ID code: '4C8K' 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' --------------------------------------------------------------------------------- 8659 C1' DG B 101 alpha beta 8655 8677 8660 8658 8693 C1' DA B 102 alpha beta 8689 8710 8694 8692 8725 C1' DC B 103 alpha beta 8721 8740 8726 8724 8755 C1' DC B 104 alpha beta 8751 8770 8756 8754 8785 C1' DA B 105 alpha beta 8781 8802 8786 8784 8817 C1' DC B 106 alpha beta 8813 8832 8818 8816 8847 C1' DG B 107 alpha beta 8843 8865 8848 8846 8880 C1' DG B 108 alpha beta 8876 8898 8881 8879 8913 C1' DC B 109 alpha beta 8909 8928 8914 8912 8943 C1' DG B 110 alpha beta 8939 8961 8944 8942 8976 C1' DC B 111 alpha beta 8972 8991 8977 8975 9004 C1' DOC B 112 alpha beta 9008 9018 8996 9005 9037 C1' DC C 203 alpha beta 9033 9052 9038 9036 9069 C1' LHO C 204 alpha beta 9076 9084 9059 9072 9106 C1' DG C 205 alpha beta 9102 9124 9107 9105 9139 C1' DG C 206 alpha beta 9135 9157 9140 9138 9172 C1' DC C 207 alpha beta 9168 9187 9173 9171 9202 C1' DG C 208 alpha beta 9198 9220 9203 9201 9235 C1' DC C 209 alpha beta 9231 9250 9236 9234 9265 C1' DC C 210 alpha beta 9261 9280 9266 9264 9295 C1' DG C 211 alpha beta 9291 9313 9296 9294 9328 C1' DT C 212 alpha beta 9324 9344 9329 9327 9360 C1' DG C 213 alpha beta 9356 9378 9361 9359 9393 C1' DG C 214 alpha beta 9389 9411 9394 9392 9426 C1' DT C 215 alpha beta 9422 9442 9427 9425 9458 C1' DC C 216 alpha beta 9454 9474 9459 9457 9503 C1' BMR A1834 alpha 9523 9530 9507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8658 C2' DG B 101 OK OK 8659 8656 8675 8676 8692 C2' DA B 102 OK OK 8693 8690 8708 8709 8724 C2' DC B 103 OK OK 8725 8722 8738 8739 8754 C2' DC B 104 OK OK 8755 8752 8768 8769 8784 C2' DA B 105 OK OK 8785 8782 8800 8801 8816 C2' DC B 106 OK OK 8817 8814 8830 8831 8846 C2' DG B 107 OK OK 8847 8844 8863 8864 8879 C2' DG B 108 OK OK 8880 8877 8896 8897 8912 C2' DC B 109 OK OK 8913 8910 8926 8927 8942 C2' DG B 110 OK OK 8943 8940 8959 8960 8975 C2' DC B 111 OK OK 8976 8973 8989 8990 9005 C2' DOC B 112 distorted distorted 9004 9006 9019 9020 9036 C2' DC C 203 OK OK 9037 9034 9050 9051 9072 C2' LHO C 204 9069 9073 9105 C2' DG C 205 OK OK 9106 9103 9122 9123 9138 C2' DG C 206 OK OK 9139 9136 9155 9156 9171 C2' DC C 207 OK OK 9172 9169 9185 9186 9201 C2' DG C 208 OK OK 9202 9199 9218 9219 9234 C2' DC C 209 OK OK 9235 9232 9248 9249 9264 C2' DC C 210 OK OK 9265 9262 9278 9279 9294 C2' DG C 211 OK OK 9295 9292 9311 9312 9327 C2' DT C 212 OK OK 9328 9325 9342 9343 9359 C2' DG C 213 OK OK 9360 9357 9376 9377 9392 C2' DG C 214 OK OK 9393 9390 9409 9410 9425 C2' DT C 215 OK OK 9426 9423 9440 9441 9457 C2' DC C 216 OK OK 9458 9455 9472 9473 9507 C2' BMR A1834 distorted 9503 9515 9528 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8656 C3' DG B 101 OK OK 8654 8674 8657 8658 8690 C3' DA B 102 OK OK 8688 8707 8691 8692 8722 C3' DC B 103 OK OK 8720 8737 8723 8724 8752 C3' DC B 104 OK OK 8750 8767 8753 8754 8782 C3' DA B 105 OK OK 8780 8799 8783 8784 8814 C3' DC B 106 OK OK 8812 8829 8815 8816 8844 C3' DG B 107 OK OK 8842 8862 8845 8846 8877 C3' DG B 108 OK OK 8875 8895 8878 8879 8910 C3' DC B 109 OK OK 8908 8925 8911 8912 8940 C3' DG B 110 OK OK 8938 8958 8941 8942 8973 C3' DC B 111 OK OK 8971 8988 8974 8975 9006 C3' DOC B 112 9007 9005 9034 C3' DC C 203 OK OK 9032 9049 9035 9036 9073 C3' LHO C 204 OK OK 9075 9090 9074 9072 9103 C3' DG C 205 OK OK 9101 9121 9104 9105 9136 C3' DG C 206 OK OK 9134 9154 9137 9138 9169 C3' DC C 207 OK OK 9167 9184 9170 9171 9199 C3' DG C 208 OK OK 9197 9217 9200 9201 9232 C3' DC C 209 OK OK 9230 9247 9233 9234 9262 C3' DC C 210 OK OK 9260 9277 9263 9264 9292 C3' DG C 211 OK OK 9290 9310 9293 9294 9325 C3' DT C 212 OK OK 9323 9341 9326 9327 9357 C3' DG C 213 OK OK 9355 9375 9358 9359 9390 C3' DG C 214 OK OK 9388 9408 9391 9392 9423 C3' DT C 215 OK OK 9421 9439 9424 9425 9455 C3' DC C 216 OK OK 9453 9470 9456 9457 9515 C3' BMR A1834 OK OK 9522 9536 9516 9507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8654 C4' DG B 101 OK OK 8656 8673 8653 8655 8688 C4' DA B 102 OK OK 8690 8706 8687 8689 8720 C4' DC B 103 OK OK 8722 8736 8719 8721 8750 C4' DC B 104 OK OK 8752 8766 8749 8751 8780 C4' DA B 105 OK OK 8782 8798 8779 8781 8812 C4' DC B 106 OK OK 8814 8828 8811 8813 8842 C4' DG B 107 OK OK 8844 8861 8841 8843 8875 C4' DG B 108 OK OK 8877 8894 8874 8876 8908 C4' DC B 109 OK OK 8910 8924 8907 8909 8938 C4' DG B 110 OK OK 8940 8957 8937 8939 8971 C4' DC B 111 OK OK 8973 8987 8970 8972 9007 C4' DOC B 112 OK OK 9006 9023 9009 9008 9032 C4' DC C 203 OK OK 9034 9048 9031 9033 9075 C4' LHO C 204 OK OK 9073 9091 9077 9076 9101 C4' DG C 205 OK OK 9103 9120 9100 9102 9134 C4' DG C 206 OK OK 9136 9153 9133 9135 9167 C4' DC C 207 OK OK 9169 9183 9166 9168 9197 C4' DG C 208 OK OK 9199 9216 9196 9198 9230 C4' DC C 209 OK OK 9232 9246 9229 9231 9260 C4' DC C 210 OK OK 9262 9276 9259 9261 9290 C4' DG C 211 OK OK 9292 9309 9289 9291 9323 C4' DT C 212 OK OK 9325 9340 9322 9324 9355 C4' DG C 213 OK OK 9357 9374 9354 9356 9388 C4' DG C 214 OK OK 9390 9407 9387 9389 9421 C4' DT C 215 OK OK 9423 9438 9420 9422 9453 C4' DC C 216 OK OK 9455 9469 9452 9454 9522 C4' BMR A1834 OK OK 9515 9539 9524 9523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8653 C5' DG B 101 OK OK 8652 8671 8672 8654 8687 C5' DA B 102 OK OK 8686 8704 8705 8688 8719 C5' DC B 103 OK OK 8718 8734 8735 8720 8749 C5' DC B 104 OK OK 8748 8764 8765 8750 8779 C5' DA B 105 OK OK 8778 8796 8797 8780 8811 C5' DC B 106 OK OK 8810 8826 8827 8812 8841 C5' DG B 107 OK OK 8840 8859 8860 8842 8874 C5' DG B 108 OK OK 8873 8892 8893 8875 8907 C5' DC B 109 OK OK 8906 8922 8923 8908 8937 C5' DG B 110 OK OK 8936 8955 8956 8938 8970 C5' DC B 111 OK OK 8969 8985 8986 8971 9009 C5' DOC B 112 OK OK 9010 9024 9025 9007 9031 C5' DC C 203 OK OK 9030 9046 9047 9032 9077 C5' LHO C 204 9078 9075 9100 C5' DG C 205 OK OK 9099 9118 9119 9101 9133 C5' DG C 206 OK OK 9132 9151 9152 9134 9166 C5' DC C 207 OK OK 9165 9181 9182 9167 9196 C5' DG C 208 OK OK 9195 9214 9215 9197 9229 C5' DC C 209 OK OK 9228 9244 9245 9230 9259 C5' DC C 210 OK OK 9258 9274 9275 9260 9289 C5' DG C 211 OK OK 9288 9307 9308 9290 9322 C5' DT C 212 OK OK 9321 9338 9339 9323 9354 C5' DG C 213 OK OK 9353 9372 9373 9355 9387 C5' DG C 214 OK OK 9386 9405 9406 9388 9420 C5' DT C 215 OK OK 9419 9436 9437 9421 9452 C5' DC C 216 OK OK 9451 9467 9468 9453 9524 C5' BMR A1834 9525 9522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8683 P DA B 102 distorted distorted 8657 8684 8685 8686 8715 P DC B 103 distorted distorted 8691 8716 8717 8718 8745 P DC B 104 distorted distorted 8723 8746 8747 8748 8775 P DA B 105 distorted distorted 8753 8776 8777 8778 8807 P DC B 106 distorted distorted 8783 8808 8809 8810 8837 P DG B 107 distorted distorted 8815 8838 8839 8840 8870 P DG B 108 distorted distorted 8845 8871 8872 8873 8903 P DC B 109 distorted distorted 8878 8904 8905 8906 8933 P DG B 110 distorted distorted 8911 8934 8935 8936 8966 P DC B 111 distorted distorted 8941 8967 8968 8969 9011 P DOC B 112 distorted distorted 8974 9012 9013 9010 9027 P DC C 203 OK OK 9028 9029 9030 9057 P LHO C 204 OK OK 9035 9094 9071 9078 9096 P DG C 205 distorted distorted 9074 9097 9098 9099 9129 P DG C 206 distorted distorted 9104 9130 9131 9132 9162 P DC C 207 distorted distorted 9137 9163 9164 9165 9192 P DG C 208 distorted distorted 9170 9193 9194 9195 9225 P DC C 209 distorted distorted 9200 9226 9227 9228 9255 P DC C 210 distorted distorted 9233 9256 9257 9258 9285 P DG C 211 distorted distorted 9263 9286 9287 9288 9318 P DT C 212 distorted distorted 9293 9319 9320 9321 9350 P DG C 213 distorted distorted 9326 9351 9352 9353 9383 P DG C 214 distorted distorted 9358 9384 9385 9386 9416 P DT C 215 distorted distorted 9391 9417 9418 9419 9448 P DC C 216 distorted distorted 9424 9449 9450 9451 ---------------------------------------------------------------------------------