ID code: '4J1G' 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' --------------------------------------------------------------------------------- 7225 C1' U E 1 beta 7220 7226 7223 7245 C1' U E 2 beta 7240 7246 7243 7265 C1' U E 3 beta 7260 7266 7263 7285 C1' U E 4 beta 7280 7286 7283 7305 C1' U E 5 beta 7300 7306 7303 7325 C1' U E 6 beta 7320 7326 7323 7345 C1' U E 7 beta 7340 7346 7343 7365 C1' U E 8 beta 7360 7366 7363 7385 C1' U E 9 beta 7380 7386 7383 7405 C1' U E 10 beta 7400 7406 7403 7425 C1' U E 11 beta 7420 7426 7423 7445 C1' U E 12 beta 7440 7446 7443 7465 C1' U E 13 beta 7460 7466 7463 7485 C1' U E 14 beta 7480 7486 7483 7505 C1' U E 15 beta 7500 7506 7503 7525 C1' U E 16 beta 7520 7526 7523 7545 C1' U E 17 beta 7540 7546 7543 7565 C1' U E 18 beta 7560 7566 7563 7585 C1' U E 19 beta 7580 7586 7583 7605 C1' U E 20 beta 7600 7606 7603 7625 C1' U E 21 beta 7620 7626 7623 7645 C1' U E 22 beta 7640 7646 7643 7665 C1' U E 23 beta 7660 7666 7663 7685 C1' U E 24 beta 7680 7686 7683 7705 C1' U E 25 beta 7700 7706 7703 7725 C1' U E 26 beta 7720 7726 7723 7745 C1' U E 27 beta 7740 7746 7743 7765 C1' U E 28 beta 7760 7766 7763 7785 C1' U E 29 beta 7780 7786 7783 7805 C1' U E 30 beta 7800 7806 7803 7825 C1' U E 31 beta 7820 7826 7823 7845 C1' U E 32 beta 7840 7846 7843 7865 C1' U E 33 beta 7860 7866 7863 7885 C1' U E 34 beta 7880 7886 7883 7905 C1' U E 35 beta 7900 7906 7903 7925 C1' U E 36 beta 7920 7926 7923 7945 C1' U E 37 beta 7940 7946 7943 7965 C1' U E 38 beta 7960 7966 7963 7985 C1' U E 39 beta 7980 7986 7983 8005 C1' U E 40 beta 8000 8006 8003 8025 C1' U E 41 beta 8020 8026 8023 8045 C1' U E 42 beta 8040 8046 8043 8065 C1' U E 43 beta 8060 8066 8063 8085 C1' U E 44 beta 8080 8086 8083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7223 C2' U E 1 OK 7225 7221 7224 7243 C2' U E 2 OK 7245 7241 7244 7263 C2' U E 3 OK 7265 7261 7264 7283 C2' U E 4 OK 7285 7281 7284 7303 C2' U E 5 OK 7305 7301 7304 7323 C2' U E 6 OK 7325 7321 7324 7343 C2' U E 7 OK 7345 7341 7344 7363 C2' U E 8 OK 7365 7361 7364 7383 C2' U E 9 OK 7385 7381 7384 7403 C2' U E 10 OK 7405 7401 7404 7423 C2' U E 11 OK 7425 7421 7424 7443 C2' U E 12 OK 7445 7441 7444 7463 C2' U E 13 OK 7465 7461 7464 7483 C2' U E 14 OK 7485 7481 7484 7503 C2' U E 15 OK 7505 7501 7504 7523 C2' U E 16 OK 7525 7521 7524 7543 C2' U E 17 OK 7545 7541 7544 7563 C2' U E 18 OK 7565 7561 7564 7583 C2' U E 19 OK 7585 7581 7584 7603 C2' U E 20 OK 7605 7601 7604 7623 C2' U E 21 OK 7625 7621 7624 7643 C2' U E 22 OK 7645 7641 7644 7663 C2' U E 23 OK 7665 7661 7664 7683 C2' U E 24 OK 7685 7681 7684 7703 C2' U E 25 OK 7705 7701 7704 7723 C2' U E 26 OK 7725 7721 7724 7743 C2' U E 27 OK 7745 7741 7744 7763 C2' U E 28 OK 7765 7761 7764 7783 C2' U E 29 OK 7785 7781 7784 7803 C2' U E 30 OK 7805 7801 7804 7823 C2' U E 31 OK 7825 7821 7824 7843 C2' U E 32 OK 7845 7841 7844 7863 C2' U E 33 OK 7865 7861 7864 7883 C2' U E 34 OK 7885 7881 7884 7903 C2' U E 35 OK 7905 7901 7904 7923 C2' U E 36 OK 7925 7921 7924 7943 C2' U E 37 OK 7945 7941 7944 7963 C2' U E 38 OK 7965 7961 7964 7983 C2' U E 39 OK 7985 7981 7984 8003 C2' U E 40 OK 8005 8001 8004 8023 C2' U E 41 OK 8025 8021 8024 8043 C2' U E 42 OK 8045 8041 8044 8063 C2' U E 43 OK 8065 8061 8064 8083 C2' U E 44 OK 8085 8081 8084 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7221 C3' U E 1 OK 7219 7222 7223 7241 C3' U E 2 OK 7239 7242 7243 7261 C3' U E 3 OK 7259 7262 7263 7281 C3' U E 4 OK 7279 7282 7283 7301 C3' U E 5 OK 7299 7302 7303 7321 C3' U E 6 OK 7319 7322 7323 7341 C3' U E 7 OK 7339 7342 7343 7361 C3' U E 8 OK 7359 7362 7363 7381 C3' U E 9 OK 7379 7382 7383 7401 C3' U E 10 OK 7399 7402 7403 7421 C3' U E 11 OK 7419 7422 7423 7441 C3' U E 12 OK 7439 7442 7443 7461 C3' U E 13 OK 7459 7462 7463 7481 C3' U E 14 OK 7479 7482 7483 7501 C3' U E 15 OK 7499 7502 7503 7521 C3' U E 16 OK 7519 7522 7523 7541 C3' U E 17 OK 7539 7542 7543 7561 C3' U E 18 OK 7559 7562 7563 7581 C3' U E 19 OK 7579 7582 7583 7601 C3' U E 20 OK 7599 7602 7603 7621 C3' U E 21 OK 7619 7622 7623 7641 C3' U E 22 OK 7639 7642 7643 7661 C3' U E 23 OK 7659 7662 7663 7681 C3' U E 24 OK 7679 7682 7683 7701 C3' U E 25 OK 7699 7702 7703 7721 C3' U E 26 OK 7719 7722 7723 7741 C3' U E 27 OK 7739 7742 7743 7761 C3' U E 28 OK 7759 7762 7763 7781 C3' U E 29 OK 7779 7782 7783 7801 C3' U E 30 OK 7799 7802 7803 7821 C3' U E 31 OK 7819 7822 7823 7841 C3' U E 32 OK 7839 7842 7843 7861 C3' U E 33 OK 7859 7862 7863 7881 C3' U E 34 OK 7879 7882 7883 7901 C3' U E 35 OK 7899 7902 7903 7921 C3' U E 36 OK 7919 7922 7923 7941 C3' U E 37 OK 7939 7942 7943 7961 C3' U E 38 OK 7959 7962 7963 7981 C3' U E 39 OK 7979 7982 7983 8001 C3' U E 40 OK 7999 8002 8003 8021 C3' U E 41 OK 8019 8022 8023 8041 C3' U E 42 OK 8039 8042 8043 8061 C3' U E 43 OK 8059 8062 8063 8081 C3' U E 44 OK 8079 8082 8083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7219 C4' U E 1 OK 7221 7218 7220 7239 C4' U E 2 OK 7241 7238 7240 7259 C4' U E 3 OK 7261 7258 7260 7279 C4' U E 4 OK 7281 7278 7280 7299 C4' U E 5 OK 7301 7298 7300 7319 C4' U E 6 OK 7321 7318 7320 7339 C4' U E 7 OK 7341 7338 7340 7359 C4' U E 8 OK 7361 7358 7360 7379 C4' U E 9 OK 7381 7378 7380 7399 C4' U E 10 OK 7401 7398 7400 7419 C4' U E 11 OK 7421 7418 7420 7439 C4' U E 12 OK 7441 7438 7440 7459 C4' U E 13 OK 7461 7458 7460 7479 C4' U E 14 OK 7481 7478 7480 7499 C4' U E 15 OK 7501 7498 7500 7519 C4' U E 16 OK 7521 7518 7520 7539 C4' U E 17 OK 7541 7538 7540 7559 C4' U E 18 OK 7561 7558 7560 7579 C4' U E 19 OK 7581 7578 7580 7599 C4' U E 20 OK 7601 7598 7600 7619 C4' U E 21 OK 7621 7618 7620 7639 C4' U E 22 OK 7641 7638 7640 7659 C4' U E 23 OK 7661 7658 7660 7679 C4' U E 24 OK 7681 7678 7680 7699 C4' U E 25 OK 7701 7698 7700 7719 C4' U E 26 OK 7721 7718 7720 7739 C4' U E 27 OK 7741 7738 7740 7759 C4' U E 28 OK 7761 7758 7760 7779 C4' U E 29 OK 7781 7778 7780 7799 C4' U E 30 OK 7801 7798 7800 7819 C4' U E 31 OK 7821 7818 7820 7839 C4' U E 32 OK 7841 7838 7840 7859 C4' U E 33 OK 7861 7858 7860 7879 C4' U E 34 OK 7881 7878 7880 7899 C4' U E 35 OK 7901 7898 7900 7919 C4' U E 36 OK 7921 7918 7920 7939 C4' U E 37 OK 7941 7938 7940 7959 C4' U E 38 OK 7961 7958 7960 7979 C4' U E 39 OK 7981 7978 7980 7999 C4' U E 40 OK 8001 7998 8000 8019 C4' U E 41 OK 8021 8018 8020 8039 C4' U E 42 OK 8041 8038 8040 8059 C4' U E 43 OK 8061 8058 8060 8079 C4' U E 44 OK 8081 8078 8080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7218 C5' U E 1 7217 7219 7238 C5' U E 2 7237 7239 7258 C5' U E 3 7257 7259 7278 C5' U E 4 7277 7279 7298 C5' U E 5 7297 7299 7318 C5' U E 6 7317 7319 7338 C5' U E 7 7337 7339 7358 C5' U E 8 7357 7359 7378 C5' U E 9 7377 7379 7398 C5' U E 10 7397 7399 7418 C5' U E 11 7417 7419 7438 C5' U E 12 7437 7439 7458 C5' U E 13 7457 7459 7478 C5' U E 14 7477 7479 7498 C5' U E 15 7497 7499 7518 C5' U E 16 7517 7519 7538 C5' U E 17 7537 7539 7558 C5' U E 18 7557 7559 7578 C5' U E 19 7577 7579 7598 C5' U E 20 7597 7599 7618 C5' U E 21 7617 7619 7638 C5' U E 22 7637 7639 7658 C5' U E 23 7657 7659 7678 C5' U E 24 7677 7679 7698 C5' U E 25 7697 7699 7718 C5' U E 26 7717 7719 7738 C5' U E 27 7737 7739 7758 C5' U E 28 7757 7759 7778 C5' U E 29 7777 7779 7798 C5' U E 30 7797 7799 7818 C5' U E 31 7817 7819 7838 C5' U E 32 7837 7839 7858 C5' U E 33 7857 7859 7878 C5' U E 34 7877 7879 7898 C5' U E 35 7897 7899 7918 C5' U E 36 7917 7919 7938 C5' U E 37 7937 7939 7958 C5' U E 38 7957 7959 7978 C5' U E 39 7977 7979 7998 C5' U E 40 7997 7999 8018 C5' U E 41 8017 8019 8038 C5' U E 42 8037 8039 8058 C5' U E 43 8057 8059 8078 C5' U E 44 8077 8079 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7234 P U E 2 distorted distorted 7222 7235 7236 7237 7254 P U E 3 distorted distorted 7242 7255 7256 7257 7274 P U E 4 distorted distorted 7262 7275 7276 7277 7294 P U E 5 distorted distorted 7282 7295 7296 7297 7314 P U E 6 distorted distorted 7302 7315 7316 7317 7334 P U E 7 distorted distorted 7322 7335 7336 7337 7354 P U E 8 distorted distorted 7342 7355 7356 7357 7374 P U E 9 distorted distorted 7362 7375 7376 7377 7394 P U E 10 distorted distorted 7382 7395 7396 7397 7414 P U E 11 distorted distorted 7402 7415 7416 7417 7434 P U E 12 distorted distorted 7422 7435 7436 7437 7454 P U E 13 distorted distorted 7442 7455 7456 7457 7474 P U E 14 distorted distorted 7462 7475 7476 7477 7494 P U E 15 distorted distorted 7482 7495 7496 7497 7514 P U E 16 distorted distorted 7502 7515 7516 7517 7534 P U E 17 distorted distorted 7522 7535 7536 7537 7554 P U E 18 distorted distorted 7542 7555 7556 7557 7574 P U E 19 distorted distorted 7562 7575 7576 7577 7594 P U E 20 distorted distorted 7582 7595 7596 7597 7614 P U E 21 distorted distorted 7602 7615 7616 7617 7634 P U E 22 distorted distorted 7622 7635 7636 7637 7654 P U E 23 distorted distorted 7642 7655 7656 7657 7674 P U E 24 distorted distorted 7662 7675 7676 7677 7694 P U E 25 distorted distorted 7682 7695 7696 7697 7714 P U E 26 distorted distorted 7702 7715 7716 7717 7734 P U E 27 distorted distorted 7722 7735 7736 7737 7754 P U E 28 distorted distorted 7742 7755 7756 7757 7774 P U E 29 distorted distorted 7762 7775 7776 7777 7794 P U E 30 distorted distorted 7782 7795 7796 7797 7814 P U E 31 distorted distorted 7802 7815 7816 7817 7834 P U E 32 distorted distorted 7822 7835 7836 7837 7854 P U E 33 distorted distorted 7842 7855 7856 7857 7874 P U E 34 distorted distorted 7862 7875 7876 7877 7894 P U E 35 distorted distorted 7882 7895 7896 7897 7914 P U E 36 distorted distorted 7902 7915 7916 7917 7934 P U E 37 distorted distorted 7922 7935 7936 7937 7954 P U E 38 distorted distorted 7942 7955 7956 7957 7974 P U E 39 distorted distorted 7962 7975 7976 7977 7994 P U E 40 distorted distorted 7982 7995 7996 7997 8014 P U E 41 distorted distorted 8002 8015 8016 8017 8034 P U E 42 distorted distorted 8022 8035 8036 8037 8054 P U E 43 distorted distorted 8042 8055 8056 8057 8074 P U E 44 distorted distorted 8062 8075 8076 8077 8094 P U E 45 distorted distorted 8082 8095 8096 8097 ---------------------------------------------------------------------------------