ID code: '3KK2' 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' --------------------------------------------------------------------------------- 7935 C1' DG P 805 beta 7931 7936 7934 7957 C1' DT P 806 beta 7953 7958 7956 7977 C1' DC P 807 beta 7973 7978 7976 7996 C1' DC P 808 beta 7992 7997 7995 8015 C1' DC P 809 beta 8011 8016 8014 8034 C1' DT P 810 beta 8030 8035 8033 8054 C1' DG P 811 beta 8050 8055 8053 8076 C1' DT P 812 beta 8072 8077 8075 8096 C1' DT P 813 beta 8092 8097 8095 8116 C1' DC P 814 beta 8112 8117 8115 8135 C1' DG P 815 beta 8131 8136 8134 8157 C1' DG P 816 beta 8153 8158 8156 8179 C1' DG P 817 beta 8175 8180 8178 8201 C1' DC P 818 beta 8197 8202 8200 8220 C1' DG P 819 beta 8216 8221 8219 8242 C1' DC P 820 beta 8238 8243 8241 8261 C1' DC P 821 beta 8257 8262 8260 8278 C1' DOC P 822 beta 8282 8270 8279 8296 C1' DT T 702 beta 8292 8297 8295 8316 C1' DG T 703 beta 8312 8317 8315 8338 C1' DG T 704 beta 8334 8339 8337 8360 C1' DT T 705 beta 8356 8361 8359 8380 C1' DG T 706 beta 8376 8381 8379 8402 C1' DG T 707 beta 8398 8403 8401 8424 C1' DG T 708 beta 8420 8425 8423 8446 C1' DC T 709 beta 8442 8447 8445 8465 C1' DG T 710 beta 8461 8466 8464 8487 C1' DC T 711 beta 8483 8488 8486 8506 C1' DC T 712 beta 8502 8507 8505 8525 C1' DC T 713 beta 8521 8526 8524 8544 C1' DG T 714 beta 8540 8545 8543 8566 C1' DA T 715 beta 8562 8567 8565 8587 C1' DA T 716 beta 8583 8588 8586 8608 C1' DC T 717 beta 8604 8609 8607 8627 C1' DA T 718 beta 8623 8628 8626 8648 C1' DG T 719 beta 8644 8649 8647 8670 C1' DG T 720 beta 8666 8671 8669 8692 C1' DG T 721 beta 8688 8693 8691 8714 C1' DA T 722 beta 8710 8715 8713 8735 C1' DC T 723 beta 8731 8736 8734 8754 C1' DT T 724 beta 8750 8755 8753 8774 C1' DG T 725 beta 8770 8775 8773 8818 C1' DTP A 563 beta 8814 8819 8817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7934 C2' DG P 805 7935 7932 7956 C2' DT P 806 7957 7954 7976 C2' DC P 807 7977 7974 7995 C2' DC P 808 7996 7993 8014 C2' DC P 809 8015 8012 8033 C2' DT P 810 8034 8031 8053 C2' DG P 811 8054 8051 8075 C2' DT P 812 8076 8073 8095 C2' DT P 813 8096 8093 8115 C2' DC P 814 8116 8113 8134 C2' DG P 815 8135 8132 8156 C2' DG P 816 8157 8154 8178 C2' DG P 817 8179 8176 8200 C2' DC P 818 8201 8198 8219 C2' DG P 819 8220 8217 8241 C2' DC P 820 8242 8239 8260 C2' DC P 821 8261 8258 8279 C2' DOC P 822 8278 8280 8295 C2' DT T 702 8296 8293 8315 C2' DG T 703 8316 8313 8337 C2' DG T 704 8338 8335 8359 C2' DT T 705 8360 8357 8379 C2' DG T 706 8380 8377 8401 C2' DG T 707 8402 8399 8423 C2' DG T 708 8424 8421 8445 C2' DC T 709 8446 8443 8464 C2' DG T 710 8465 8462 8486 C2' DC T 711 8487 8484 8505 C2' DC T 712 8506 8503 8524 C2' DC T 713 8525 8522 8543 C2' DG T 714 8544 8541 8565 C2' DA T 715 8566 8563 8586 C2' DA T 716 8587 8584 8607 C2' DC T 717 8608 8605 8626 C2' DA T 718 8627 8624 8647 C2' DG T 719 8648 8645 8669 C2' DG T 720 8670 8667 8691 C2' DG T 721 8692 8689 8713 C2' DA T 722 8714 8711 8734 C2' DC T 723 8735 8732 8753 C2' DT T 724 8754 8751 8773 C2' DG T 725 8774 8771 8817 C2' DTP A 563 8818 8815 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7932 C3' DG P 805 OK 7930 7933 7934 7954 C3' DT P 806 OK 7952 7955 7956 7974 C3' DC P 807 OK 7972 7975 7976 7993 C3' DC P 808 OK 7991 7994 7995 8012 C3' DC P 809 OK 8010 8013 8014 8031 C3' DT P 810 OK 8029 8032 8033 8051 C3' DG P 811 OK 8049 8052 8053 8073 C3' DT P 812 OK 8071 8074 8075 8093 C3' DT P 813 OK 8091 8094 8095 8113 C3' DC P 814 OK 8111 8114 8115 8132 C3' DG P 815 OK 8130 8133 8134 8154 C3' DG P 816 OK 8152 8155 8156 8176 C3' DG P 817 OK 8174 8177 8178 8198 C3' DC P 818 OK 8196 8199 8200 8217 C3' DG P 819 OK 8215 8218 8219 8239 C3' DC P 820 OK 8237 8240 8241 8258 C3' DC P 821 OK 8256 8259 8260 8280 C3' DOC P 822 8281 8279 8293 C3' DT T 702 OK 8291 8294 8295 8313 C3' DG T 703 OK 8311 8314 8315 8335 C3' DG T 704 OK 8333 8336 8337 8357 C3' DT T 705 OK 8355 8358 8359 8377 C3' DG T 706 OK 8375 8378 8379 8399 C3' DG T 707 OK 8397 8400 8401 8421 C3' DG T 708 OK 8419 8422 8423 8443 C3' DC T 709 OK 8441 8444 8445 8462 C3' DG T 710 OK 8460 8463 8464 8484 C3' DC T 711 OK 8482 8485 8486 8503 C3' DC T 712 OK 8501 8504 8505 8522 C3' DC T 713 OK 8520 8523 8524 8541 C3' DG T 714 OK 8539 8542 8543 8563 C3' DA T 715 OK 8561 8564 8565 8584 C3' DA T 716 OK 8582 8585 8586 8605 C3' DC T 717 OK 8603 8606 8607 8624 C3' DA T 718 OK 8622 8625 8626 8645 C3' DG T 719 OK 8643 8646 8647 8667 C3' DG T 720 OK 8665 8668 8669 8689 C3' DG T 721 OK 8687 8690 8691 8711 C3' DA T 722 OK 8709 8712 8713 8732 C3' DC T 723 OK 8730 8733 8734 8751 C3' DT T 724 OK 8749 8752 8753 8771 C3' DG T 725 OK 8769 8772 8773 8815 C3' DTP A 563 OK 8813 8816 8817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7930 C4' DG P 805 OK 7932 7929 7931 7952 C4' DT P 806 OK 7954 7951 7953 7972 C4' DC P 807 OK 7974 7971 7973 7991 C4' DC P 808 OK 7993 7990 7992 8010 C4' DC P 809 OK 8012 8009 8011 8029 C4' DT P 810 OK 8031 8028 8030 8049 C4' DG P 811 OK 8051 8048 8050 8071 C4' DT P 812 OK 8073 8070 8072 8091 C4' DT P 813 OK 8093 8090 8092 8111 C4' DC P 814 OK 8113 8110 8112 8130 C4' DG P 815 OK 8132 8129 8131 8152 C4' DG P 816 OK 8154 8151 8153 8174 C4' DG P 817 OK 8176 8173 8175 8196 C4' DC P 818 OK 8198 8195 8197 8215 C4' DG P 819 OK 8217 8214 8216 8237 C4' DC P 820 OK 8239 8236 8238 8256 C4' DC P 821 OK 8258 8255 8257 8281 C4' DOC P 822 OK 8280 8283 8282 8291 C4' DT T 702 OK 8293 8290 8292 8311 C4' DG T 703 OK 8313 8310 8312 8333 C4' DG T 704 OK 8335 8332 8334 8355 C4' DT T 705 OK 8357 8354 8356 8375 C4' DG T 706 OK 8377 8374 8376 8397 C4' DG T 707 OK 8399 8396 8398 8419 C4' DG T 708 OK 8421 8418 8420 8441 C4' DC T 709 OK 8443 8440 8442 8460 C4' DG T 710 OK 8462 8459 8461 8482 C4' DC T 711 OK 8484 8481 8483 8501 C4' DC T 712 OK 8503 8500 8502 8520 C4' DC T 713 OK 8522 8519 8521 8539 C4' DG T 714 OK 8541 8538 8540 8561 C4' DA T 715 OK 8563 8560 8562 8582 C4' DA T 716 OK 8584 8581 8583 8603 C4' DC T 717 OK 8605 8602 8604 8622 C4' DA T 718 OK 8624 8621 8623 8643 C4' DG T 719 OK 8645 8642 8644 8665 C4' DG T 720 OK 8667 8664 8666 8687 C4' DG T 721 OK 8689 8686 8688 8709 C4' DA T 722 OK 8711 8708 8710 8730 C4' DC T 723 OK 8732 8729 8731 8749 C4' DT T 724 OK 8751 8748 8750 8769 C4' DG T 725 OK 8771 8768 8770 8813 C4' DTP A 563 OK 8815 8812 8814 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7929 C5' DG P 805 7928 7930 7951 C5' DT P 806 7950 7952 7971 C5' DC P 807 7970 7972 7990 C5' DC P 808 7989 7991 8009 C5' DC P 809 8008 8010 8028 C5' DT P 810 8027 8029 8048 C5' DG P 811 8047 8049 8070 C5' DT P 812 8069 8071 8090 C5' DT P 813 8089 8091 8110 C5' DC P 814 8109 8111 8129 C5' DG P 815 8128 8130 8151 C5' DG P 816 8150 8152 8173 C5' DG P 817 8172 8174 8195 C5' DC P 818 8194 8196 8214 C5' DG P 819 8213 8215 8236 C5' DC P 820 8235 8237 8255 C5' DC P 821 8254 8256 8283 C5' DOC P 822 8284 8281 8290 C5' DT T 702 8289 8291 8310 C5' DG T 703 8309 8311 8332 C5' DG T 704 8331 8333 8354 C5' DT T 705 8353 8355 8374 C5' DG T 706 8373 8375 8396 C5' DG T 707 8395 8397 8418 C5' DG T 708 8417 8419 8440 C5' DC T 709 8439 8441 8459 C5' DG T 710 8458 8460 8481 C5' DC T 711 8480 8482 8500 C5' DC T 712 8499 8501 8519 C5' DC T 713 8518 8520 8538 C5' DG T 714 8537 8539 8560 C5' DA T 715 8559 8561 8581 C5' DA T 716 8580 8582 8602 C5' DC T 717 8601 8603 8621 C5' DA T 718 8620 8622 8642 C5' DG T 719 8641 8643 8664 C5' DG T 720 8663 8665 8686 C5' DG T 721 8685 8687 8708 C5' DA T 722 8707 8709 8729 C5' DC T 723 8728 8730 8748 C5' DT T 724 8747 8749 8768 C5' DG T 725 8767 8769 8812 C5' DTP A 563 8811 8813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7947 P DT P 806 distorted distorted 7933 7948 7949 7950 7967 P DC P 807 distorted distorted 7955 7968 7969 7970 7986 P DC P 808 distorted distorted 7975 7987 7988 7989 8005 P DC P 809 distorted distorted 7994 8006 8007 8008 8024 P DT P 810 distorted distorted 8013 8025 8026 8027 8044 P DG P 811 distorted distorted 8032 8045 8046 8047 8066 P DT P 812 distorted distorted 8052 8067 8068 8069 8086 P DT P 813 distorted distorted 8074 8087 8088 8089 8106 P DC P 814 distorted distorted 8094 8107 8108 8109 8125 P DG P 815 distorted distorted 8114 8126 8127 8128 8147 P DG P 816 distorted distorted 8133 8148 8149 8150 8169 P DG P 817 distorted distorted 8155 8170 8171 8172 8191 P DC P 818 distorted distorted 8177 8192 8193 8194 8210 P DG P 819 distorted distorted 8199 8211 8212 8213 8232 P DC P 820 distorted distorted 8218 8233 8234 8235 8251 P DC P 821 distorted distorted 8240 8252 8253 8254 8285 P DOC P 822 distorted distorted 8259 8286 8287 8284 8306 P DG T 703 distorted distorted 8294 8307 8308 8309 8328 P DG T 704 distorted distorted 8314 8329 8330 8331 8350 P DT T 705 distorted distorted 8336 8351 8352 8353 8370 P DG T 706 distorted distorted 8358 8371 8372 8373 8392 P DG T 707 distorted distorted 8378 8393 8394 8395 8414 P DG T 708 distorted distorted 8400 8415 8416 8417 8436 P DC T 709 distorted distorted 8422 8437 8438 8439 8455 P DG T 710 distorted distorted 8444 8456 8457 8458 8477 P DC T 711 distorted distorted 8463 8478 8479 8480 8496 P DC T 712 distorted distorted 8485 8497 8498 8499 8515 P DC T 713 distorted distorted 8504 8516 8517 8518 8534 P DG T 714 distorted distorted 8523 8535 8536 8537 8556 P DA T 715 distorted distorted 8542 8557 8558 8559 8577 P DA T 716 distorted distorted 8564 8578 8579 8580 8598 P DC T 717 distorted distorted 8585 8599 8600 8601 8617 P DA T 718 distorted distorted 8606 8618 8619 8620 8638 P DG T 719 distorted distorted 8625 8639 8640 8641 8660 P DG T 720 distorted distorted 8646 8661 8662 8663 8682 P DG T 721 distorted distorted 8668 8683 8684 8685 8704 P DA T 722 distorted distorted 8690 8705 8706 8707 8725 P DC T 723 distorted distorted 8712 8726 8727 8728 8744 P DT T 724 distorted distorted 8733 8745 8746 8747 8764 P DG T 725 distorted distorted 8752 8765 8766 8767 ---------------------------------------------------------------------------------