ID code: '2BH2' 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' --------------------------------------------------------------------------------- 6485 C1' A C1932 beta 6480 6486 6483 6507 C1' G C1933 beta 6502 6508 6505 6530 C1' C C1934 beta 6525 6531 6528 6550 C1' G C1935 beta 6545 6551 6548 6573 C1' A C1936 beta 6568 6574 6571 6595 C1' A C1937 beta 6590 6596 6593 6617 C1' A C1938 beta 6612 6618 6615 6635 C1' FMU C1939 beta 6643 6628 6638 6661 C1' U C1940 beta 6656 6662 6659 6681 C1' C C1941 beta 6676 6682 6679 6701 C1' C C1942 beta 6696 6702 6699 6721 C1' U C1943 beta 6716 6722 6719 6741 C1' U C1944 beta 6736 6742 6739 6761 C1' G C1945 beta 6756 6762 6759 6784 C1' U C1946 beta 6779 6785 6782 6804 C1' C C1947 beta 6799 6805 6802 6824 C1' G C1948 beta 6819 6825 6822 6847 C1' G C1949 beta 6842 6848 6845 6870 C1' G C1950 beta 6865 6871 6868 6893 C1' U C1951 beta 6888 6894 6891 6913 C1' A C1952 beta 6908 6914 6911 6935 C1' A C1953 beta 6930 6936 6933 6957 C1' G C1954 beta 6952 6958 6955 6980 C1' U C1955 beta 6975 6981 6978 7000 C1' U C1956 beta 6995 7001 6998 7020 C1' C C1957 beta 7015 7021 7018 7040 C1' C C1958 beta 7035 7041 7038 7060 C1' G C1959 beta 7055 7061 7058 7083 C1' A C1960 beta 7078 7084 7081 7105 C1' C C1961 beta 7100 7106 7103 7123 C1' A D1932 beta 7118 7124 7121 7145 C1' G D1933 beta 7140 7146 7143 7168 C1' C D1934 beta 7163 7169 7166 7188 C1' G D1935 beta 7183 7189 7186 7211 C1' A D1936 beta 7206 7212 7209 7233 C1' A D1937 beta 7228 7234 7231 7255 C1' A D1938 beta 7250 7256 7253 7273 C1' FMU D1939 beta 7281 7266 7276 7299 C1' U D1940 beta 7294 7300 7297 7319 C1' C D1941 beta 7314 7320 7317 7339 C1' C D1942 beta 7334 7340 7337 7359 C1' U D1943 beta 7354 7360 7357 7379 C1' U D1944 beta 7374 7380 7377 7399 C1' G D1945 beta 7394 7400 7397 7422 C1' U D1946 beta 7417 7423 7420 7442 C1' C D1947 beta 7437 7443 7440 7462 C1' G D1948 beta 7457 7463 7460 7485 C1' G D1949 beta 7480 7486 7483 7508 C1' G D1950 beta 7503 7509 7506 7531 C1' U D1951 beta 7526 7532 7529 7551 C1' A D1952 beta 7546 7552 7549 7573 C1' A D1953 beta 7568 7574 7571 7595 C1' G D1954 beta 7590 7596 7593 7618 C1' U D1955 beta 7613 7619 7616 7638 C1' U D1956 beta 7633 7639 7636 7658 C1' C D1957 beta 7653 7659 7656 7678 C1' C D1958 beta 7673 7679 7676 7698 C1' G D1959 beta 7693 7699 7696 7721 C1' A D1960 beta 7716 7722 7719 7743 C1' C D1961 beta 7738 7744 7741 7768 C1' SAH A 500 beta 7763 7769 7766 7802 C1' SAH B 500 beta 7797 7803 7800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6483 C2' A C1932 OK 6485 6481 6484 6505 C2' G C1933 OK 6507 6503 6506 6528 C2' C C1934 OK 6530 6526 6529 6548 C2' G C1935 OK 6550 6546 6549 6571 C2' A C1936 OK 6573 6569 6572 6593 C2' A C1937 OK 6595 6591 6594 6615 C2' A C1938 OK 6617 6613 6616 6638 C2' FMU C1939 OK 6635 6640 6639 6659 C2' U C1940 OK 6661 6657 6660 6679 C2' C C1941 OK 6681 6677 6680 6699 C2' C C1942 OK 6701 6697 6700 6719 C2' U C1943 OK 6721 6717 6720 6739 C2' U C1944 OK 6741 6737 6740 6759 C2' G C1945 OK 6761 6757 6760 6782 C2' U C1946 OK 6784 6780 6783 6802 C2' C C1947 OK 6804 6800 6803 6822 C2' G C1948 OK 6824 6820 6823 6845 C2' G C1949 OK 6847 6843 6846 6868 C2' G C1950 OK 6870 6866 6869 6891 C2' U C1951 OK 6893 6889 6892 6911 C2' A C1952 OK 6913 6909 6912 6933 C2' A C1953 OK 6935 6931 6934 6955 C2' G C1954 OK 6957 6953 6956 6978 C2' U C1955 OK 6980 6976 6979 6998 C2' U C1956 OK 7000 6996 6999 7018 C2' C C1957 OK 7020 7016 7019 7038 C2' C C1958 OK 7040 7036 7039 7058 C2' G C1959 OK 7060 7056 7059 7081 C2' A C1960 OK 7083 7079 7082 7103 C2' C C1961 OK 7105 7101 7104 7121 C2' A D1932 OK 7123 7119 7122 7143 C2' G D1933 OK 7145 7141 7144 7166 C2' C D1934 OK 7168 7164 7167 7186 C2' G D1935 OK 7188 7184 7187 7209 C2' A D1936 OK 7211 7207 7210 7231 C2' A D1937 OK 7233 7229 7232 7253 C2' A D1938 OK 7255 7251 7254 7276 C2' FMU D1939 OK 7273 7278 7277 7297 C2' U D1940 OK 7299 7295 7298 7317 C2' C D1941 OK 7319 7315 7318 7337 C2' C D1942 OK 7339 7335 7338 7357 C2' U D1943 OK 7359 7355 7358 7377 C2' U D1944 OK 7379 7375 7378 7397 C2' G D1945 OK 7399 7395 7398 7420 C2' U D1946 OK 7422 7418 7421 7440 C2' C D1947 OK 7442 7438 7441 7460 C2' G D1948 OK 7462 7458 7461 7483 C2' G D1949 OK 7485 7481 7484 7506 C2' G D1950 OK 7508 7504 7507 7529 C2' U D1951 OK 7531 7527 7530 7549 C2' A D1952 OK 7551 7547 7550 7571 C2' A D1953 OK 7573 7569 7572 7593 C2' G D1954 OK 7595 7591 7594 7616 C2' U D1955 OK 7618 7614 7617 7636 C2' U D1956 OK 7638 7634 7637 7656 C2' C D1957 OK 7658 7654 7657 7676 C2' C D1958 OK 7678 7674 7677 7696 C2' G D1959 OK 7698 7694 7697 7719 C2' A D1960 OK 7721 7717 7720 7741 C2' C D1961 OK 7743 7739 7742 7766 C2' SAH A 500 OK 7768 7764 7767 7800 C2' SAH B 500 OK 7802 7798 7801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6481 C3' A C1932 OK 6479 6482 6483 6503 C3' G C1933 OK 6501 6504 6505 6526 C3' C C1934 OK 6524 6527 6528 6546 C3' G C1935 OK 6544 6547 6548 6569 C3' A C1936 OK 6567 6570 6571 6591 C3' A C1937 OK 6589 6592 6593 6613 C3' A C1938 OK 6611 6614 6615 6640 C3' FMU C1939 OK 6641 6642 6638 6657 C3' U C1940 OK 6655 6658 6659 6677 C3' C C1941 OK 6675 6678 6679 6697 C3' C C1942 OK 6695 6698 6699 6717 C3' U C1943 OK 6715 6718 6719 6737 C3' U C1944 OK 6735 6738 6739 6757 C3' G C1945 OK 6755 6758 6759 6780 C3' U C1946 OK 6778 6781 6782 6800 C3' C C1947 OK 6798 6801 6802 6820 C3' G C1948 OK 6818 6821 6822 6843 C3' G C1949 OK 6841 6844 6845 6866 C3' G C1950 OK 6864 6867 6868 6889 C3' U C1951 OK 6887 6890 6891 6909 C3' A C1952 OK 6907 6910 6911 6931 C3' A C1953 OK 6929 6932 6933 6953 C3' G C1954 OK 6951 6954 6955 6976 C3' U C1955 OK 6974 6977 6978 6996 C3' U C1956 OK 6994 6997 6998 7016 C3' C C1957 OK 7014 7017 7018 7036 C3' C C1958 OK 7034 7037 7038 7056 C3' G C1959 OK 7054 7057 7058 7079 C3' A C1960 OK 7077 7080 7081 7101 C3' C C1961 OK 7099 7102 7103 7119 C3' A D1932 OK 7117 7120 7121 7141 C3' G D1933 OK 7139 7142 7143 7164 C3' C D1934 OK 7162 7165 7166 7184 C3' G D1935 OK 7182 7185 7186 7207 C3' A D1936 OK 7205 7208 7209 7229 C3' A D1937 OK 7227 7230 7231 7251 C3' A D1938 OK 7249 7252 7253 7278 C3' FMU D1939 OK 7279 7280 7276 7295 C3' U D1940 OK 7293 7296 7297 7315 C3' C D1941 OK 7313 7316 7317 7335 C3' C D1942 OK 7333 7336 7337 7355 C3' U D1943 OK 7353 7356 7357 7375 C3' U D1944 OK 7373 7376 7377 7395 C3' G D1945 OK 7393 7396 7397 7418 C3' U D1946 OK 7416 7419 7420 7438 C3' C D1947 OK 7436 7439 7440 7458 C3' G D1948 OK 7456 7459 7460 7481 C3' G D1949 OK 7479 7482 7483 7504 C3' G D1950 OK 7502 7505 7506 7527 C3' U D1951 OK 7525 7528 7529 7547 C3' A D1952 OK 7545 7548 7549 7569 C3' A D1953 OK 7567 7570 7571 7591 C3' G D1954 OK 7589 7592 7593 7614 C3' U D1955 OK 7612 7615 7616 7634 C3' U D1956 OK 7632 7635 7636 7654 C3' C D1957 OK 7652 7655 7656 7674 C3' C D1958 OK 7672 7675 7676 7694 C3' G D1959 OK 7692 7695 7696 7717 C3' A D1960 OK 7715 7718 7719 7739 C3' C D1961 OK 7737 7740 7741 7764 C3' SAH A 500 OK 7762 7765 7766 7798 C3' SAH B 500 OK 7796 7799 7800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6479 C4' A C1932 OK 6481 6478 6480 6501 C4' G C1933 OK 6503 6500 6502 6524 C4' C C1934 OK 6526 6523 6525 6544 C4' G C1935 OK 6546 6543 6545 6567 C4' A C1936 OK 6569 6566 6568 6589 C4' A C1937 OK 6591 6588 6590 6611 C4' A C1938 OK 6613 6610 6612 6641 C4' FMU C1939 OK 6640 6644 6643 6655 C4' U C1940 OK 6657 6654 6656 6675 C4' C C1941 OK 6677 6674 6676 6695 C4' C C1942 OK 6697 6694 6696 6715 C4' U C1943 OK 6717 6714 6716 6735 C4' U C1944 OK 6737 6734 6736 6755 C4' G C1945 OK 6757 6754 6756 6778 C4' U C1946 OK 6780 6777 6779 6798 C4' C C1947 OK 6800 6797 6799 6818 C4' G C1948 OK 6820 6817 6819 6841 C4' G C1949 OK 6843 6840 6842 6864 C4' G C1950 OK 6866 6863 6865 6887 C4' U C1951 OK 6889 6886 6888 6907 C4' A C1952 OK 6909 6906 6908 6929 C4' A C1953 OK 6931 6928 6930 6951 C4' G C1954 OK 6953 6950 6952 6974 C4' U C1955 OK 6976 6973 6975 6994 C4' U C1956 OK 6996 6993 6995 7014 C4' C C1957 OK 7016 7013 7015 7034 C4' C C1958 OK 7036 7033 7035 7054 C4' G C1959 OK 7056 7053 7055 7077 C4' A C1960 OK 7079 7076 7078 7099 C4' C C1961 OK 7101 7098 7100 7117 C4' A D1932 OK 7119 7116 7118 7139 C4' G D1933 OK 7141 7138 7140 7162 C4' C D1934 OK 7164 7161 7163 7182 C4' G D1935 OK 7184 7181 7183 7205 C4' A D1936 OK 7207 7204 7206 7227 C4' A D1937 OK 7229 7226 7228 7249 C4' A D1938 OK 7251 7248 7250 7279 C4' FMU D1939 OK 7278 7282 7281 7293 C4' U D1940 OK 7295 7292 7294 7313 C4' C D1941 OK 7315 7312 7314 7333 C4' C D1942 OK 7335 7332 7334 7353 C4' U D1943 OK 7355 7352 7354 7373 C4' U D1944 OK 7375 7372 7374 7393 C4' G D1945 OK 7395 7392 7394 7416 C4' U D1946 OK 7418 7415 7417 7436 C4' C D1947 OK 7438 7435 7437 7456 C4' G D1948 OK 7458 7455 7457 7479 C4' G D1949 OK 7481 7478 7480 7502 C4' G D1950 OK 7504 7501 7503 7525 C4' U D1951 OK 7527 7524 7526 7545 C4' A D1952 OK 7547 7544 7546 7567 C4' A D1953 OK 7569 7566 7568 7589 C4' G D1954 OK 7591 7588 7590 7612 C4' U D1955 OK 7614 7611 7613 7632 C4' U D1956 OK 7634 7631 7633 7652 C4' C D1957 OK 7654 7651 7653 7672 C4' C D1958 OK 7674 7671 7673 7692 C4' G D1959 OK 7694 7691 7693 7715 C4' A D1960 OK 7717 7714 7716 7737 C4' C D1961 OK 7739 7736 7738 7762 C4' SAH A 500 OK 7764 7761 7763 7796 C4' SAH B 500 OK 7798 7795 7797 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6478 C5' A C1932 6477 6479 6500 C5' G C1933 6499 6501 6523 C5' C C1934 6522 6524 6543 C5' G C1935 6542 6544 6566 C5' A C1936 6565 6567 6588 C5' A C1937 6587 6589 6610 C5' A C1938 6609 6611 6644 C5' FMU C1939 6645 6641 6654 C5' U C1940 6653 6655 6674 C5' C C1941 6673 6675 6694 C5' C C1942 6693 6695 6714 C5' U C1943 6713 6715 6734 C5' U C1944 6733 6735 6754 C5' G C1945 6753 6755 6777 C5' U C1946 6776 6778 6797 C5' C C1947 6796 6798 6817 C5' G C1948 6816 6818 6840 C5' G C1949 6839 6841 6863 C5' G C1950 6862 6864 6886 C5' U C1951 6885 6887 6906 C5' A C1952 6905 6907 6928 C5' A C1953 6927 6929 6950 C5' G C1954 6949 6951 6973 C5' U C1955 6972 6974 6993 C5' U C1956 6992 6994 7013 C5' C C1957 7012 7014 7033 C5' C C1958 7032 7034 7053 C5' G C1959 7052 7054 7076 C5' A C1960 7075 7077 7098 C5' C C1961 7097 7099 7116 C5' A D1932 7115 7117 7138 C5' G D1933 7137 7139 7161 C5' C D1934 7160 7162 7181 C5' G D1935 7180 7182 7204 C5' A D1936 7203 7205 7226 C5' A D1937 7225 7227 7248 C5' A D1938 7247 7249 7282 C5' FMU D1939 7283 7279 7292 C5' U D1940 7291 7293 7312 C5' C D1941 7311 7313 7332 C5' C D1942 7331 7333 7352 C5' U D1943 7351 7353 7372 C5' U D1944 7371 7373 7392 C5' G D1945 7391 7393 7415 C5' U D1946 7414 7416 7435 C5' C D1947 7434 7436 7455 C5' G D1948 7454 7456 7478 C5' G D1949 7477 7479 7501 C5' G D1950 7500 7502 7524 C5' U D1951 7523 7525 7544 C5' A D1952 7543 7545 7566 C5' A D1953 7565 7567 7588 C5' G D1954 7587 7589 7611 C5' U D1955 7610 7612 7631 C5' U D1956 7630 7632 7651 C5' C D1957 7650 7652 7671 C5' C D1958 7670 7672 7691 C5' G D1959 7690 7692 7714 C5' A D1960 7713 7715 7736 C5' C D1961 7735 7737 7761 C5' SAH A 500 7762 7795 C5' SAH B 500 7796 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6496 P G C1933 distorted distorted 6482 6497 6498 6499 6519 P C C1934 distorted distorted 6504 6520 6521 6522 6539 P G C1935 distorted distorted 6527 6540 6541 6542 6562 P A C1936 distorted distorted 6547 6563 6564 6565 6584 P A C1937 distorted distorted 6570 6585 6586 6587 6606 P A C1938 distorted distorted 6592 6607 6608 6609 6646 P FMU C1939 distorted distorted 6614 6648 6647 6645 6650 P U C1940 distorted distorted 6642 6651 6652 6653 6670 P C C1941 distorted distorted 6658 6671 6672 6673 6690 P C C1942 distorted distorted 6678 6691 6692 6693 6710 P U C1943 distorted distorted 6698 6711 6712 6713 6730 P U C1944 distorted distorted 6718 6731 6732 6733 6750 P G C1945 distorted distorted 6738 6751 6752 6753 6773 P U C1946 distorted distorted 6758 6774 6775 6776 6793 P C C1947 distorted distorted 6781 6794 6795 6796 6813 P G C1948 distorted distorted 6801 6814 6815 6816 6836 P G C1949 distorted distorted 6821 6837 6838 6839 6859 P G C1950 distorted distorted 6844 6860 6861 6862 6882 P U C1951 distorted distorted 6867 6883 6884 6885 6902 P A C1952 distorted distorted 6890 6903 6904 6905 6924 P A C1953 distorted distorted 6910 6925 6926 6927 6946 P G C1954 distorted distorted 6932 6947 6948 6949 6969 P U C1955 distorted distorted 6954 6970 6971 6972 6989 P U C1956 distorted distorted 6977 6990 6991 6992 7009 P C C1957 distorted distorted 6997 7010 7011 7012 7029 P C C1958 distorted distorted 7017 7030 7031 7032 7049 P G C1959 distorted distorted 7037 7050 7051 7052 7072 P A C1960 distorted distorted 7057 7073 7074 7075 7094 P C C1961 distorted distorted 7080 7095 7096 7097 7134 P G D1933 distorted distorted 7120 7135 7136 7137 7157 P C D1934 distorted distorted 7142 7158 7159 7160 7177 P G D1935 distorted distorted 7165 7178 7179 7180 7200 P A D1936 distorted distorted 7185 7201 7202 7203 7222 P A D1937 distorted distorted 7208 7223 7224 7225 7244 P A D1938 distorted distorted 7230 7245 7246 7247 7284 P FMU D1939 distorted distorted 7252 7286 7285 7283 7288 P U D1940 distorted distorted 7280 7289 7290 7291 7308 P C D1941 distorted distorted 7296 7309 7310 7311 7328 P C D1942 distorted distorted 7316 7329 7330 7331 7348 P U D1943 distorted distorted 7336 7349 7350 7351 7368 P U D1944 distorted distorted 7356 7369 7370 7371 7388 P G D1945 distorted distorted 7376 7389 7390 7391 7411 P U D1946 distorted distorted 7396 7412 7413 7414 7431 P C D1947 distorted distorted 7419 7432 7433 7434 7451 P G D1948 distorted distorted 7439 7452 7453 7454 7474 P G D1949 distorted distorted 7459 7475 7476 7477 7497 P G D1950 distorted distorted 7482 7498 7499 7500 7520 P U D1951 distorted distorted 7505 7521 7522 7523 7540 P A D1952 distorted distorted 7528 7541 7542 7543 7562 P A D1953 distorted distorted 7548 7563 7564 7565 7584 P G D1954 distorted distorted 7570 7585 7586 7587 7607 P U D1955 distorted distorted 7592 7608 7609 7610 7627 P U D1956 distorted distorted 7615 7628 7629 7630 7647 P C D1957 distorted distorted 7635 7648 7649 7650 7667 P C D1958 distorted distorted 7655 7668 7669 7670 7687 P G D1959 distorted distorted 7675 7688 7689 7690 7710 P A D1960 distorted distorted 7695 7711 7712 7713 7732 P C D1961 distorted distorted 7718 7733 7734 7735 ---------------------------------------------------------------------------------