ID code: '4IJS' 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' --------------------------------------------------------------------------------- 7476 C1' A E1001 beta 7471 7477 7474 7498 C1' A E1002 beta 7493 7499 7496 7520 C1' A E1003 beta 7515 7521 7518 7542 C1' A E1004 beta 7537 7543 7540 7564 C1' A E1005 beta 7559 7565 7562 7586 C1' A E1006 beta 7581 7587 7584 7608 C1' A E1007 beta 7603 7609 7606 7630 C1' A E1008 beta 7625 7631 7628 7652 C1' A E1009 beta 7647 7653 7650 7674 C1' A E1010 beta 7669 7675 7672 7697 C1' A F1002 beta 7692 7698 7695 7719 C1' A F1003 beta 7714 7720 7717 7741 C1' A F1004 beta 7736 7742 7739 7763 C1' A F1005 beta 7758 7764 7761 7785 C1' A F1006 beta 7780 7786 7783 7807 C1' A F1007 beta 7802 7808 7805 7829 C1' A F1008 beta 7824 7830 7827 7851 C1' A F1009 beta 7846 7852 7849 7873 C1' A F1010 beta 7868 7874 7871 7896 C1' A G1001 beta 7891 7897 7894 7918 C1' A G1002 beta 7913 7919 7916 7940 C1' A G1003 beta 7935 7941 7938 7962 C1' A G1004 beta 7957 7963 7960 7984 C1' A G1005 beta 7979 7985 7982 8006 C1' A G1006 beta 8001 8007 8004 8028 C1' A G1007 beta 8023 8029 8026 8050 C1' A G1008 beta 8045 8051 8048 8072 C1' A G1009 beta 8067 8073 8070 8095 C1' A H1001 beta 8090 8096 8093 8117 C1' A H1002 beta 8112 8118 8115 8139 C1' A H1003 beta 8134 8140 8137 8161 C1' A H1004 beta 8156 8162 8159 8183 C1' A H1005 beta 8178 8184 8181 8205 C1' A H1006 beta 8200 8206 8203 8227 C1' A H1007 beta 8222 8228 8225 8249 C1' A H1008 beta 8244 8250 8247 8271 C1' A H1009 beta 8266 8272 8269 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7474 C2' A E1001 OK 7476 7472 7475 7496 C2' A E1002 OK 7498 7494 7497 7518 C2' A E1003 OK 7520 7516 7519 7540 C2' A E1004 OK 7542 7538 7541 7562 C2' A E1005 OK 7564 7560 7563 7584 C2' A E1006 OK 7586 7582 7585 7606 C2' A E1007 OK 7608 7604 7607 7628 C2' A E1008 OK 7630 7626 7629 7650 C2' A E1009 OK 7652 7648 7651 7672 C2' A E1010 OK 7674 7670 7673 7695 C2' A F1002 OK 7697 7693 7696 7717 C2' A F1003 OK 7719 7715 7718 7739 C2' A F1004 OK 7741 7737 7740 7761 C2' A F1005 OK 7763 7759 7762 7783 C2' A F1006 OK 7785 7781 7784 7805 C2' A F1007 OK 7807 7803 7806 7827 C2' A F1008 OK 7829 7825 7828 7849 C2' A F1009 OK 7851 7847 7850 7871 C2' A F1010 OK 7873 7869 7872 7894 C2' A G1001 OK 7896 7892 7895 7916 C2' A G1002 OK 7918 7914 7917 7938 C2' A G1003 OK 7940 7936 7939 7960 C2' A G1004 OK 7962 7958 7961 7982 C2' A G1005 OK 7984 7980 7983 8004 C2' A G1006 OK 8006 8002 8005 8026 C2' A G1007 OK 8028 8024 8027 8048 C2' A G1008 OK 8050 8046 8049 8070 C2' A G1009 OK 8072 8068 8071 8093 C2' A H1001 OK 8095 8091 8094 8115 C2' A H1002 OK 8117 8113 8116 8137 C2' A H1003 OK 8139 8135 8138 8159 C2' A H1004 OK 8161 8157 8160 8181 C2' A H1005 OK 8183 8179 8182 8203 C2' A H1006 OK 8205 8201 8204 8225 C2' A H1007 OK 8227 8223 8226 8247 C2' A H1008 OK 8249 8245 8248 8269 C2' A H1009 OK 8271 8267 8270 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7472 C3' A E1001 OK 7470 7473 7474 7494 C3' A E1002 OK 7492 7495 7496 7516 C3' A E1003 OK 7514 7517 7518 7538 C3' A E1004 OK 7536 7539 7540 7560 C3' A E1005 OK 7558 7561 7562 7582 C3' A E1006 OK 7580 7583 7584 7604 C3' A E1007 OK 7602 7605 7606 7626 C3' A E1008 OK 7624 7627 7628 7648 C3' A E1009 OK 7646 7649 7650 7670 C3' A E1010 OK 7668 7671 7672 7693 C3' A F1002 OK 7691 7694 7695 7715 C3' A F1003 OK 7713 7716 7717 7737 C3' A F1004 OK 7735 7738 7739 7759 C3' A F1005 OK 7757 7760 7761 7781 C3' A F1006 OK 7779 7782 7783 7803 C3' A F1007 OK 7801 7804 7805 7825 C3' A F1008 OK 7823 7826 7827 7847 C3' A F1009 OK 7845 7848 7849 7869 C3' A F1010 OK 7867 7870 7871 7892 C3' A G1001 OK 7890 7893 7894 7914 C3' A G1002 OK 7912 7915 7916 7936 C3' A G1003 OK 7934 7937 7938 7958 C3' A G1004 OK 7956 7959 7960 7980 C3' A G1005 OK 7978 7981 7982 8002 C3' A G1006 OK 8000 8003 8004 8024 C3' A G1007 OK 8022 8025 8026 8046 C3' A G1008 OK 8044 8047 8048 8068 C3' A G1009 OK 8066 8069 8070 8091 C3' A H1001 OK 8089 8092 8093 8113 C3' A H1002 OK 8111 8114 8115 8135 C3' A H1003 OK 8133 8136 8137 8157 C3' A H1004 OK 8155 8158 8159 8179 C3' A H1005 OK 8177 8180 8181 8201 C3' A H1006 OK 8199 8202 8203 8223 C3' A H1007 OK 8221 8224 8225 8245 C3' A H1008 OK 8243 8246 8247 8267 C3' A H1009 OK 8265 8268 8269 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7470 C4' A E1001 OK 7472 7469 7471 7492 C4' A E1002 OK 7494 7491 7493 7514 C4' A E1003 OK 7516 7513 7515 7536 C4' A E1004 OK 7538 7535 7537 7558 C4' A E1005 OK 7560 7557 7559 7580 C4' A E1006 OK 7582 7579 7581 7602 C4' A E1007 OK 7604 7601 7603 7624 C4' A E1008 OK 7626 7623 7625 7646 C4' A E1009 OK 7648 7645 7647 7668 C4' A E1010 OK 7670 7667 7669 7691 C4' A F1002 OK 7693 7690 7692 7713 C4' A F1003 OK 7715 7712 7714 7735 C4' A F1004 OK 7737 7734 7736 7757 C4' A F1005 OK 7759 7756 7758 7779 C4' A F1006 OK 7781 7778 7780 7801 C4' A F1007 OK 7803 7800 7802 7823 C4' A F1008 OK 7825 7822 7824 7845 C4' A F1009 OK 7847 7844 7846 7867 C4' A F1010 OK 7869 7866 7868 7890 C4' A G1001 OK 7892 7889 7891 7912 C4' A G1002 OK 7914 7911 7913 7934 C4' A G1003 OK 7936 7933 7935 7956 C4' A G1004 OK 7958 7955 7957 7978 C4' A G1005 OK 7980 7977 7979 8000 C4' A G1006 OK 8002 7999 8001 8022 C4' A G1007 OK 8024 8021 8023 8044 C4' A G1008 OK 8046 8043 8045 8066 C4' A G1009 OK 8068 8065 8067 8089 C4' A H1001 OK 8091 8088 8090 8111 C4' A H1002 OK 8113 8110 8112 8133 C4' A H1003 OK 8135 8132 8134 8155 C4' A H1004 OK 8157 8154 8156 8177 C4' A H1005 OK 8179 8176 8178 8199 C4' A H1006 OK 8201 8198 8200 8221 C4' A H1007 OK 8223 8220 8222 8243 C4' A H1008 OK 8245 8242 8244 8265 C4' A H1009 OK 8267 8264 8266 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7469 C5' A E1001 7468 7470 7491 C5' A E1002 7490 7492 7513 C5' A E1003 7512 7514 7535 C5' A E1004 7534 7536 7557 C5' A E1005 7556 7558 7579 C5' A E1006 7578 7580 7601 C5' A E1007 7600 7602 7623 C5' A E1008 7622 7624 7645 C5' A E1009 7644 7646 7667 C5' A E1010 7666 7668 7690 C5' A F1002 7689 7691 7712 C5' A F1003 7711 7713 7734 C5' A F1004 7733 7735 7756 C5' A F1005 7755 7757 7778 C5' A F1006 7777 7779 7800 C5' A F1007 7799 7801 7822 C5' A F1008 7821 7823 7844 C5' A F1009 7843 7845 7866 C5' A F1010 7865 7867 7889 C5' A G1001 7888 7890 7911 C5' A G1002 7910 7912 7933 C5' A G1003 7932 7934 7955 C5' A G1004 7954 7956 7977 C5' A G1005 7976 7978 7999 C5' A G1006 7998 8000 8021 C5' A G1007 8020 8022 8043 C5' A G1008 8042 8044 8065 C5' A G1009 8064 8066 8088 C5' A H1001 8087 8089 8110 C5' A H1002 8109 8111 8132 C5' A H1003 8131 8133 8154 C5' A H1004 8153 8155 8176 C5' A H1005 8175 8177 8198 C5' A H1006 8197 8199 8220 C5' A H1007 8219 8221 8242 C5' A H1008 8241 8243 8264 C5' A H1009 8263 8265 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7465 P A E1001 distorted distorted 7466 7467 7468 7487 P A E1002 distorted distorted 7473 7488 7489 7490 7509 P A E1003 distorted distorted 7495 7510 7511 7512 7531 P A E1004 distorted distorted 7517 7532 7533 7534 7553 P A E1005 distorted distorted 7539 7554 7555 7556 7575 P A E1006 distorted distorted 7561 7576 7577 7578 7597 P A E1007 distorted distorted 7583 7598 7599 7600 7619 P A E1008 distorted distorted 7605 7620 7621 7622 7641 P A E1009 distorted distorted 7627 7642 7643 7644 7663 P A E1010 distorted distorted 7649 7664 7665 7666 7686 P A F1002 distorted distorted 7687 7688 7689 7708 P A F1003 distorted distorted 7694 7709 7710 7711 7730 P A F1004 distorted distorted 7716 7731 7732 7733 7752 P A F1005 distorted distorted 7738 7753 7754 7755 7774 P A F1006 distorted distorted 7760 7775 7776 7777 7796 P A F1007 distorted distorted 7782 7797 7798 7799 7818 P A F1008 distorted distorted 7804 7819 7820 7821 7840 P A F1009 distorted distorted 7826 7841 7842 7843 7862 P A F1010 distorted distorted 7848 7863 7864 7865 7885 P A G1001 distorted distorted 7886 7887 7888 7907 P A G1002 distorted distorted 7893 7908 7909 7910 7929 P A G1003 distorted distorted 7915 7930 7931 7932 7951 P A G1004 distorted distorted 7937 7952 7953 7954 7973 P A G1005 distorted distorted 7959 7974 7975 7976 7995 P A G1006 distorted distorted 7981 7996 7997 7998 8017 P A G1007 distorted distorted 8003 8018 8019 8020 8039 P A G1008 distorted distorted 8025 8040 8041 8042 8061 P A G1009 distorted distorted 8047 8062 8063 8064 8084 P A H1001 OK OK 8085 8086 8087 8106 P A H1002 distorted distorted 8092 8107 8108 8109 8128 P A H1003 distorted distorted 8114 8129 8130 8131 8150 P A H1004 distorted distorted 8136 8151 8152 8153 8172 P A H1005 distorted distorted 8158 8173 8174 8175 8194 P A H1006 distorted distorted 8180 8195 8196 8197 8216 P A H1007 distorted distorted 8202 8217 8218 8219 8238 P A H1008 distorted distorted 8224 8239 8240 8241 8260 P A H1009 distorted distorted 8246 8261 8262 8263 ---------------------------------------------------------------------------------