted distorted 8137 8153 8154 8155 8173 P C G 692 distorted distorted 8174 8175 8176 8193 P G G 693 distorted distorted 8181 8194 8195 8196 8216 P A G 694 distorted distorted 8201 8217 8218 8219 8238 P G G 695 distorted distorted 8224 8239 8240 8241 8261 P A G 696 distorted distorted 8246 8262 8263 8264 8283 P G G 697 distorted distorted 8269 8284 8285 8286 8306 P A G 698 distorted distorted 8291 8307 8308 8309 8328 P G G 699 distorted distorted 8314 8329 8330 8331 8351 P A G 700 distorted distorted 8336 8352 8353 8354 8373 P DC G 701 distorted distorted 8359 8374 8375 8376 ---------------------------------------------------------------------------------