ID code: '5WQE' 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' --------------------------------------------------------------------------------- 8001 C1' G B 1 beta 7996 8002 7999 8024 C1' U B 2 beta 8019 8025 8022 8044 C1' C B 3 beta 8039 8045 8042 8064 C1' U B 4 beta 8059 8065 8062 8084 C1' A B 5 beta 8079 8085 8082 8106 C1' G B 6 beta 8101 8107 8104 8129 C1' A B 7 beta 8124 8130 8127 8151 C1' G B 8 beta 8146 8152 8149 8174 C1' G B 9 beta 8169 8175 8172 8197 C1' A B 10 beta 8192 8198 8195 8219 C1' C B 11 beta 8214 8220 8217 8239 C1' A B 12 beta 8234 8240 8237 8261 C1' G B 13 beta 8256 8262 8259 8284 C1' A B 23 beta 8279 8285 8282 8306 C1' C B 24 beta 8301 8307 8304 8326 C1' G B 25 beta 8321 8327 8324 8349 C1' G B 26 beta 8344 8350 8347 8372 C1' G B 27 beta 8367 8373 8370 8395 C1' U B 28 beta 8390 8396 8393 8415 C1' G B 29 beta 8410 8416 8413 8438 C1' U B 30 beta 8433 8439 8436 8458 C1' G B 31 beta 8453 8459 8456 8481 C1' C B 32 beta 8476 8482 8479 8501 C1' C B 33 beta 8496 8502 8499 8521 C1' A B 34 beta 8516 8522 8519 8543 C1' A B 35 beta 8538 8544 8541 8565 C1' U B 36 beta 8560 8566 8563 8585 C1' G B 37 beta 8580 8586 8583 8608 C1' G B 38 beta 8603 8609 8606 8631 C1' C B 39 beta 8626 8632 8629 8651 C1' C B 40 beta 8646 8652 8649 8671 C1' A B 41 beta 8666 8672 8669 8693 C1' C B 42 beta 8688 8694 8691 8713 C1' U B 43 beta 8708 8714 8711 8737 C1' C B 47 beta 8732 8738 8735 8757 C1' A B 48 beta 8752 8758 8755 8779 C1' G B 49 beta 8774 8780 8777 8802 C1' G B 50 beta 8797 8803 8800 8825 C1' U B 51 beta 8820 8826 8823 8845 C1' G B 52 beta 8840 8846 8843 8868 C1' G B 53 beta 8863 8869 8866 8891 C1' C B 54 beta 8886 8892 8889 8911 C1' A B 55 beta 8906 8912 8909 8933 C1' G B 58 beta 8928 8934 8931 8956 C1' C B 59 beta 8951 8957 8954 8976 C1' C B 60 beta 8971 8977 8974 8996 C1' C B 61 beta 8991 8997 8994 9016 C1' G B 62 beta 9011 9017 9014 9039 C1' U B 86 beta 9034 9040 9037 9059 C1' G B 87 beta 9054 9060 9057 9082 C1' G B 88 beta 9077 9083 9080 9105 C1' C B 89 beta 9100 9106 9103 9125 C1' A B 90 beta 9120 9126 9123 9147 C1' C B 91 beta 9142 9148 9145 9167 C1' G B 92 beta 9162 9168 9165 9190 C1' A B 93 beta 9185 9191 9188 9212 C1' G B 94 beta 9207 9213 9210 9235 C1' A B 95 beta 9230 9236 9233 9257 C1' A B 96 beta 9252 9258 9255 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7999 C2' G B 1 OK 8001 7997 8000 8022 C2' U B 2 OK 8024 8020 8023 8042 C2' C B 3 OK 8044 8040 8043 8062 C2' U B 4 OK 8064 8060 8063 8082 C2' A B 5 OK 8084 8080 8083 8104 C2' G B 6 OK 8106 8102 8105 8127 C2' A B 7 OK 8129 8125 8128 8149 C2' G B 8 OK 8151 8147 8150 8172 C2' G B 9 OK 8174 8170 8173 8195 C2' A B 10 OK 8197 8193 8196 8217 C2' C B 11 OK 8219 8215 8218 8237 C2' A B 12 OK 8239 8235 8238 8259 C2' G B 13 OK 8261 8257 8260 8282 C2' A B 23 OK 8284 8280 8283 8304 C2' C B 24 OK 8306 8302 8305 8324 C2' G B 25 OK 8326 8322 8325 8347 C2' G B 26 OK 8349 8345 8348 8370 C2' G B 27 OK 8372 8368 8371 8393 C2' U B 28 OK 8395 8391 8394 8413 C2' G B 29 OK 8415 8411 8414 8436 C2' U B 30 OK 8438 8434 8437 8456 C2' G B 31 OK 8458 8454 8457 8479 C2' C B 32 OK 8481 8477 8480 8499 C2' C B 33 OK 8501 8497 8500 8519 C2' A B 34 OK 8521 8517 8520 8541 C2' A B 35 OK 8543 8539 8542 8563 C2' U B 36 OK 8565 8561 8564 8583 C2' G B 37 OK 8585 8581 8584 8606 C2' G B 38 OK 8608 8604 8607 8629 C2' C B 39 OK 8631 8627 8630 8649 C2' C B 40 OK 8651 8647 8650 8669 C2' A B 41 OK 8671 8667 8670 8691 C2' C B 42 OK 8693 8689 8692 8711 C2' U B 43 OK 8713 8709 8712 8735 C2' C B 47 OK 8737 8733 8736 8755 C2' A B 48 OK 8757 8753 8756 8777 C2' G B 49 OK 8779 8775 8778 8800 C2' G B 50 OK 8802 8798 8801 8823 C2' U B 51 OK 8825 8821 8824 8843 C2' G B 52 OK 8845 8841 8844 8866 C2' G B 53 OK 8868 8864 8867 8889 C2' C B 54 OK 8891 8887 8890 8909 C2' A B 55 OK 8911 8907 8910 8931 C2' G B 58 OK 8933 8929 8932 8954 C2' C B 59 OK 8956 8952 8955 8974 C2' C B 60 OK 8976 8972 8975 8994 C2' C B 61 OK 8996 8992 8995 9014 C2' G B 62 OK 9016 9012 9015 9037 C2' U B 86 OK 9039 9035 9038 9057 C2' G B 87 OK 9059 9055 9058 9080 C2' G B 88 OK 9082 9078 9081 9103 C2' C B 89 OK 9105 9101 9104 9123 C2' A B 90 OK 9125 9121 9124 9145 C2' C B 91 OK 9147 9143 9146 9165 C2' G B 92 OK 9167 9163 9166 9188 C2' A B 93 OK 9190 9186 9189 9210 C2' G B 94 OK 9212 9208 9211 9233 C2' A B 95 OK 9235 9231 9234 9255 C2' A B 96 OK 9257 9253 9256 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7997 C3' G B 1 OK 7995 7998 7999 8020 C3' U B 2 OK 8018 8021 8022 8040 C3' C B 3 OK 8038 8041 8042 8060 C3' U B 4 OK 8058 8061 8062 8080 C3' A B 5 OK 8078 8081 8082 8102 C3' G B 6 OK 8100 8103 8104 8125 C3' A B 7 OK 8123 8126 8127 8147 C3' G B 8 OK 8145 8148 8149 8170 C3' G B 9 OK 8168 8171 8172 8193 C3' A B 10 OK 8191 8194 8195 8215 C3' C B 11 OK 8213 8216 8217 8235 C3' A B 12 OK 8233 8236 8237 8257 C3' G B 13 OK 8255 8258 8259 8280 C3' A B 23 OK 8278 8281 8282 8302 C3' C B 24 OK 8300 8303 8304 8322 C3' G B 25 OK 8320 8323 8324 8345 C3' G B 26 OK 8343 8346 8347 8368 C3' G B 27 OK 8366 8369 8370 8391 C3' U B 28 OK 8389 8392 8393 8411 C3' G B 29 OK 8409 8412 8413 8434 C3' U B 30 OK 8432 8435 8436 8454 C3' G B 31 OK 8452 8455 8456 8477 C3' C B 32 OK 8475 8478 8479 8497 C3' C B 33 OK 8495 8498 8499 8517 C3' A B 34 OK 8515 8518 8519 8539 C3' A B 35 OK 8537 8540 8541 8561 C3' U B 36 OK 8559 8562 8563 8581 C3' G B 37 OK 8579 8582 8583 8604 C3' G B 38 OK 8602 8605 8606 8627 C3' C B 39 OK 8625 8628 8629 8647 C3' C B 40 OK 8645 8648 8649 8667 C3' A B 41 OK 8665 8668 8669 8689 C3' C B 42 OK 8687 8690 8691 8709 C3' U B 43 OK 8707 8710 8711 8733 C3' C B 47 OK 8731 8734 8735 8753 C3' A B 48 OK 8751 8754 8755 8775 C3' G B 49 OK 8773 8776 8777 8798 C3' G B 50 OK 8796 8799 8800 8821 C3' U B 51 OK 8819 8822 8823 8841 C3' G B 52 OK 8839 8842 8843 8864 C3' G B 53 OK 8862 8865 8866 8887 C3' C B 54 OK 8885 8888 8889 8907 C3' A B 55 OK 8905 8908 8909 8929 C3' G B 58 OK 8927 8930 8931 8952 C3' C B 59 OK 8950 8953 8954 8972 C3' C B 60 OK 8970 8973 8974 8992 C3' C B 61 OK 8990 8993 8994 9012 C3' G B 62 OK 9010 9013 9014 9035 C3' U B 86 OK 9033 9036 9037 9055 C3' G B 87 OK 9053 9056 9057 9078 C3' G B 88 OK 9076 9079 9080 9101 C3' C B 89 OK 9099 9102 9103 9121 C3' A B 90 OK 9119 9122 9123 9143 C3' C B 91 OK 9141 9144 9145 9163 C3' G B 92 OK 9161 9164 9165 9186 C3' A B 93 OK 9184 9187 9188 9208 C3' G B 94 OK 9206 9209 9210 9231 C3' A B 95 OK 9229 9232 9233 9253 C3' A B 96 OK 9251 9254 9255 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7995 C4' G B 1 OK 7997 7994 7996 8018 C4' U B 2 OK 8020 8017 8019 8038 C4' C B 3 OK 8040 8037 8039 8058 C4' U B 4 OK 8060 8057 8059 8078 C4' A B 5 OK 8080 8077 8079 8100 C4' G B 6 OK 8102 8099 8101 8123 C4' A B 7 OK 8125 8122 8124 8145 C4' G B 8 OK 8147 8144 8146 8168 C4' G B 9 OK 8170 8167 8169 8191 C4' A B 10 OK 8193 8190 8192 8213 C4' C B 11 OK 8215 8212 8214 8233 C4' A B 12 OK 8235 8232 8234 8255 C4' G B 13 OK 8257 8254 8256 8278 C4' A B 23 OK 8280 8277 8279 8300 C4' C B 24 OK 8302 8299 8301 8320 C4' G B 25 OK 8322 8319 8321 8343 C4' G B 26 OK 8345 8342 8344 8366 C4' G B 27 OK 8368 8365 8367 8389 C4' U B 28 OK 8391 8388 8390 8409 C4' G B 29 OK 8411 8408 8410 8432 C4' U B 30 OK 8434 8431 8433 8452 C4' G B 31 OK 8454 8451 8453 8475 C4' C B 32 OK 8477 8474 8476 8495 C4' C B 33 OK 8497 8494 8496 8515 C4' A B 34 OK 8517 8514 8516 8537 C4' A B 35 OK 8539 8536 8538 8559 C4' U B 36 OK 8561 8558 8560 8579 C4' G B 37 OK 8581 8578 8580 8602 C4' G B 38 OK 8604 8601 8603 8625 C4' C B 39 OK 8627 8624 8626 8645 C4' C B 40 OK 8647 8644 8646 8665 C4' A B 41 OK 8667 8664 8666 8687 C4' C B 42 OK 8689 8686 8688 8707 C4' U B 43 OK 8709 8706 8708 8731 C4' C B 47 OK 8733 8730 8732 8751 C4' A B 48 OK 8753 8750 8752 8773 C4' G B 49 OK 8775 8772 8774 8796 C4' G B 50 OK 8798 8795 8797 8819 C4' U B 51 OK 8821 8818 8820 8839 C4' G B 52 OK 8841 8838 8840 8862 C4' G B 53 OK 8864 8861 8863 8885 C4' C B 54 OK 8887 8884 8886 8905 C4' A B 55 OK 8907 8904 8906 8927 C4' G B 58 OK 8929 8926 8928 8950 C4' C B 59 OK 8952 8949 8951 8970 C4' C B 60 OK 8972 8969 8971 8990 C4' C B 61 OK 8992 8989 8991 9010 C4' G B 62 OK 9012 9009 9011 9033 C4' U B 86 OK 9035 9032 9034 9053 C4' G B 87 OK 9055 9052 9054 9076 C4' G B 88 OK 9078 9075 9077 9099 C4' C B 89 OK 9101 9098 9100 9119 C4' A B 90 OK 9121 9118 9120 9141 C4' C B 91 OK 9143 9140 9142 9161 C4' G B 92 OK 9163 9160 9162 9184 C4' A B 93 OK 9186 9183 9185 9206 C4' G B 94 OK 9208 9205 9207 9229 C4' A B 95 OK 9231 9228 9230 9251 C4' A B 96 OK 9253 9250 9252 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7994 C5' G B 1 7993 7995 8017 C5' U B 2 8016 8018 8037 C5' C B 3 8036 8038 8057 C5' U B 4 8056 8058 8077 C5' A B 5 8076 8078 8099 C5' G B 6 8098 8100 8122 C5' A B 7 8121 8123 8144 C5' G B 8 8143 8145 8167 C5' G B 9 8166 8168 8190 C5' A B 10 8189 8191 8212 C5' C B 11 8211 8213 8232 C5' A B 12 8231 8233 8254 C5' G B 13 8253 8255 8277 C5' A B 23 8276 8278 8299 C5' C B 24 8298 8300 8319 C5' G B 25 8318 8320 8342 C5' G B 26 8341 8343 8365 C5' G B 27 8364 8366 8388 C5' U B 28 8387 8389 8408 C5' G B 29 8407 8409 8431 C5' U B 30 8430 8432 8451 C5' G B 31 8450 8452 8474 C5' C B 32 8473 8475 8494 C5' C B 33 8493 8495 8514 C5' A B 34 8513 8515 8536 C5' A B 35 8535 8537 8558 C5' U B 36 8557 8559 8578 C5' G B 37 8577 8579 8601 C5' G B 38 8600 8602 8624 C5' C B 39 8623 8625 8644 C5' C B 40 8643 8645 8664 C5' A B 41 8663 8665 8686 C5' C B 42 8685 8687 8706 C5' U B 43 8705 8707 8730 C5' C B 47 8729 8731 8750 C5' A B 48 8749 8751 8772 C5' G B 49 8771 8773 8795 C5' G B 50 8794 8796 8818 C5' U B 51 8817 8819 8838 C5' G B 52 8837 8839 8861 C5' G B 53 8860 8862 8884 C5' C B 54 8883 8885 8904 C5' A B 55 8903 8905 8926 C5' G B 58 8925 8927 8949 C5' C B 59 8948 8950 8969 C5' C B 60 8968 8970 8989 C5' C B 61 8988 8990 9009 C5' G B 62 9008 9010 9032 C5' U B 86 9031 9033 9052 C5' G B 87 9051 9053 9075 C5' G B 88 9074 9076 9098 C5' C B 89 9097 9099 9118 C5' A B 90 9117 9119 9140 C5' C B 91 9139 9141 9160 C5' G B 92 9159 9161 9183 C5' A B 93 9182 9184 9205 C5' G B 94 9204 9206 9228 C5' A B 95 9227 9229 9250 C5' A B 96 9249 9251 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7990 P G B 1 distorted distorted 7991 7992 7993 8013 P U B 2 distorted distorted 7998 8014 8015 8016 8033 P C B 3 distorted distorted 8021 8034 8035 8036 8053 P U B 4 distorted distorted 8041 8054 8055 8056 8073 P A B 5 distorted distorted 8061 8074 8075 8076 8095 P G B 6 distorted distorted 8081 8096 8097 8098 8118 P A B 7 distorted distorted 8103 8119 8120 8121 8140 P G B 8 distorted distorted 8126 8141 8142 8143 8163 P G B 9 distorted distorted 8148 8164 8165 8166 8186 P A B 10 distorted distorted 8171 8187 8188 8189 8208 P C B 11 distorted distorted 8194 8209 8210 8211 8228 P A B 12 distorted distorted 8216 8229 8230 8231 8250 P G B 13 distorted distorted 8236 8251 8252 8253 8273 P A B 23 distorted distorted 8274 8275 8276 8295 P C B 24 distorted distorted 8281 8296 8297 8298 8315 P G B 25 distorted distorted 8303 8316 8317 8318 8338 P G B 26 distorted distorted 8323 8339 8340 8341 8361 P G B 27 distorted distorted 8346 8362 8363 8364 8384 P U B 28 distorted distorted 8369 8385 8386 8387 8404 P G B 29 distorted distorted 8392 8405 8406 8407 8427 P U B 30 distorted distorted 8412 8428 8429 8430 8447 P G B 31 distorted distorted 8435 8448 8449 8450 8470 P C B 32 distorted distorted 8455 8471 8472 8473 8490 P C B 33 distorted distorted 8478 8491 8492 8493 8510 P A B 34 distorted distorted 8498 8511 8512 8513 8532 P A B 35 distorted distorted 8518 8533 8534 8535 8554 P U B 36 distorted distorted 8540 8555 8556 8557 8574 P G B 37 distorted distorted 8562 8575 8576 8577 8597 P G B 38 distorted distorted 8582 8598 8599 8600 8620 P C B 39 distorted distorted 8605 8621 8622 8623 8640 P C B 40 distorted distorted 8628 8641 8642 8643 8660 P A B 41 distorted distorted 8648 8661 8662 8663 8682 P C B 42 distorted distorted 8668 8683 8684 8685 8702 P U B 43 distorted distorted 8690 8703 8704 8705 8722 P U B 44 distorted distorted 8710 8723 8724 8725 8726 P C B 47 OK OK 8727 8728 8729 8746 P A B 48 distorted distorted 8734 8747 8748 8749 8768 P G B 49 distorted distorted 8754 8769 8770 8771 8791 P G B 50 distorted distorted 8776 8792 8793 8794 8814 P U B 51 distorted distorted 8799 8815 8816 8817 8834 P G B 52 distorted distorted 8822 8835 8836 8837 8857 P G B 53 distorted distorted 8842 8858 8859 8860 8880 P C B 54 distorted distorted 8865 8881 8882 8883 8900 P A B 55 distorted distorted 8888 8901 8902 8903 8922 P G B 58 distorted distorted 8923 8924 8925 8945 P C B 59 distorted distorted 8930 8946 8947 8948 8965 P C B 60 distorted distorted 8953 8966 8967 8968 8985 P C B 61 distorted distorted 8973 8986 8987 8988 9005 P G B 62 distorted distorted 8993 9006 9007 9008 9028 P U B 86 distorted distorted 9029 9030 9031 9048 P G B 87 distorted distorted 9036 9049 9050 9051 9071 P G B 88 distorted distorted 9056 9072 9073 9074 9094 P C B 89 distorted distorted 9079 9095 9096 9097 9114 P A B 90 distorted distorted 9102 9115 9116 9117 9136 P C B 91 distorted distorted 9122 9137 9138 9139 9156 P G B 92 distorted distorted 9144 9157 9158 9159 9179 P A B 93 distorted distorted 9164 9180 9181 9182 9201 P G B 94 distorted distorted 9187 9202 9203 9204 9224 P A B 95 distorted distorted 9209 9225 9226 9227 9246 P A B 96 distorted distorted 9232 9247 9248 9249 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