ID code: '4CCH' 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' --------------------------------------------------------------------------------- 8467 C1' DG B 101 alpha beta 8463 8485 8468 8466 8501 C1' DA B 102 alpha beta 8497 8518 8502 8500 8533 C1' DC B 103 alpha beta 8529 8548 8534 8532 8563 C1' DC B 104 alpha beta 8559 8578 8564 8562 8593 C1' DA B 105 alpha beta 8589 8610 8594 8592 8625 C1' DC B 106 alpha beta 8621 8640 8626 8624 8655 C1' DG B 107 alpha beta 8651 8673 8656 8654 8688 C1' DG B 108 alpha beta 8684 8706 8689 8687 8721 C1' DC B 109 alpha beta 8717 8736 8722 8720 8751 C1' DG B 110 alpha beta 8747 8769 8752 8750 8784 C1' DC B 111 alpha beta 8780 8799 8785 8783 8812 C1' DOC B 112 alpha beta 8816 8826 8804 8813 8847 C1' LHO C 204 alpha beta 8855 8863 8837 8850 8883 C1' DG C 205 alpha beta 8879 8901 8884 8882 8916 C1' DG C 206 alpha beta 8912 8934 8917 8915 8949 C1' DC C 207 alpha beta 8945 8964 8950 8948 8979 C1' DG C 208 alpha beta 8975 8997 8980 8978 9012 C1' DC C 209 alpha beta 9008 9027 9013 9011 9042 C1' DC C 210 alpha beta 9038 9057 9043 9041 9072 C1' DG C 211 alpha beta 9068 9090 9073 9071 9105 C1' DT C 212 alpha beta 9101 9121 9106 9104 9137 C1' DG C 213 alpha beta 9133 9155 9138 9136 9170 C1' DG C 214 alpha beta 9166 9188 9171 9169 9203 C1' DT C 215 alpha beta 9199 9219 9204 9202 9235 C1' DC C 216 alpha beta 9231 9251 9236 9234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8466 C2' DG B 101 OK OK 8467 8464 8483 8484 8500 C2' DA B 102 OK OK 8501 8498 8516 8517 8532 C2' DC B 103 OK OK 8533 8530 8546 8547 8562 C2' DC B 104 OK OK 8563 8560 8576 8577 8592 C2' DA B 105 OK OK 8593 8590 8608 8609 8624 C2' DC B 106 OK OK 8625 8622 8638 8639 8654 C2' DG B 107 OK OK 8655 8652 8671 8672 8687 C2' DG B 108 OK OK 8688 8685 8704 8705 8720 C2' DC B 109 OK OK 8721 8718 8734 8735 8750 C2' DG B 110 OK OK 8751 8748 8767 8768 8783 C2' DC B 111 OK OK 8784 8781 8797 8798 8813 C2' DOC B 112 distorted distorted 8812 8814 8827 8828 8850 C2' LHO C 204 8847 8852 8882 C2' DG C 205 OK OK 8883 8880 8899 8900 8915 C2' DG C 206 OK OK 8916 8913 8932 8933 8948 C2' DC C 207 OK OK 8949 8946 8962 8963 8978 C2' DG C 208 OK OK 8979 8976 8995 8996 9011 C2' DC C 209 OK OK 9012 9009 9025 9026 9041 C2' DC C 210 OK OK 9042 9039 9055 9056 9071 C2' DG C 211 OK OK 9072 9069 9088 9089 9104 C2' DT C 212 OK OK 9105 9102 9119 9120 9136 C2' DG C 213 OK OK 9137 9134 9153 9154 9169 C2' DG C 214 OK OK 9170 9167 9186 9187 9202 C2' DT C 215 OK OK 9203 9200 9217 9218 9234 C2' DC C 216 OK OK 9235 9232 9249 9250 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8464 C3' DG B 101 OK OK 8462 8482 8465 8466 8498 C3' DA B 102 OK OK 8496 8515 8499 8500 8530 C3' DC B 103 OK OK 8528 8545 8531 8532 8560 C3' DC B 104 OK OK 8558 8575 8561 8562 8590 C3' DA B 105 OK OK 8588 8607 8591 8592 8622 C3' DC B 106 OK OK 8620 8637 8623 8624 8652 C3' DG B 107 OK OK 8650 8670 8653 8654 8685 C3' DG B 108 OK OK 8683 8703 8686 8687 8718 C3' DC B 109 OK OK 8716 8733 8719 8720 8748 C3' DG B 110 OK OK 8746 8766 8749 8750 8781 C3' DC B 111 OK OK 8779 8796 8782 8783 8814 C3' DOC B 112 8815 8813 8852 C3' LHO C 204 OK OK 8854 8869 8853 8850 8880 C3' DG C 205 OK OK 8878 8898 8881 8882 8913 C3' DG C 206 OK OK 8911 8931 8914 8915 8946 C3' DC C 207 OK OK 8944 8961 8947 8948 8976 C3' DG C 208 OK OK 8974 8994 8977 8978 9009 C3' DC C 209 OK OK 9007 9024 9010 9011 9039 C3' DC C 210 OK OK 9037 9054 9040 9041 9069 C3' DG C 211 OK OK 9067 9087 9070 9071 9102 C3' DT C 212 OK OK 9100 9118 9103 9104 9134 C3' DG C 213 OK OK 9132 9152 9135 9136 9167 C3' DG C 214 OK OK 9165 9185 9168 9169 9200 C3' DT C 215 OK OK 9198 9216 9201 9202 9232 C3' DC C 216 OK OK 9230 9247 9233 9234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8462 C4' DG B 101 OK OK 8464 8481 8461 8463 8496 C4' DA B 102 OK OK 8498 8514 8495 8497 8528 C4' DC B 103 OK OK 8530 8544 8527 8529 8558 C4' DC B 104 OK OK 8560 8574 8557 8559 8588 C4' DA B 105 OK OK 8590 8606 8587 8589 8620 C4' DC B 106 OK OK 8622 8636 8619 8621 8650 C4' DG B 107 OK OK 8652 8669 8649 8651 8683 C4' DG B 108 OK OK 8685 8702 8682 8684 8716 C4' DC B 109 OK OK 8718 8732 8715 8717 8746 C4' DG B 110 OK OK 8748 8765 8745 8747 8779 C4' DC B 111 OK OK 8781 8795 8778 8780 8815 C4' DOC B 112 OK OK 8814 8831 8817 8816 8854 C4' LHO C 204 OK OK 8852 8870 8856 8855 8878 C4' DG C 205 OK OK 8880 8897 8877 8879 8911 C4' DG C 206 OK OK 8913 8930 8910 8912 8944 C4' DC C 207 OK OK 8946 8960 8943 8945 8974 C4' DG C 208 OK OK 8976 8993 8973 8975 9007 C4' DC C 209 OK OK 9009 9023 9006 9008 9037 C4' DC C 210 OK OK 9039 9053 9036 9038 9067 C4' DG C 211 OK OK 9069 9086 9066 9068 9100 C4' DT C 212 OK OK 9102 9117 9099 9101 9132 C4' DG C 213 OK OK 9134 9151 9131 9133 9165 C4' DG C 214 OK OK 9167 9184 9164 9166 9198 C4' DT C 215 OK OK 9200 9215 9197 9199 9230 C4' DC C 216 OK OK 9232 9246 9229 9231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8461 C5' DG B 101 OK OK 8460 8479 8480 8462 8495 C5' DA B 102 OK OK 8494 8512 8513 8496 8527 C5' DC B 103 OK OK 8526 8542 8543 8528 8557 C5' DC B 104 OK OK 8556 8572 8573 8558 8587 C5' DA B 105 OK OK 8586 8604 8605 8588 8619 C5' DC B 106 OK OK 8618 8634 8635 8620 8649 C5' DG B 107 OK OK 8648 8667 8668 8650 8682 C5' DG B 108 OK OK 8681 8700 8701 8683 8715 C5' DC B 109 OK OK 8714 8730 8731 8716 8745 C5' DG B 110 OK OK 8744 8763 8764 8746 8778 C5' DC B 111 OK OK 8777 8793 8794 8779 8817 C5' DOC B 112 OK OK 8818 8832 8833 8815 8856 C5' LHO C 204 8857 8854 8877 C5' DG C 205 OK OK 8876 8895 8896 8878 8910 C5' DG C 206 OK OK 8909 8928 8929 8911 8943 C5' DC C 207 OK OK 8942 8958 8959 8944 8973 C5' DG C 208 OK OK 8972 8991 8992 8974 9006 C5' DC C 209 OK OK 9005 9021 9022 9007 9036 C5' DC C 210 OK OK 9035 9051 9052 9037 9066 C5' DG C 211 OK OK 9065 9084 9085 9067 9099 C5' DT C 212 OK OK 9098 9115 9116 9100 9131 C5' DG C 213 OK OK 9130 9149 9150 9132 9164 C5' DG C 214 OK OK 9163 9182 9183 9165 9197 C5' DT C 215 OK OK 9196 9213 9214 9198 9229 C5' DC C 216 OK OK 9228 9244 9245 9230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8491 P DA B 102 distorted distorted 8465 8492 8493 8494 8523 P DC B 103 distorted distorted 8499 8524 8525 8526 8553 P DC B 104 distorted distorted 8531 8554 8555 8556 8583 P DA B 105 distorted distorted 8561 8584 8585 8586 8615 P DC B 106 distorted distorted 8591 8616 8617 8618 8645 P DG B 107 distorted distorted 8623 8646 8647 8648 8678 P DG B 108 distorted distorted 8653 8679 8680 8681 8711 P DC B 109 distorted distorted 8686 8712 8713 8714 8741 P DG B 110 distorted distorted 8719 8742 8743 8744 8774 P DC B 111 distorted distorted 8749 8775 8776 8777 8819 P DOC B 112 distorted distorted 8782 8820 8821 8818 8835 P LHO C 204 8849 8857 8873 P DG C 205 distorted distorted 8853 8874 8875 8876 8906 P DG C 206 distorted distorted 8881 8907 8908 8909 8939 P DC C 207 distorted distorted 8914 8940 8941 8942 8969 P DG C 208 distorted distorted 8947 8970 8971 8972 9002 P DC C 209 distorted distorted 8977 9003 9004 9005 9032 P DC C 210 distorted distorted 9010 9033 9034 9035 9062 P DG C 211 distorted distorted 9040 9063 9064 9065 9095 P DT C 212 distorted distorted 9070 9096 9097 9098 9127 P DG C 213 distorted distorted 9103 9128 9129 9130 9160 P DG C 214 distorted distorted 9135 9161 9162 9163 9193 P DT C 215 distorted distorted 9168 9194 9195 9196 9225 P DC C 216 distorted distorted 9201 9226 9227 9228 ---------------------------------------------------------------------------------