ID code: '4BWJ' 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' --------------------------------------------------------------------------------- 8786 C1' DG B 101 alpha beta 8782 8804 8787 8785 8820 C1' DA B 102 alpha beta 8816 8837 8821 8819 8852 C1' DC B 103 alpha beta 8848 8867 8853 8851 8882 C1' DC B 104 alpha beta 8878 8897 8883 8881 8912 C1' DA B 105 alpha beta 8908 8929 8913 8911 8944 C1' DC B 106 alpha beta 8940 8959 8945 8943 8974 C1' DG B 107 alpha beta 8970 8992 8975 8973 9007 C1' DG B 108 alpha beta 9003 9025 9008 9006 9040 C1' DC B 109 alpha beta 9036 9055 9041 9039 9070 C1' DG B 110 alpha beta 9066 9088 9071 9069 9103 C1' DC B 111 alpha beta 9099 9118 9104 9102 9131 C1' DOC B 112 alpha beta 9135 9145 9123 9132 9164 C1' DA C 203 alpha beta 9160 9181 9165 9163 9196 C1' DG C 204 alpha beta 9192 9214 9197 9195 9229 C1' DG C 205 alpha beta 9225 9247 9230 9228 9262 C1' DG C 206 alpha beta 9258 9280 9263 9261 9295 C1' DC C 207 alpha beta 9291 9310 9296 9294 9325 C1' DG C 208 alpha beta 9321 9343 9326 9324 9358 C1' DC C 209 alpha beta 9354 9373 9359 9357 9388 C1' DC C 210 alpha beta 9384 9403 9389 9387 9418 C1' DG C 211 alpha beta 9414 9436 9419 9417 9451 C1' DT C 212 alpha beta 9447 9467 9452 9450 9483 C1' DG C 213 alpha beta 9479 9501 9484 9482 9516 C1' DG C 214 alpha beta 9512 9534 9517 9515 9549 C1' DT C 215 alpha beta 9545 9565 9550 9548 9581 C1' DC C 216 alpha beta 9577 9597 9582 9580 9611 C1' DCT A1833 alpha beta 9615 9634 9603 9612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8785 C2' DG B 101 OK OK 8786 8783 8802 8803 8819 C2' DA B 102 OK OK 8820 8817 8835 8836 8851 C2' DC B 103 OK OK 8852 8849 8865 8866 8881 C2' DC B 104 OK OK 8882 8879 8895 8896 8911 C2' DA B 105 OK OK 8912 8909 8927 8928 8943 C2' DC B 106 OK OK 8944 8941 8957 8958 8973 C2' DG B 107 OK OK 8974 8971 8990 8991 9006 C2' DG B 108 OK OK 9007 9004 9023 9024 9039 C2' DC B 109 OK OK 9040 9037 9053 9054 9069 C2' DG B 110 OK OK 9070 9067 9086 9087 9102 C2' DC B 111 OK OK 9103 9100 9116 9117 9132 C2' DOC B 112 distorted distorted 9131 9133 9146 9147 9163 C2' DA C 203 OK OK 9164 9161 9179 9180 9195 C2' DG C 204 OK OK 9196 9193 9212 9213 9228 C2' DG C 205 OK OK 9229 9226 9245 9246 9261 C2' DG C 206 OK OK 9262 9259 9278 9279 9294 C2' DC C 207 OK OK 9295 9292 9308 9309 9324 C2' DG C 208 OK OK 9325 9322 9341 9342 9357 C2' DC C 209 OK OK 9358 9355 9371 9372 9387 C2' DC C 210 OK OK 9388 9385 9401 9402 9417 C2' DG C 211 OK OK 9418 9415 9434 9435 9450 C2' DT C 212 OK OK 9451 9448 9465 9466 9482 C2' DG C 213 OK OK 9483 9480 9499 9500 9515 C2' DG C 214 OK OK 9516 9513 9532 9533 9548 C2' DT C 215 OK OK 9549 9546 9563 9564 9580 C2' DC C 216 OK OK 9581 9578 9595 9596 9612 C2' DCT A1833 distorted distorted 9611 9613 9635 9636 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8783 C3' DG B 101 OK OK 8781 8801 8784 8785 8817 C3' DA B 102 OK OK 8815 8834 8818 8819 8849 C3' DC B 103 OK OK 8847 8864 8850 8851 8879 C3' DC B 104 OK OK 8877 8894 8880 8881 8909 C3' DA B 105 OK OK 8907 8926 8910 8911 8941 C3' DC B 106 OK OK 8939 8956 8942 8943 8971 C3' DG B 107 OK OK 8969 8989 8972 8973 9004 C3' DG B 108 OK OK 9002 9022 9005 9006 9037 C3' DC B 109 OK OK 9035 9052 9038 9039 9067 C3' DG B 110 OK OK 9065 9085 9068 9069 9100 C3' DC B 111 OK OK 9098 9115 9101 9102 9133 C3' DOC B 112 9134 9132 9161 C3' DA C 203 OK OK 9159 9178 9162 9163 9193 C3' DG C 204 OK OK 9191 9211 9194 9195 9226 C3' DG C 205 OK OK 9224 9244 9227 9228 9259 C3' DG C 206 OK OK 9257 9277 9260 9261 9292 C3' DC C 207 OK OK 9290 9307 9293 9294 9322 C3' DG C 208 OK OK 9320 9340 9323 9324 9355 C3' DC C 209 OK OK 9353 9370 9356 9357 9385 C3' DC C 210 OK OK 9383 9400 9386 9387 9415 C3' DG C 211 OK OK 9413 9433 9416 9417 9448 C3' DT C 212 OK OK 9446 9464 9449 9450 9480 C3' DG C 213 OK OK 9478 9498 9481 9482 9513 C3' DG C 214 OK OK 9511 9531 9514 9515 9546 C3' DT C 215 OK OK 9544 9562 9547 9548 9578 C3' DC C 216 OK OK 9576 9593 9579 9580 9613 C3' DCT A1833 9614 9612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8781 C4' DG B 101 OK OK 8783 8800 8780 8782 8815 C4' DA B 102 OK OK 8817 8833 8814 8816 8847 C4' DC B 103 OK OK 8849 8863 8846 8848 8877 C4' DC B 104 OK OK 8879 8893 8876 8878 8907 C4' DA B 105 OK OK 8909 8925 8906 8908 8939 C4' DC B 106 OK OK 8941 8955 8938 8940 8969 C4' DG B 107 OK OK 8971 8988 8968 8970 9002 C4' DG B 108 OK OK 9004 9021 9001 9003 9035 C4' DC B 109 OK OK 9037 9051 9034 9036 9065 C4' DG B 110 OK OK 9067 9084 9064 9066 9098 C4' DC B 111 OK OK 9100 9114 9097 9099 9134 C4' DOC B 112 OK OK 9133 9150 9136 9135 9159 C4' DA C 203 OK OK 9161 9177 9158 9160 9191 C4' DG C 204 OK OK 9193 9210 9190 9192 9224 C4' DG C 205 OK OK 9226 9243 9223 9225 9257 C4' DG C 206 OK OK 9259 9276 9256 9258 9290 C4' DC C 207 OK OK 9292 9306 9289 9291 9320 C4' DG C 208 OK OK 9322 9339 9319 9321 9353 C4' DC C 209 OK OK 9355 9369 9352 9354 9383 C4' DC C 210 OK OK 9385 9399 9382 9384 9413 C4' DG C 211 OK OK 9415 9432 9412 9414 9446 C4' DT C 212 OK OK 9448 9463 9445 9447 9478 C4' DG C 213 OK OK 9480 9497 9477 9479 9511 C4' DG C 214 OK OK 9513 9530 9510 9512 9544 C4' DT C 215 OK OK 9546 9561 9543 9545 9576 C4' DC C 216 OK OK 9578 9592 9575 9577 9614 C4' DCT A1833 OK OK 9613 9639 9616 9615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8780 C5' DG B 101 OK OK 8779 8798 8799 8781 8814 C5' DA B 102 OK OK 8813 8831 8832 8815 8846 C5' DC B 103 OK OK 8845 8861 8862 8847 8876 C5' DC B 104 OK OK 8875 8891 8892 8877 8906 C5' DA B 105 OK OK 8905 8923 8924 8907 8938 C5' DC B 106 OK OK 8937 8953 8954 8939 8968 C5' DG B 107 OK OK 8967 8986 8987 8969 9001 C5' DG B 108 OK OK 9000 9019 9020 9002 9034 C5' DC B 109 OK OK 9033 9049 9050 9035 9064 C5' DG B 110 OK OK 9063 9082 9083 9065 9097 C5' DC B 111 OK OK 9096 9112 9113 9098 9136 C5' DOC B 112 OK OK 9137 9151 9152 9134 9158 C5' DA C 203 OK OK 9157 9175 9176 9159 9190 C5' DG C 204 OK OK 9189 9208 9209 9191 9223 C5' DG C 205 OK OK 9222 9241 9242 9224 9256 C5' DG C 206 OK OK 9255 9274 9275 9257 9289 C5' DC C 207 OK OK 9288 9304 9305 9290 9319 C5' DG C 208 OK OK 9318 9337 9338 9320 9352 C5' DC C 209 OK OK 9351 9367 9368 9353 9382 C5' DC C 210 OK OK 9381 9397 9398 9383 9412 C5' DG C 211 OK OK 9411 9430 9431 9413 9445 C5' DT C 212 OK OK 9444 9461 9462 9446 9477 C5' DG C 213 OK OK 9476 9495 9496 9478 9510 C5' DG C 214 OK OK 9509 9528 9529 9511 9543 C5' DT C 215 OK OK 9542 9559 9560 9544 9575 C5' DC C 216 OK OK 9574 9590 9591 9576 9616 C5' DCT A1833 OK OK 9617 9640 9641 9614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8810 P DA B 102 distorted distorted 8784 8811 8812 8813 8842 P DC B 103 distorted distorted 8818 8843 8844 8845 8872 P DC B 104 distorted distorted 8850 8873 8874 8875 8902 P DA B 105 distorted distorted 8880 8903 8904 8905 8934 P DC B 106 distorted distorted 8910 8935 8936 8937 8964 P DG B 107 distorted distorted 8942 8965 8966 8967 8997 P DG B 108 distorted distorted 8972 8998 8999 9000 9030 P DC B 109 distorted distorted 9005 9031 9032 9033 9060 P DG B 110 distorted distorted 9038 9061 9062 9063 9093 P DC B 111