ID code: '5M0I' 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' --------------------------------------------------------------------------------- 7606 C1' G E 1 beta 7601 7607 7604 7629 C1' A E 2 beta 7624 7630 7627 7651 C1' U E 3 beta 7646 7652 7649 7671 C1' A E 4 beta 7666 7672 7669 7693 C1' A E 5 beta 7688 7694 7691 7715 C1' C E 6 beta 7710 7716 7713 7735 C1' U E 7 beta 7730 7736 7733 7755 C1' G E 8 beta 7750 7756 7753 7778 C1' A E 9 beta 7773 7779 7776 7800 C1' A E 10 beta 7795 7801 7798 7822 C1' U E 11 beta 7817 7823 7820 7842 C1' C E 12 beta 7837 7843 7840 7862 C1' G E 13 beta 7857 7863 7860 7885 C1' A E 14 beta 7880 7886 7883 7907 C1' A E 15 beta 7902 7908 7905 7929 C1' A E 16 beta 7924 7930 7927 7951 C1' G E 17 beta 7946 7952 7949 7974 C1' A E 18 beta 7969 7975 7972 7996 C1' C E 19 beta 7991 7997 7994 8016 C1' A E 20 beta 8011 8017 8014 8038 C1' U E 21 beta 8033 8039 8036 8058 C1' U E 22 beta 8053 8059 8056 8078 C1' A E 23 beta 8073 8079 8076 8100 C1' U E 24 beta 8095 8101 8098 8120 C1' C E 25 beta 8115 8121 8118 8140 C1' A E 26 beta 8135 8141 8138 8162 C1' C E 27 beta 8157 8163 8160 8182 C1' G E 28 beta 8177 8183 8180 8203 C1' G F 1 beta 8198 8204 8201 8226 C1' A F 2 beta 8221 8227 8224 8248 C1' U F 3 beta 8243 8249 8246 8268 C1' A F 4 beta 8263 8269 8266 8290 C1' A F 5 beta 8285 8291 8288 8312 C1' C F 6 beta 8307 8313 8310 8332 C1' U F 7 beta 8327 8333 8330 8352 C1' G F 8 beta 8347 8353 8350 8375 C1' A F 9 beta 8370 8376 8373 8397 C1' A F 10 beta 8392 8398 8395 8419 C1' U F 11 beta 8414 8420 8417 8439 C1' C F 12 beta 8434 8440 8437 8459 C1' G F 13 beta 8454 8460 8457 8482 C1' A F 14 beta 8477 8483 8480 8504 C1' A F 15 beta 8499 8505 8502 8526 C1' A F 16 beta 8521 8527 8524 8548 C1' G F 17 beta 8543 8549 8546 8571 C1' A F 18 beta 8566 8572 8569 8593 C1' C F 19 beta 8588 8594 8591 8613 C1' A F 20 beta 8608 8614 8611 8635 C1' U F 21 beta 8630 8636 8633 8655 C1' U F 22 beta 8650 8656 8653 8675 C1' A F 23 beta 8670 8676 8673 8697 C1' U F 24 beta 8692 8698 8695 8717 C1' C F 25 beta 8712 8718 8715 8737 C1' A F 26 beta 8732 8738 8735 8759 C1' C F 27 beta 8754 8760 8757 8779 C1' G F 28 beta 8774 8780 8777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7604 C2' G E 1 OK 7606 7602 7605 7627 C2' A E 2 OK 7629 7625 7628 7649 C2' U E 3 OK 7651 7647 7650 7669 C2' A E 4 OK 7671 7667 7670 7691 C2' A E 5 OK 7693 7689 7692 7713 C2' C E 6 OK 7715 7711 7714 7733 C2' U E 7 OK 7735 7731 7734 7753 C2' G E 8 OK 7755 7751 7754 7776 C2' A E 9 OK 7778 7774 7777 7798 C2' A E 10 OK 7800 7796 7799 7820 C2' U E 11 OK 7822 7818 7821 7840 C2' C E 12 OK 7842 7838 7841 7860 C2' G E 13 OK 7862 7858 7861 7883 C2' A E 14 OK 7885 7881 7884 7905 C2' A E 15 OK 7907 7903 7906 7927 C2' A E 16 OK 7929 7925 7928 7949 C2' G E 17 OK 7951 7947 7950 7972 C2' A E 18 OK 7974 7970 7973 7994 C2' C E 19 OK 7996 7992 7995 8014 C2' A E 20 OK 8016 8012 8015 8036 C2' U E 21 OK 8038 8034 8037 8056 C2' U E 22 OK 8058 8054 8057 8076 C2' A E 23 OK 8078 8074 8077 8098 C2' U E 24 OK 8100 8096 8099 8118 C2' C E 25 OK 8120 8116 8119 8138 C2' A E 26 OK 8140 8136 8139 8160 C2' C E 27 OK 8162 8158 8161 8180 C2' G E 28 OK 8182 8178 8181 8201 C2' G F 1 OK 8203 8199 8202 8224 C2' A F 2 OK 8226 8222 8225 8246 C2' U F 3 OK 8248 8244 8247 8266 C2' A F 4 OK 8268 8264 8267 8288 C2' A F 5 OK 8290 8286 8289 8310 C2' C F 6 OK 8312 8308 8311 8330 C2' U F 7 OK 8332 8328 8331 8350 C2' G F 8 OK 8352 8348 8351 8373 C2' A F 9 OK 8375 8371 8374 8395 C2' A F 10 OK 8397 8393 8396 8417 C2' U F 11 OK 8419 8415 8418 8437 C2' C F 12 OK 8439 8435 8438 8457 C2' G F 13 OK 8459 8455 8458 8480 C2' A F 14 OK 8482 8478 8481 8502 C2' A F 15 OK 8504 8500 8503 8524 C2' A F 16 OK 8526 8522 8525 8546 C2' G F 17 OK 8548 8544 8547 8569 C2' A F 18 OK 8571 8567 8570 8591 C2' C F 19 OK 8593 8589 8592 8611 C2' A F 20 OK 8613 8609 8612 8633 C2' U F 21 OK 8635 8631 8634 8653 C2' U F 22 OK 8655 8651 8654 8673 C2' A F 23 OK 8675 8671 8674 8695 C2' U F 24 OK 8697 8693 8696 8715 C2' C F 25 OK 8717 8713 8716 8735 C2' A F 26 OK 8737 8733 8736 8757 C2' C F 27 OK 8759 8755 8758 8777 C2' G F 28 OK 8779 8775 8778 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7602 C3' G E 1 OK 7600 7603 7604 7625 C3' A E 2 OK 7623 7626 7627 7647 C3' U E 3 OK 7645 7648 7649 7667 C3' A E 4 OK 7665 7668 7669 7689 C3' A E 5 OK 7687 7690 7691 7711 C3' C E 6 OK 7709 7712 7713 7731 C3' U E 7 OK 7729 7732 7733 7751 C3' G E 8 OK 7749 7752 7753 7774 C3' A E 9 OK 7772 7775 7776 7796 C3' A E 10 OK 7794 7797 7798 7818 C3' U E 11 OK 7816 7819 7820 7838 C3' C E 12 OK 7836 7839 7840 7858 C3' G E 13 OK 7856 7859 7860 7881 C3' A E 14 OK 7879 7882 7883 7903 C3' A E 15 OK 7901 7904 7905 7925 C3' A E 16 OK 7923 7926 7927 7947 C3' G E 17 OK 7945 7948 7949 7970 C3' A E 18 OK 7968 7971 7972 7992 C3' C E 19 OK 7990 7993 7994 8012 C3' A E 20 OK 8010 8013 8014 8034 C3' U E 21 OK 8032 8035 8036 8054 C3' U E 22 OK 8052 8055 8056 8074 C3' A E 23 OK 8072 8075 8076 8096 C3' U E 24 OK 8094 8097 8098 8116 C3' C E 25 OK 8114 8117 8118 8136 C3' A E 26 OK 8134 8137 8138 8158 C3' C E 27 OK 8156 8159 8160 8178 C3' G E 28 OK 8176 8179 8180 8199 C3' G F 1 OK 8197 8200 8201 8222 C3' A F 2 OK 8220 8223 8224 8244 C3' U F 3 OK 8242 8245 8246 8264 C3' A F 4 OK 8262 8265 8266 8286 C3' A F 5 OK 8284 8287 8288 8308 C3' C F 6 OK 8306 8309 8310 8328 C3' U F 7 OK 8326 8329 8330 8348 C3' G F 8 OK 8346 8349 8350 8371 C3' A F 9 OK 8369 8372 8373 8393 C3' A F 10 OK 8391 8394 8395 8415 C3' U F 11 OK 8413 8416 8417 8435 C3' C F 12 OK 8433 8436 8437 8455 C3' G F 13 OK 8453 8456 8457 8478 C3' A F 14 OK 8476 8479 8480 8500 C3' A F 15 OK 8498 8501 8502 8522 C3' A F 16 OK 8520 8523 8524 8544 C3' G F 17 OK 8542 8545 8546 8567 C3' A F 18 OK 8565 8568 8569 8589 C3' C F 19 OK 8587 8590 8591 8609 C3' A F 20 OK 8607 8610 8611 8631 C3' U F 21 OK 8629 8632 8633 8651 C3' U F 22 OK 8649 8652 8653 8671 C3' A F 23 OK 8669 8672 8673 8693 C3' U F 24 OK 8691 8694 8695 8713 C3' C F 25 OK 8711 8714 8715 8733 C3' A F 26 OK 8731 8734 8735 8755 C3' C F 27 OK 8753 8756 8757 8775 C3' G F 28 OK 8773 8776 8777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7600 C4' G E 1 OK 7602 7599 7601 7623 C4' A E 2 OK 7625 7622 7624 7645 C4' U E 3 OK 7647 7644 7646 7665 C4' A E 4 OK 7667 7664 7666 7687 C4' A E 5 OK 7689 7686 7688 7709 C4' C E 6 OK 7711 7708 7710 7729 C4' U E 7 OK 7731 7728 7730 7749 C4' G E 8 OK 7751 7748 7750 7772 C4' A E 9 OK 7774 7771 7773 7794 C4' A E 10 OK 7796 7793 7795 7816 C4' U E 11 OK 7818 7815 7817 7836 C4' C E 12 OK 7838 7835 7837 7856 C4' G E 13 OK 7858 7855 7857 7879 C4' A E 14 OK 7881 7878 7880 7901 C4' A E 15 OK 7903 7900 7902 7923 C4' A E 16 OK 7925 7922 7924 7945 C4' G E 17 OK 7947 7944 7946 7968 C4' A E 18 OK 7970 7967 7969 7990 C4' C E 19 OK 7992 7989 7991 8010 C4' A E 20 OK 8012 8009 8011 8032 C4' U E 21 OK 8034 8031 8033 8052 C4' U E 22 OK 8054 8051 8053 8072 C4' A E 23 OK 8074 8071 8073 8094 C4' U E 24 OK 8096 8093 8095 8114 C4' C E 25 OK 8116 8113 8115 8134 C4' A E 26 OK 8136 8133 8135 8156 C4' C E 27 OK 8158 8155 8157 8176 C4' G E 28 OK 8178 8175 8177 8197 C4' G F 1 OK 8199 8196 8198 8220 C4' A F 2 OK 8222 8219 8221 8242 C4' U F 3 OK 8244 8241 8243 8262 C4' A F 4 OK 8264 8261 8263 8284 C4' A F 5 OK 8286 8283 8285 8306 C4' C F 6 OK 8308 8305 8307 8326 C4' U F 7 OK 8328 8325 8327 8346 C4' G F 8 OK 8348 8345 8347 8369 C4' A F 9 OK 8371 8368 8370 8391 C4' A F 10 OK 8393 8390 8392 8413 C4' U F 11 OK 8415 8412 8414 8433 C4' C F 12 OK 8435 8432 8434 8453 C4' G F 13 OK 8455 8452 8454 8476 C4' A F 14 OK 8478 8475 8477 8498 C4' A F 15 OK 8500 8497 8499 8520 C4' A F 16 OK 8522 8519 8521 8542 C4' G F 17 OK 8544 8541 8543 8565 C4' A F 18 OK 8567 8564 8566 8587 C4' C F 19 OK 8589 8586 8588 8607 C4' A F 20 OK 8609 8606 8608 8629 C4' U F 21 OK 8631 8628 8630 8649 C4' U F 22 OK 8651 8648 8650 8669 C4' A F 23 OK 8671 8668 8670 8691 C4' U F 24 OK 8693 8690 8692 8711 C4' C F 25 OK 8713 8710 8712 8731 C4' A F 26 OK 8733 8730 8732 8753 C4' C F 27 OK 8755 8752 8754 8773 C4' G F 28 OK 8775 8772 8774 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7599 C5' G E 1 7598 7600 7622 C5' A E 2 7621 7623 7644 C5' U E 3 7643 7645 7664 C5' A E 4 7663 7665 7686 C5' A E 5 7685 7687 7708 C5' C E 6 7707 7709 7728 C5' U E 7 7727 7729 7748 C5' G E 8 7747 7749 7771 C5' A E 9 7770 7772 7793 C5' A E 10 7792 7794 7815 C5' U E 11 7814 7816 7835 C5' C E 12 7834 7836 7855 C5' G E 13 7854 7856 7878 C5' A E 14 7877 7879 7900 C5' A E 15 7899 7901 7922 C5' A E 16 7921 7923 7944 C5' G E 17 7943 7945 7967 C5' A E 18 7966 7968 7989 C5' C E 19 7988 7990 8009 C5' A E 20 8008 8010 8031 C5' U E 21 8030 8032 8051 C5' U E 22 8050 8052 8071 C5' A E 23 8070 8072 8093 C5' U E 24 8092 8094 8113 C5' C E 25 8112 8114 8133 C5' A E 26 8132 8134 8155 C5' C E 27 8154 8156 8175 C5' G E 28 8174 8176 8196 C5' G F 1 8195 8197 8219 C5' A F 2 8218 8220 8241 C5' U F 3 8240 8242 8261 C5' A F 4 8260 8262 8283 C5' A F 5 8282 8284 8305 C5' C F 6 8304 8306 8325 C5' U F 7 8324 8326 8345 C5' G F 8 8344 8346 8368 C5' A F 9 8367 8369 8390 C5' A F 10 8389 8391 8412 C5' U F 11 8411 8413 8432 C5' C F 12 8431 8433 8452 C5' G F 13 8451 8453 8475 C5' A F 14 8474 8476 8497 C5' A F 15 8496 8498 8519 C5' A F 16 8518 8520 8541 C5' G F 17 8540 8542 8564 C5' A F 18 8563 8565 8586 C5' C F 19 8585 8587 8606 C5' A F 20 8605 8607 8628 C5' U F 21 8627 8629 8648 C5' U F 22 8647 8649 8668 C5' A F 23 8667 8669 8690 C5' U F 24 8689 8691 8710 C5' C F 25 8709 8711 8730 C5' A F 26 8729 8731 8752 C5' C F 27 8751 8753 8772 C5' G F 28 8771 8773 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7618 P A E 2 distorted distorted 7603 7619 7620 7621 7640 P U E 3 distorted distorted 7626 7641 7642 7643 7660 P A E 4 distorted distorted 7648 7661 7662 7663 7682 P A E 5 distorted distorted 7668 7683 7684 7685 7704 P C E 6 distorted distorted 7690 7705 7706 7707 7724 P U E 7 distorted distorted 7712 7725 7726 7727 7744 P G E 8 distorted distorted 7732 7745 7746 7747 7767 P A E 9 distorted distorted 7752 7768 7769 7770 7789 P A E 10 distorted distorted 7775 7790 7791 7792 7811 P U E 11 distorted distorted 7797 7812 7813 7814 7831 P C E 12 distorted distorted 7819 7832 7833 7834 7851 P G E 13 distorted distorted 7839 7852 7853 7854 7874 P A E 14 distorted distorted 7859 7875 7876 7877 7896 P A E 15 distorted distorted 7882 7897 7898 7899 7918 P A E 16 distorted distorted 7904 7919 7920 7921 7940 P G E 17 distorted distorted 7926 7941 7942 7943 7963 P A E 18 distorted distorted 7948 7964 7965 7966 7985 P C E 19 distorted distorted 7971 7986 7987 7988 8005 P A E 20 distorted distorted 7993 8006 8007 8008 8027 P U E 21 distorted distorted 8013 8028 8029 8030 8047 P U E 22 distorted distorted 8035 8048 8049 8050 8067 P A E 23 distorted distorted 8055 8068 8069 8070 8089 P U E 24 distorted distorted 8075 8090 8091 8092 8109 P C E 25 distorted distorted 8097 8110 8111 8112 8129 P A E 26 distorted distorted 8117 8130 8131 8132 8151 P C E 27 distorted distorted 8137 8152 8153 8154 8171 P G E 28 distorted distorted 8159 8172 8173 8174 8215 P A F 2 distorted distorted 8200 8216 8217 8218 8237 P U F 3 distorted distorted 8223 8238 8239 8240 8257 P A F 4 distorted distorted 8245 8258 8259 8260 8279 P A F 5 distorted distorted 8265 8280 8281 8282 8301 P C F 6 distorted distorted 8287 8302 8303 8304 8321 P U F 7 distorted distorted 8309 8322 8323 8324 8341 P G F 8 distorted distorted 8329 8342 8343 8344 8364 P A F 9 distorted distorted 8349 8365 8366 8367 8386 P A F 10 distorted distorted 8372 8387 8388 8389 8408 P U F 11 distorted distorted 8394 8409 8410 8411 8428 P C F 12 distorted distorted 8416 8429 8430 8431 8448 P G F 13 distorted distorted 8436 8449 8450 8451 8471 P A F 14 distorted distorted 8456 8472 8473 8474 8493 P A F 15 distorted distorted 8479 8494 8495 8496 8515 P A F 16 distorted distorted 8501 8516 8517 8518 8537 P G F 17 distorted distorted 8523 8538 8539 8540 8560 P A F 18 distorted distorted 8545 8561 8562 8563 8582 P C F 19 distorted distorted 8568 8583 8584 8585 8602 P A F 20 distorted distorted 8590 8603 8604 8605 8624 P U F 21 distorted distorted 8610 8625 8626 8627 8644 P U F 22 distorted distorted 8632 8645 8646 8647 8664 P A F 23 distorted distorted 8652 8665 8666 8667 8686 P U F 24 distorted distorted 8672 8687 8688 8689 8706 P C F 25 distorted distorted 8694 8707 8708 8709 8726 P A F 26 distorted distorted 8714 8727 8728 8729 8748 P C F 27 distorted distorted 8734 8749 8750 8751 8768 P G F 28 distorted distorted 8756 8769 8770 8771 ---------------------------------------------------------------------------------