ID code: '1IXY' 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' A C 8 beta 7 12 10 32 C1' G C 9 beta 28 33 31 54 C1' A C 10 beta 50 55 53 75 C1' T C 11 beta 71 76 74 95 C1' A C 12 beta 91 96 94 116 C1' G C 13 beta 112 117 115 136 C1' C E 14 beta 132 137 135 155 C1' T E 15 beta 151 156 154 175 C1' A E 16 beta 171 176 174 196 C1' T E 17 beta 192 197 195 216 C1' C E 18 beta 212 217 215 235 C1' T E 19 beta 231 236 234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 8 11 8 31 C2' G C 9 32 29 53 C2' A C 10 54 51 74 C2' T C 11 75 72 94 C2' A C 12 95 92 115 C2' G C 13 116 113 135 C2' C E 14 136 133 154 C2' T E 15 155 152 174 C2' A E 16 175 172 195 C2' T E 17 196 193 215 C2' C E 18 216 213 234 C2' T E 19 235 232 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 8 OK 6 9 10 29 C3' G C 9 OK 27 30 31 51 C3' A C 10 OK 49 52 53 72 C3' T C 11 OK 70 73 74 92 C3' A C 12 OK 90 93 94 113 C3' G C 13 OK 111 114 115 133 C3' C E 14 OK 131 134 135 152 C3' T E 15 OK 150 153 154 172 C3' A E 16 OK 170 173 174 193 C3' T E 17 OK 191 194 195 213 C3' C E 18 OK 211 214 215 232 C3' T E 19 OK 230 233 234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 8 OK 8 5 7 27 C4' G C 9 OK 29 26 28 49 C4' A C 10 OK 51 48 50 70 C4' T C 11 OK 72 69 71 90 C4' A C 12 OK 92 89 91 111 C4' G C 13 OK 113 110 112 131 C4' C E 14 OK 133 130 132 150 C4' T E 15 OK 152 149 151 170 C4' A E 16 OK 172 169 171 191 C4' T E 17 OK 193 190 192 211 C4' C E 18 OK 213 210 212 230 C4' T E 19 OK 232 229 231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 8 4 6 26 C5' G C 9 25 27 48 C5' A C 10 47 49 69 C5' T C 11 68 70 89 C5' A C 12 88 90 110 C5' G C 13 109 111 130 C5' C E 14 129 131 149 C5' T E 15 148 150 169 C5' A E 16 168 170 190 C5' T E 17 189 191 210 C5' C E 18 209 211 229 C5' T E 19 228 230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 8 distorted distorted 2 3 4 22 P G C 9 distorted distorted 9 23 24 25 44 P A C 10 distorted distorted 30 45 46 47 65 P T C 11 distorted distorted 52 66 67 68 85 P A C 12 distorted distorted 73 86 87 88 106 P G C 13 distorted distorted 93 107 108 109 145 P T E 15 distorted distorted 134 146 147 148 165 P A E 16 distorted distorted 153 166 167 168 186 P T E 17 distorted distorted 173 187 188 189 206 P C E 18 distorted distorted 194 207 208 209 225 P T E 19 distorted distorted 214 226 227 228 ---------------------------------------------------------------------------------