ID code: '2FLL' 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' --------------------------------------------------------------------------------- 8 C1' DA P 867 beta 4 9 7 29 C1' DG P 868 beta 25 30 28 51 C1' DG P 869 beta 47 52 50 73 C1' DA P 870 beta 69 74 72 94 C1' DC P 871 beta 90 95 93 113 C1' DC P 872 beta 109 114 112 130 C1' DOC P 873 beta 134 122 131 148 C1' DT T 839 beta 144 149 147 168 C1' DA T 840 beta 164 169 167 189 C1' DG T 841 beta 185 190 188 211 C1' DG T 842 beta 207 212 210 233 C1' DG T 843 beta 229 234 232 255 C1' DT T 844 beta 251 256 254 275 C1' DC T 845 beta 271 276 274 294 C1' DC T 846 beta 290 295 293 313 C1' DT T 847 beta 309 314 312 3212 C1' TTP A 875 beta 3208 3213 3211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DA P 867 8 5 28 C2' DG P 868 29 26 50 C2' DG P 869 51 48 72 C2' DA P 870 73 70 93 C2' DC P 871 94 91 112 C2' DC P 872 113 110 131 C2' DOC P 873 130 132 147 C2' DT T 839 148 145 167 C2' DA T 840 168 165 188 C2' DG T 841 189 186 210 C2' DG T 842 211 208 232 C2' DG T 843 233 230 254 C2' DT T 844 255 252 274 C2' DC T 845 275 272 293 C2' DC T 846 294 291 312 C2' DT T 847 313 310 3211 C2' TTP A 875 3212 3209 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DA P 867 OK 3 6 7 26 C3' DG P 868 OK 24 27 28 48 C3' DG P 869 OK 46 49 50 70 C3' DA P 870 OK 68 71 72 91 C3' DC P 871 OK 89 92 93 110 C3' DC P 872 OK 108 111 112 132 C3' DOC P 873 133 131 145 C3' DT T 839 OK 143 146 147 165 C3' DA T 840 OK 163 166 167 186 C3' DG T 841 OK 184 187 188 208 C3' DG T 842 OK 206 209 210 230 C3' DG T 843 OK 228 231 232 252 C3' DT T 844 OK 250 253 254 272 C3' DC T 845 OK 270 273 274 291 C3' DC T 846 OK 289 292 293 310 C3' DT T 847 OK 308 311 312 3209 C3' TTP A 875 OK 3207 3210 3211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DA P 867 OK 5 2 4 24 C4' DG P 868 OK 26 23 25 46 C4' DG P 869 OK 48 45 47 68 C4' DA P 870 OK 70 67 69 89 C4' DC P 871 OK 91 88 90 108 C4' DC P 872 OK 110 107 109 133 C4' DOC P 873 OK 132 135 134 143 C4' DT T 839 OK 145 142 144 163 C4' DA T 840 OK 165 162 164 184 C4' DG T 841 OK 186 183 185 206 C4' DG T 842 OK 208 205 207 228 C4' DG T 843 OK 230 227 229 250 C4' DT T 844 OK 252 249 251 270 C4' DC T 845 OK 272 269 271 289 C4' DC T 846 OK 291 288 290 308 C4' DT T 847 OK 310 307 309 3207 C4' TTP A 875 OK 3209 3206 3208 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DA P 867 1 3 23 C5' DG P 868 22 24 45 C5' DG P 869 44 46 67 C5' DA P 870 66 68 88 C5' DC P 871 87 89 107 C5' DC P 872 106 108 135 C5' DOC P 873 136 133 142 C5' DT T 839 141 143 162 C5' DA T 840 161 163 183 C5' DG T 841 182 184 205 C5' DG T 842 204 206 227 C5' DG T 843 226 228 249 C5' DT T 844 248 250 269 C5' DC T 845 268 270 288 C5' DC T 846 287 289 307 C5' DT T 847 306 308 3206 C5' TTP A 875 3205 3207 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P DG P 868 distorted distorted 6 20 21 22 41 P DG P 869 distorted distorted 27 42 43 44 63 P DA P 870 distorted distorted 49 64 65 66 84 P DC P 871 distorted distorted 71 85 86 87 103 P DC P 872 distorted distorted 92 104 105 106 137 P DOC P 873 distorted distorted 111 138 139 136 158 P DA T 840 distorted distorted 146 159 160 161 179 P DG T 841 distorted distorted 166 180 181 182 201 P DG T 842 distorted distorted 187 202 203 204 223 P DG T 843 distorted distorted 209 224 225 226 245 P DT T 844 distorted distorted 231 246 247 248 265 P DC T 845 distorted distorted 253 266 267 268 284 P DC T 846 distorted distorted 273 285 286 287 303 P DT T 847 distorted distorted 292 304 305 306 ---------------------------------------------------------------------------------