ID code: '2ALZ' 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' DT T 839 beta 4 9 7 28 C1' DG T 840 beta 24 29 27 50 C1' DG T 841 beta 46 51 49 72 C1' DG T 842 beta 68 73 71 94 C1' DG T 843 beta 90 95 93 116 C1' DT T 844 beta 112 117 115 136 C1' DC T 845 beta 132 137 135 155 C1' DC T 846 beta 151 156 154 174 C1' DT T 847 beta 170 175 173 192 C1' DA P 867 beta 188 193 191 213 C1' DG P 868 beta 209 214 212 235 C1' DG P 869 beta 231 236 234 257 C1' DA P 870 beta 253 258 256 278 C1' DC P 871 beta 274 279 277 297 C1' DC P 872 beta 293 298 296 314 C1' DOC P 873 beta 318 306 315 3210 C1' DCP A 875 beta 3214 3202 3211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DT T 839 8 5 27 C2' DG T 840 28 25 49 C2' DG T 841 50 47 71 C2' DG T 842 72 69 93 C2' DG T 843 94 91 115 C2' DT T 844 116 113 135 C2' DC T 845 136 133 154 C2' DC T 846 155 152 173 C2' DT T 847 174 171 191 C2' DA P 867 192 189 212 C2' DG P 868 213 210 234 C2' DG P 869 235 232 256 C2' DA P 870 257 254 277 C2' DC P 871 278 275 296 C2' DC P 872 297 294 315 C2' DOC P 873 314 316 3211 C2' DCP A 875 3210 3212 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DT T 839 OK 3 6 7 25 C3' DG T 840 OK 23 26 27 47 C3' DG T 841 OK 45 48 49 69 C3' DG T 842 OK 67 70 71 91 C3' DG T 843 OK 89 92 93 113 C3' DT T 844 OK 111 114 115 133 C3' DC T 845 OK 131 134 135 152 C3' DC T 846 OK 150 153 154 171 C3' DT T 847 OK 169 172 173 189 C3' DA P 867 OK 187 190 191 210 C3' DG P 868 OK 208 211 212 232 C3' DG P 869 OK 230 233 234 254 C3' DA P 870 OK 252 255 256 275 C3' DC P 871 OK 273 276 277 294 C3' DC P 872 OK 292 295 296 316 C3' DOC P 873 317 315 3212 C3' DCP A 875 OK 3213 3215 3211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DT T 839 OK 5 2 4 23 C4' DG T 840 OK 25 22 24 45 C4' DG T 841 OK 47 44 46 67 C4' DG T 842 OK 69 66 68 89 C4' DG T 843 OK 91 88 90 111 C4' DT T 844 OK 113 110 112 131 C4' DC T 845 OK 133 130 132 150 C4' DC T 846 OK 152 149 151 169 C4' DT T 847 OK 171 168 170 187 C4' DA P 867 OK 189 186 188 208 C4' DG P 868 OK 210 207 209 230 C4' DG P 869 OK 232 229 231 252 C4' DA P 870 OK 254 251 253 273 C4' DC P 871 OK 275 272 274 292 C4' DC P 872 OK 294 291 293 317 C4' DOC P 873 OK 316 319 318 3213 C4' DCP A 875 OK 3212 3216 3214 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DT T 839 1 3 22 C5' DG T 840 21 23 44 C5' DG T 841 43 45 66 C5' DG T 842 65 67 88 C5' DG T 843 87 89 110 C5' DT T 844 109 111 130 C5' DC T 845 129 131 149 C5' DC T 846 148 150 168 C5' DT T 847 167 169 186 C5' DA P 867 185 187 207 C5' DG P 868 206 208 229 C5' DG P 869 228 230 251 C5' DA P 870 250 252 272 C5' DC P 871 271 273 291 C5' DC P 872 290 292 319 C5' DOC P 873 320 317 3216 C5' DCP A 875 3217 3213 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P DG T 840 distorted distorted 6 19 20 21 40 P DG T 841 distorted distorted 26 41 42 43 62 P DG T 842 distorted distorted 48 63 64 65 84 P DG T 843 distorted distorted 70 85 86 87 106 P DT T 844 distorted distorted 92 107 108 109 126 P DC T 845 distorted distorted 114 127 128 129 145 P DC T 846 distorted distorted 134 146 147 148 164 P DT T 847 distorted distorted 153 165 166 167 203 P DG P 868 distorted distorted 190 204 205 206 225 P DG P 869 distorted distorted 211 226 227 228 247 P DA P 870 distorted distorted 233 248 249 250 268 P DC P 871 distorted distorted 255 269 270 271 287 P DC P 872 distorted distorted 276 288 289 290 321 P DOC P 873 distorted distorted 295 322 323 320 ---------------------------------------------------------------------------------