ID code: '1I1V' 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' --------------------------------------------------------------------------------- 11 C1' G A 1 beta 7 12 10 36 C1' G A 2 beta 32 37 35 61 C1' G A 3 beta 57 62 60 87 C1' C B 4 beta 83 88 86 108 C1' C B 5 beta 104 109 107 129 C1' C B 6 beta 125 130 128 151 C1' C C 7 beta 147 152 150 172 C1' C C 8 beta 168 173 171 193 C1' C C 9 beta 189 194 192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 11 8 35 C2' G A 2 36 33 60 C2' G A 3 61 58 86 C2' C B 4 87 84 107 C2' C B 5 108 105 128 C2' C B 6 129 126 150 C2' C C 7 151 148 171 C2' C C 8 172 169 192 C2' C C 9 193 190 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 33 C3' G A 2 OK 31 34 35 58 C3' G A 3 OK 56 59 60 84 C3' C B 4 OK 82 85 86 105 C3' C B 5 OK 103 106 107 126 C3' C B 6 OK 124 127 128 148 C3' C C 7 OK 146 149 150 169 C3' C C 8 OK 167 170 171 190 C3' C C 9 OK 188 191 192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 31 C4' G A 2 OK 33 30 32 56 C4' G A 3 OK 58 55 57 82 C4' C B 4 OK 84 81 83 103 C4' C B 5 OK 105 102 104 124 C4' C B 6 OK 126 123 125 146 C4' C C 7 OK 148 145 147 167 C4' C C 8 OK 169 166 168 188 C4' C C 9 OK 190 187 189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 30 C5' G A 2 29 31 55 C5' G A 3 54 56 81 C5' C B 4 80 82 102 C5' C B 5 101 103 123 C5' C B 6 122 124 145 C5' C C 7 144 146 166 C5' C C 8 165 167 187 C5' C C 9 186 188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 26 P G A 2 distorted distorted 9 27 28 29 51 P G A 3 distorted distorted 34 52 53 54 77 P C B 4 OK OK 78 79 80 98 P C B 5 distorted distorted 85 99 100 101 119 P C B 6 distorted distorted 106 120 121 122 141 P C C 7 OK OK 142 143 144 162 P C C 8 distorted distorted 149 163 164 165 183 P C C 9 distorted distorted 170 184 185 186 ---------------------------------------------------------------------------------