ID code: '4BOC' 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' --------------------------------------------------------------------------------- 7892 C1' DA N -26 beta 7888 7893 7891 7913 C1' DT N -25 beta 7909 7914 7912 7933 C1' DG N -24 beta 7929 7934 7932 7955 C1' DG N -23 beta 7951 7956 7954 7977 C1' DG N -22 beta 7973 7978 7976 7999 C1' DG N -21 beta 7995 8000 7998 8021 C1' DT N -20 beta 8017 8022 8020 8041 C1' DA N -19 beta 8037 8042 8040 8062 C1' DA N -18 beta 8058 8063 8061 8083 C1' DC N -11 beta 8079 8084 8082 8102 C1' DG N -10 beta 8098 8103 8101 8124 C1' DA N -9 beta 8120 8125 8123 8145 C1' DC N -8 beta 8141 8146 8144 8164 C1' DG N -7 beta 8160 8165 8163 8186 C1' DC N -6 beta 8182 8187 8185 8205 C1' DC N -5 beta 8201 8206 8204 8224 C1' DA N -4 beta 8220 8225 8223 8245 C1' DG N -3 beta 8241 8246 8244 8267 C1' DA N -2 beta 8263 8268 8266 8288 C1' DC N -1 beta 8284 8289 8287 8307 C1' DG N 0 beta 8303 8308 8306 8331 C1' G R 1 beta 8326 8332 8329 8354 C1' C R 2 beta 8349 8355 8352 8374 C1' G R 3 beta 8369 8375 8372 8397 C1' G R 4 beta 8392 8398 8395 8420 C1' C R 5 beta 8415 8421 8418 8440 C1' G R 6 beta 8435 8441 8438 8463 C1' C R 7 beta 8458 8464 8461 8483 C1' G R 8 beta 8478 8484 8481 8506 C1' C R 9 beta 8501 8507 8504 8526 C1' DC T -9 beta 8522 8527 8525 8545 C1' DG T -8 beta 8541 8546 8544 8567 C1' DT T -7 beta 8563 8568 8566 8587 C1' DC T -6 beta 8583 8588 8586 8606 C1' DT T -5 beta 8602 8607 8605 8626 C1' DG T -4 beta 8622 8627 8625 8648 C1' DG T -3 beta 8644 8649 8647 8670 C1' DC T -2 beta 8666 8671 8669 8689 C1' DG T -1 beta 8685 8690 8688 8711 C1' DT T 0 beta 8707 8712 8710 8731 C1' DG T 1 beta 8727 8732 8730 8753 C1' DC T 2 beta 8749 8754 8752 8772 C1' DG T 3 beta 8768 8773 8771 8794 C1' DC T 4 beta 8790 8795 8793 8813 C1' DG T 5 beta 8809 8814 8812 8835 C1' DC T 6 beta 8831 8836 8834 8854 C1' DC T 7 beta 8850 8855 8853 8873 C1' DG T 8 beta 8869 8874 8872 8895 C1' DC T 9 beta 8891 8896 8894 8914 C1' DT T 10 beta 8910 8915 8913 8934 C1' DA T 11 beta 8930 8935 8933 8955 C1' DC T 12 beta 8951 8956 8954 8974 C1' DC T 13 beta 8970 8975 8973 8993 C1' DC T 14 beta 8989 8994 8992 9012 C1' DC T 15 beta 9008 9013 9011 9031 C1' DA T 16 beta 9027 9032 9030 9052 C1' DT T 17 beta 9048 9053 9051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7891 C2' DA N -26 7892 7889 7912 C2' DT N -25 7913 7910 7932 C2' DG N -24 7933 7930 7954 C2' DG N -23 7955 7952 7976 C2' DG N -22 7977 7974 7998 C2' DG N -21 7999 7996 8020 C2' DT N -20 8021 8018 8040 C2' DA N -19 8041 8038 8061 C2' DA N -18 8062 8059 8082 C2' DC N -11 8083 8080 8101 C2' DG N -10 8102 8099 8123 C2' DA N -9 8124 8121 8144 C2' DC N -8 8145 8142 8163 C2' DG N -7 8164 8161 8185 C2' DC N -6 8186 8183 8204 C2' DC N -5 8205 8202 8223 C2' DA N -4 8224 8221 8244 C2' DG N -3 8245 8242 8266 C2' DA N -2 8267 8264 8287 C2' DC N -1 8288 8285 8306 C2' DG N 0 8307 8304 8329 C2' G R 1 OK 8331 8327 8330 8352 C2' C R 2 OK 8354 8350 8353 8372 C2' G R 3 OK 8374 8370 8373 8395 C2' G R 4 OK 8397 8393 8396 8418 C2' C R 5 OK 8420 8416 8419 8438 C2' G R 6 OK 8440 8436 8439 8461 C2' C R 7 OK 8463 8459 8462 8481 C2' G R 8 OK 8483 8479 8482 8504 C2' C R 9 OK 8506 8502 8505 8525 C2' DC T -9 8526 8523 8544 C2' DG T -8 8545 8542 8566 C2' DT T -7 8567 8564 8586 C2' DC T -6 8587 8584 8605 C2' DT T -5 8606 8603 8625 C2' DG T -4 8626 8623 8647 C2' DG T -3 8648 8645 8669 C2' DC T -2 8670 8667 8688 C2' DG T -1 8689 8686 8710 C2' DT T 0 8711 8708 8730 C2' DG T 1 8731 8728 8752 C2' DC T 2 8753 8750 8771 C2' DG T 3 8772 8769 8793 C2' DC T 4 8794 8791 8812 C2' DG T 5 8813 8810 8834 C2' DC T 6 8835 8832 8853 C2' DC T 7 8854 8851 8872 C2' DG T 8 8873 8870 8894 C2' DC T 9 8895 8892 8913 C2' DT T 10 8914 8911 8933 C2' DA T 11 8934 8931 8954 C2' DC T 12 8955 8952 8973 C2' DC T 13 8974 8971 8992 C2' DC T 14 8993 8990 9011 C2' DC T 15 9012 9009 9030 C2' DA T 16 9031 9028 9051 C2' DT T 17 9052 9049 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7889 C3' DA N -26 OK 7887 7890 7891 7910 C3' DT N -25 OK 7908 7911 7912 7930 C3' DG N -24 OK 7928 7931 7932 7952 C3' DG N -23 OK 7950 7953 7954 7974 C3' DG N -22 OK 7972 7975 7976 7996 C3' DG N -21 OK 7994 7997 7998 8018 C3' DT N -20 OK 8016 8019 8020 8038 C3' DA N -19 OK 8036 8039 8040 8059 C3' DA N -18 OK 8057 8060 8061 8080 C3' DC N -11 OK 8078 8081 8082 8099 C3' DG N -10 OK 8097 8100 8101 8121 C3' DA N -9 OK 8119 8122 8123 8142 C3' DC N -8 OK 8140 8143 8144 8161 C3' DG N -7 OK 8159 8162 8163 8183 C3' DC N -6 OK 8181 8184 8185 8202 C3' DC N -5 OK 8200 8203 8204 8221 C3' DA N -4 OK 8219 8222 8223 8242 C3' DG N -3 OK 8240 8243 8244 8264 C3' DA N -2 OK 8262 8265 8266 8285 C3' DC N -1 OK 8283 8286 8287 8304 C3' DG N 0 OK 8302 8305 8306 8327 C3' G R 1 OK 8325 8328 8329 8350 C3' C R 2 OK 8348 8351 8352 8370 C3' G R 3 OK 8368 8371 8372 8393 C3' G R 4 OK 8391 8394 8395 8416 C3' C R 5 OK 8414 8417 8418 8436 C3' G R 6 OK 8434 8437 8438 8459 C3' C R 7 OK 8457 8460 8461 8479 C3' G R 8 OK 8477 8480 8481 8502 C3' C R 9 OK 8500 8503 8504 8523 C3' DC T -9 OK 8521 8524 8525 8542 C3' DG T -8 OK 8540 8543 8544 8564 C3' DT T -7 OK 8562 8565 8566 8584 C3' DC T -6 OK 8582 8585 8586 8603 C3' DT T -5 OK 8601 8604 8605 8623 C3' DG T -4 OK 8621 8624 8625 8645 C3' DG T -3 OK 8643 8646 8647 8667 C3' DC T -2 OK 8665 8668 8669 8686 C3' DG T -1 OK 8684 8687 8688 8708 C3' DT T 0 OK 8706 8709 8710 8728 C3' DG T 1 OK 8726 8729 8730 8750 C3' DC T 2 OK 8748 8751 8752 8769 C3' DG T 3 OK 8767 8770 8771 8791 C3' DC T 4 OK 8789 8792 8793 8810 C3' DG T 5 OK 8808 8811 8812 8832 C3' DC T 6 OK 8830 8833 8834 8851 C3' DC T 7 OK 8849 8852 8853 8870 C3' DG T 8 OK 8868 8871 8872 8892 C3' DC T 9 OK 8890 8893 8894 8911 C3' DT T 10 OK 8909 8912 8913 8931 C3' DA T 11 OK 8929 8932 8933 8952 C3' DC T 12 OK 8950 8953 8954 8971 C3' DC T 13 OK 8969 8972 8973 8990 C3' DC T 14 OK 8988 8991 8992 9009 C3' DC T 15 OK 9007 9010 9011 9028 C3' DA T 16 OK 9026 9029 9030 9049 C3' DT T 17 OK 9047 9050 9051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7887 C4' DA N -26 OK 7889 7886 7888 7908 C4' DT N -25 OK 7910 7907 7909 7928 C4' DG N -24 OK 7930 7927 7929 7950 C4' DG N -23 OK 7952 7949 7951 7972 C4' DG N -22 OK 7974 7971 7973 7994 C4' DG N -21 OK 7996 7993 7995 8016 C4' DT N -20 OK 8018 8015 8017 8036 C4' DA N -19 OK 8038 8035 8037 8057 C4' DA N -18 OK 8059 8056 8058 8078 C4' DC N -11 OK 8080 8077 8079 8097 C4' DG N -10 OK 8099 8096 8098 8119 C4' DA N -9 OK 8121 8118 8120 8140 C4' DC N -8 OK 8142 8139 8141 8159 C4' DG N -7 OK 8161 8158 8160 8181 C4' DC N -6 OK 8183 8180 8182 8200 C4' DC N -5 OK 8202 8199 8201 8219 C4' DA N -4 OK 8221 8218 8220 8240 C4' DG N -3 OK 8242 8239 8241 8262 C4' DA N -2 OK 8264 8261 8263 8283 C4' DC N -1 OK 8285 8282 8284 8302 C4' DG N 0 OK 8304 8301 8303 8325 C4' G R 1 OK 8327 8324 8326 8348 C4' C R 2 OK 8350 8347 8349 8368 C4' G R 3 OK 8370 8367 8369 8391 C4' G R 4 OK 8393 8390 8392 8414 C4' C R 5 OK 8416 8413 8415 8434 C4' G R 6 OK 8436 8433 8435 8457 C4' C R 7 OK 8459 8456 8458 8477 C4' G R 8 OK 8479 8476 8478 8500 C4' C R 9 OK 8502 8499 8501 8521 C4' DC T -9 OK 8523 8520 8522 8540 C4' DG T -8 OK 8542 8539 8541 8562 C4' DT T -7 OK 8564 8561 8563 8582 C4' DC T -6 OK 8584 8581 8583 8601 C4' DT T -5 OK 8603 8600 8602 8621 C4' DG T -4 OK 8623 8620 8622 8643 C4' DG T -3 OK 8645 8642 8644 8665 C4' DC T -2 OK 8667 8664 8666 8684 C4' DG T -1 OK 8686 8683 8685 8706 C4' DT T 0 OK 8708 8705 8707 8726 C4' DG T 1 OK 8728 8725 8727 8748 C4' DC T 2 OK 8750 8747 8749 8767 C4' DG T 3 OK 8769 8766 8768 8789 C4' DC T 4 OK 8791 8788 8790 8808 C4' DG T 5 OK 8810 8807 8809 8830 C4' DC T 6 OK 8832 8829 8831 8849 C4' DC T 7 OK 8851 8848 8850 8868 C4' DG T 8 OK 8870 8867 8869 8890 C4' DC T 9 OK 8892 8889 8891 8909 C4' DT T 10 OK 8911 8908 8910 8929 C4' DA T 11 OK 8931 8928 8930 8950 C4' DC T 12 OK 8952 8949 8951 8969 C4' DC T 13 OK 8971 8968 8970 8988 C4' DC T 14 OK 8990 8987 8989 9007 C4' DC T 15 OK 9009 9006 9008 9026 C4' DA T 16 OK 9028 9025 9027 9047 C4' DT T 17 OK 9049 9046 9048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7886 C5' DA N -26 7885 7887 7907 C5' DT N -25 7906 7908 7927 C5' DG N -24 7926 7928 7949 C5' DG N -23 7948 7950 7971 C5' DG N -22 7970 7972 7993 C5' DG N -21 7992 7994 8015 C5' DT N -20 8014 8016 8035 C5' DA N -19 8034 8036 8056 C5' DA N -18 8055 8057 8077 C5' DC N -11 8076 8078 8096 C5' DG N -10 8095 8097 8118 C5' DA N -9 8117 8119 8139 C5' DC N -8 8138 8140 8158 C5' DG N -7 8157 8159 8180 C5' DC N -6 8179 8181 8199 C5' DC N -5 8198 8200 8218 C5' DA N -4 8217 8219 8239 C5' DG N -3 8238 8240 8261 C5' DA N -2 8260 8262 8282 C5' DC N -1 8281 8283 8301 C5' DG N 0 8300 8302 8324 C5' G R 1 8323 8325 8347 C5' C R 2 8346 8348 8367 C5' G R 3 8366 8368 8390 C5' G R 4 8389 8391 8413 C5' C R 5 8412 8414 8433 C5' G R 6 8432 8434 8456 C5' C R 7 8455 8457 8476 C5' G R 8 8475 8477 8499 C5' C R 9 8498 8500 8520 C5' DC T -9 8519 8521 8539 C5' DG T -8 8538 8540 8561 C5' DT T -7 8560 8562 8581 C5' DC T -6 8580 8582 8600 C5' DT T -5 8599 8601 8620 C5' DG T -4 8619 8621 8642 C5' DG T -3 8641 8643 8664 C5' DC T -2 8663 8665 8683 C5' DG T -1 8682 8684 8705 C5' DT T 0 8704 8706 8725 C5' DG T 1 8724 8726 8747 C5' DC T 2 8746 8748 8766 C5' DG T 3 8765 8767 8788 C5' DC T 4 8787 8789 8807 C5' DG T 5 8806 8808 8829 C5' DC T 6 8828 8830 8848 C5' DC T 7 8847 8849 8867 C5' DG T 8 8866 8868 8889 C5' DC T 9 8888 8890 8908 C5' DT T 10 8907 8909 8928 C5' DA T 11 8927 8929 8949 C5' DC T 12 8948 8950 8968 C5' DC T 13 8967 8969 8987 C5' DC T 14 8986 8988 9006 C5' DC T 15 9005 9007 9025 C5' DA T 16 9024 9026 9046 C5' DT T 17 9045 9047 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7882 P DA N -26 distorted distorted 7883 7884 7885 7903 P DT N -25 distorted distorted 7890 7904 7905 7906 7923 P DG N -24 distorted distorted 7911 7924 7925 7926 7945 P DG N -23 distorted distorted 7931 7946 7947 7948 7967 P DG N -22 distorted distorted 7953 7968 7969 7970 7989 P DG N -21 distorted distorted 7975 7990 7991 7992 8011 P DT N -20 distorted distorted 7997 8012 8013 8014 8031 P DA N -19 distorted distorted 8019 8032 8033 8034 8052 P DA N -18 OK OK 8039 8053 8054 8055 8073 P DC N -11 distorted distorted 8074 8075 8076 8092 P DG N -10 OK OK 8081 8093 8094 8095 8114 P DA N -9 distorted distorted 8100 8115 8116 8117 8135 P DC N -8 distorted distorted 8122 8136 8137 8138 8154 P DG N -7 distorted distorted 8143 8155 8156 8157 8176 P DC N -6 distorted distorted 8162 8177 8178 8179 8195 P DC N -5 OK OK 8184 8196 8197 8198 8214 P DA N -4 distorted distorted 8203 8215 8216 8217 8235 P DG N -3 distorted distorted 8222 8236 8237 8238 8257 P DA N -2 distorted distorted 8243 8258 8259 8260 8278 P DC N -1 distorted distorted 8265 8279 8280 8281 8297 P DG N 0 distorted distorted 8286 8298 8299 8300 8320 P G R 1 distorted distorted 8321 8322 8323 8343 P C R 2 distorted distorted 8328 8344 8345 8346 8363 P G R 3 distorted distorted 8351 8364 8365 8366 8386 P G R 4 distorted distorted 8371 8387 8388 8389 8409 P C R 5 OK OK 8394 8410 8411 8412 8429 P G R 6 distorted distorted 8417 8430 8431 8432 8452 P C R 7 distorted distorted 8437 8453 8454 8455 8472 P G R 8 distorted distorted 8460 8473 8474 8475 8495 P C R 9 distorted distorted 8480 8496 8497 8498 8516 P DC T -9 distorted distorted 8517 8518 8519 8535 P DG T -8 distorted distorted 8524 8536 8537 8538 8557 P DT T -7 distorted distorted 8543 8558 8559 8560 8577 P DC T -6 distorted distorted 8565 8578 8579 8580 8596 P DT T -5 OK OK 8585 8597 8598 8599 8616 P DG T -4 distorted distorted 8604 8617 8618 8619 8638 P DG T -3 distorted distorted 8624 8639 8640 8641 8660 P DC T -2 distorted distorted 8646 8661 8662 8663 8679 P DG T -1 distorted distorted 8668 8680 8681 8682 8701 P DT T 0 distorted distorted 8687 8702 8703 8704 8721 P DG T 1 OK OK 8709 8722 8723 8724 8743 P DC T 2 distorted distorted 8729 8744 8745 8746 8762 P DG T 3 distorted distorted 8751 8763 8764 8765 8784 P DC T 4 distorted distorted 8770 8785 8786 8787 8803 P DG T 5 distorted distorted 8792 8804 8805 8806 8825 P DC T 6 distorted distorted 8811 8826 8827 8828 8844 P DC T 7 distorted distorted 8833 8845 8846 8847 8863 P DG T 8 distorted distorted 8852 8864 8865 8866 8885 P DC T 9 distorted distorted 8871 8886 8887 8888 8904 P DT T 10 distorted distorted 8893 8905 8906 8907 8924 P DA T 11 distorted distorted 8912 8925 8926 8927 8945 P DC T 12 distorted distorted 8932 8946 8947 8948 8964 P DC T 13 distorted distorted 8953 8965 8966 8967 8983 P DC T 14 distorted distorted 8972 8984 8985 8986 9002 P DC T 15 distorted distorted 8991 9003 9004 9005 9021 P DA T 16 distorted distorted 9010 9022 9023 9024 9042 P DT T 17 distorted distorted 9029 9043 9044 9045 ---------------------------------------------------------------------------------