ID code: '3KK1' 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' --------------------------------------------------------------------------------- 7920 C1' DG P 805 beta 7916 7921 7919 7942 C1' DT P 806 beta 7938 7943 7941 7962 C1' DC P 807 beta 7958 7963 7961 7981 C1' DC P 808 beta 7977 7982 7980 8000 C1' DC P 809 beta 7996 8001 7999 8019 C1' DT P 810 beta 8015 8020 8018 8039 C1' DG P 811 beta 8035 8040 8038 8061 C1' DT P 812 beta 8057 8062 8060 8081 C1' DT P 813 beta 8077 8082 8080 8101 C1' DC P 814 beta 8097 8102 8100 8120 C1' DG P 815 beta 8116 8121 8119 8142 C1' DG P 816 beta 8138 8143 8141 8164 C1' DG P 817 beta 8160 8165 8163 8186 C1' DC P 818 beta 8182 8187 8185 8205 C1' DG P 819 beta 8201 8206 8204 8227 C1' DC P 820 beta 8223 8228 8226 8246 C1' DC P 821 beta 8242 8247 8245 8263 C1' DOC P 822 beta 8267 8255 8264 8281 C1' DT T 702 beta 8277 8282 8280 8301 C1' DG T 703 beta 8297 8302 8300 8323 C1' DG T 704 beta 8319 8324 8322 8345 C1' DT T 705 beta 8341 8346 8344 8365 C1' DG T 706 beta 8361 8366 8364 8387 C1' DG T 707 beta 8383 8388 8386 8409 C1' DG T 708 beta 8405 8410 8408 8431 C1' DC T 709 beta 8427 8432 8430 8450 C1' DG T 710 beta 8446 8451 8449 8472 C1' DC T 711 beta 8468 8473 8471 8491 C1' DC T 712 beta 8487 8492 8490 8510 C1' DC T 713 beta 8506 8511 8509 8529 C1' DG T 714 beta 8525 8530 8528 8551 C1' DA T 715 beta 8547 8552 8550 8572 C1' DA T 716 beta 8568 8573 8571 8593 C1' DC T 717 beta 8589 8594 8592 8612 C1' DA T 718 beta 8608 8613 8611 8633 C1' DG T 719 beta 8629 8634 8632 8655 C1' DG T 720 beta 8651 8656 8654 8677 C1' DG T 721 beta 8673 8678 8676 8699 C1' DA T 722 beta 8695 8700 8698 8720 C1' DC T 723 beta 8716 8721 8719 8739 C1' DT T 724 beta 8735 8740 8738 8759 C1' DG T 725 beta 8755 8760 8758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7919 C2' DG P 805 7920 7917 7941 C2' DT P 806 7942 7939 7961 C2' DC P 807 7962 7959 7980 C2' DC P 808 7981 7978 7999 C2' DC P 809 8000 7997 8018 C2' DT P 810 8019 8016 8038 C2' DG P 811 8039 8036 8060 C2' DT P 812 8061 8058 8080 C2' DT P 813 8081 8078 8100 C2' DC P 814 8101 8098 8119 C2' DG P 815 8120 8117 8141 C2' DG P 816 8142 8139 8163 C2' DG P 817 8164 8161 8185 C2' DC P 818 8186 8183 8204 C2' DG P 819 8205 8202 8226 C2' DC P 820 8227 8224 8245 C2' DC P 821 8246 8243 8264 C2' DOC P 822 8263 8265 8280 C2' DT T 702 8281 8278 8300 C2' DG T 703 8301 8298 8322 C2' DG T 704 8323 8320 8344 C2' DT T 705 8345 8342 8364 C2' DG T 706 8365 8362 8386 C2' DG T 707 8387 8384 8408 C2' DG T 708 8409 8406 8430 C2' DC T 709 8431 8428 8449 C2' DG T 710 8450 8447 8471 C2' DC T 711 8472 8469 8490 C2' DC T 712 8491 8488 8509 C2' DC T 713 8510 8507 8528 C2' DG T 714 8529 8526 8550 C2' DA T 715 8551 8548 8571 C2' DA T 716 8572 8569 8592 C2' DC T 717 8593 8590 8611 C2' DA T 718 8612 8609 8632 C2' DG T 719 8633 8630 8654 C2' DG T 720 8655 8652 8676 C2' DG T 721 8677 8674 8698 C2' DA T 722 8699 8696 8719 C2' DC T 723 8720 8717 8738 C2' DT T 724 8739 8736 8758 C2' DG T 725 8759 8756 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7917 C3' DG P 805 OK 7915 7918 7919 7939 C3' DT P 806 OK 7937 7940 7941 7959 C3' DC P 807 OK 7957 7960 7961 7978 C3' DC P 808 OK 7976 7979 7980 7997 C3' DC P 809 OK 7995 7998 7999 8016 C3' DT P 810 OK 8014 8017 8018 8036 C3' DG P 811 OK 8034 8037 8038 8058 C3' DT P 812 OK 8056 8059 8060 8078 C3' DT P 813 OK 8076 8079 8080 8098 C3' DC P 814 OK 8096 8099 8100 8117 C3' DG P 815 OK 8115 8118 8119 8139 C3' DG P 816 OK 8137 8140 8141 8161 C3' DG P 817 OK 8159 8162 8163 8183 C3' DC P 818 OK 8181 8184 8185 8202 C3' DG P 819 OK 8200 8203 8204 8224 C3' DC P 820 OK 8222 8225 8226 8243 C3' DC P 821 OK 8241 8244 8245 8265 C3' DOC P 822 8266 8264 8278 C3' DT T 702 OK 8276 8279 8280 8298 C3' DG T 703 OK 8296 8299 8300 8320 C3' DG T 704 OK 8318 8321 8322 8342 C3' DT T 705 OK 8340 8343 8344 8362 C3' DG T 706 OK 8360 8363 8364 8384 C3' DG T 707 OK 8382 8385 8386 8406 C3' DG T 708 OK 8404 8407 8408 8428 C3' DC T 709 OK 8426 8429 8430 8447 C3' DG T 710 OK 8445 8448 8449 8469 C3' DC T 711 OK 8467 8470 8471 8488 C3' DC T 712 OK 8486 8489 8490 8507 C3' DC T 713 OK 8505 8508 8509 8526 C3' DG T 714 OK 8524 8527 8528 8548 C3' DA T 715 OK 8546 8549 8550 8569 C3' DA T 716 OK 8567 8570 8571 8590 C3' DC T 717 OK 8588 8591 8592 8609 C3' DA T 718 OK 8607 8610 8611 8630 C3' DG T 719 OK 8628 8631 8632 8652 C3' DG T 720 OK 8650 8653 8654 8674 C3' DG T 721 OK 8672 8675 8676 8696 C3' DA T 722 OK 8694 8697 8698 8717 C3' DC T 723 OK 8715 8718 8719 8736 C3' DT T 724 OK 8734 8737 8738 8756 C3' DG T 725 OK 8754 8757 8758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7915 C4' DG P 805 OK 7917 7914 7916 7937 C4' DT P 806 OK 7939 7936 7938 7957 C4' DC P 807 OK 7959 7956 7958 7976 C4' DC P 808 OK 7978 7975 7977 7995 C4' DC P 809 OK 7997 7994 7996 8014 C4' DT P 810 OK 8016 8013 8015 8034 C4' DG P 811 OK 8036 8033 8035 8056 C4' DT P 812 OK 8058 8055 8057 8076 C4' DT P 813 OK 8078 8075 8077 8096 C4' DC P 814 OK 8098 8095 8097 8115 C4' DG P 815 OK 8117 8114 8116 8137 C4' DG P 816 OK 8139 8136 8138 8159 C4' DG P 817 OK 8161 8158 8160 8181 C4' DC P 818 OK 8183 8180 8182 8200 C4' DG P 819 OK 8202 8199 8201 8222 C4' DC P 820 OK 8224 8221 8223 8241 C4' DC P 821 OK 8243 8240 8242 8266 C4' DOC P 822 OK 8265 8268 8267 8276 C4' DT T 702 OK 8278 8275 8277 8296 C4' DG T 703 OK 8298 8295 8297 8318 C4' DG T 704 OK 8320 8317 8319 8340 C4' DT T 705 OK 8342 8339 8341 8360 C4' DG T 706 OK 8362 8359 8361 8382 C4' DG T 707 OK 8384 8381 8383 8404 C4' DG T 708 OK 8406 8403 8405 8426 C4' DC T 709 OK 8428 8425 8427 8445 C4' DG T 710 OK 8447 8444 8446 8467 C4' DC T 711 OK 8469 8466 8468 8486 C4' DC T 712 OK 8488 8485 8487 8505 C4' DC T 713 OK 8507 8504 8506 8524 C4' DG T 714 OK 8526 8523 8525 8546 C4' DA T 715 OK 8548 8545 8547 8567 C4' DA T 716 OK 8569 8566 8568 8588 C4' DC T 717 OK 8590 8587 8589 8607 C4' DA T 718 OK 8609 8606 8608 8628 C4' DG T 719 OK 8630 8627 8629 8650 C4' DG T 720 OK 8652 8649 8651 8672 C4' DG T 721 OK 8674 8671 8673 8694 C4' DA T 722 OK 8696 8693 8695 8715 C4' DC T 723 OK 8717 8714 8716 8734 C4' DT T 724 OK 8736 8733 8735 8754 C4' DG T 725 OK 8756 8753 8755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7914 C5' DG P 805 7913 7915 7936 C5' DT P 806 7935 7937 7956 C5' DC P 807 7955 7957 7975 C5' DC P 808 7974 7976 7994 C5' DC P 809 7993 7995 8013 C5' DT P 810 8012 8014 8033 C5' DG P 811 8032 8034 8055 C5' DT P 812 8054 8056 8075 C5' DT P 813 8074 8076 8095 C5' DC P 814 8094 8096 8114 C5' DG P 815 8113 8115 8136 C5' DG P 816 8135 8137 8158 C5' DG P 817 8157 8159 8180 C5' DC P 818 8179 8181 8199 C5' DG P 819 8198 8200 8221 C5' DC P 820 8220 8222 8240 C5' DC P 821 8239 8241 8268 C5' DOC P 822 8269 8266 8275 C5' DT T 702 8274 8276 8295 C5' DG T 703 8294 8296 8317 C5' DG T 704 8316 8318 8339 C5' DT T 705 8338 8340 8359 C5' DG T 706 8358 8360 8381 C5' DG T 707 8380 8382 8403 C5' DG T 708 8402 8404 8425 C5' DC T 709 8424 8426 8444 C5' DG T 710 8443 8445 8466 C5' DC T 711 8465 8467 8485 C5' DC T 712 8484 8486 8504 C5' DC T 713 8503 8505 8523 C5' DG T 714 8522 8524 8545 C5' DA T 715 8544 8546 8566 C5' DA T 716 8565 8567 8587 C5' DC T 717 8586 8588 8606 C5' DA T 718 8605 8607 8627 C5' DG T 719 8626 8628 8649 C5' DG T 720 8648 8650 8671 C5' DG T 721 8670 8672 8693 C5' DA T 722 8692 8694 8714 C5' DC T 723 8713 8715 8733 C5' DT T 724 8732 8734 8753 C5' DG T 725 8752 8754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7932 P DT P 806 distorted distorted 7918 7933 7934 7935 7952 P DC P 807 distorted distorted 7940 7953 7954 7955 7971 P DC P 808 distorted distorted 7960 7972 7973 7974 7990 P DC P 809 distorted distorted 7979 7991 7992 7993 8009 P DT P 810 distorted distorted 7998 8010 8011 8012 8029 P DG P 811 distorted distorted 8017 8030 8031 8032 8051 P DT P 812 distorted distorted 8037 8052 8053 8054 8071 P DT P 813 distorted distorted 8059 8072 8073 8074 8091 P DC P 814 distorted distorted 8079 8092 8093 8094 8110 P DG P 815 distorted distorted 8099 8111 8112 8113 8132 P DG P 816 distorted distorted 8118 8133 8134 8135 8154 P DG P 817 distorted distorted 8140 8155 8156 8157 8176 P DC P 818 distorted distorted 8162 8177 8178 8179 8195 P DG P 819 distorted distorted 8184 8196 8197 8198 8217 P DC P 820 distorted distorted 8203 8218 8219 8220 8236 P DC P 821 distorted distorted 8225 8237 8238 8239 8270 P DOC P 822 distorted distorted 8244 8271 8272 8269 8291 P DG T 703 distorted distorted 8279 8292 8293 8294 8313 P DG T 704 distorted distorted 8299 8314 8315 8316 8335 P DT T 705 distorted distorted 8321 8336 8337 8338 8355 P DG T 706 distorted distorted 8343 8356 8357 8358 8377 P DG T 707 distorted distorted 8363 8378 8379 8380 8399 P DG T 708 distorted distorted 8385 8400 8401 8402 8421 P DC T 709 distorted distorted 8407 8422 8423 8424 8440 P DG T 710 distorted distorted 8429 8441 8442 8443 8462 P DC T 711 distorted distorted 8448 8463 8464 8465 8481 P DC T 712 distorted distorted 8470 8482 8483 8484 8500 P DC T 713 distorted distorted 8489 8501 8502 8503 8519 P DG T 714 distorted distorted 8508 8520 8521 8522 8541 P DA T 715 distorted distorted 8527 8542 8543 8544 8562 P DA T 716 distorted distorted 8549 8563 8564 8565 8583 P DC T 717 distorted distorted 8570 8584 8585 8586 8602 P DA T 718 distorted distorted 8591 8603 8604 8605 8623 P DG T 719 distorted distorted 8610 8624 8625 8626 8645 P DG T 720 distorted distorted 8631 8646 8647 8648 8667 P DG T 721 distorted distorted 8653 8668 8669 8670 8689 P DA T 722 distorted distorted 8675 8690 8691 8692 8710 P DC T 723 distorted distorted 8697 8711 8712 8713 8729 P DT T 724 distorted distorted 8718 8730 8731 8732 8749 P DG T 725 distorted distorted 8737 8750 8751 8752 ---------------------------------------------------------------------------------