ID code: '4FS1' 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' DA B 7 beta 7 12 10 32 C1' DG B 8 beta 28 33 31 54 C1' DG B 9 beta 50 55 53 76 C1' DA B 10 beta 72 77 75 97 C1' DC B 11 beta 93 98 96 116 C1' DC B 12 beta 112 117 115 133 C1' DOC B 13 beta 137 125 134 151 C1' DT C 839 beta 147 152 150 174 C1' EFG C 840 beta 175 173 176 196 C1' DG C 841 beta 192 197 195 218 C1' DG C 842 beta 214 219 217 240 C1' DG C 843 beta 236 241 239 262 C1' DT C 844 beta 258 263 261 282 C1' DC C 845 beta 278 283 281 301 C1' DC C 846 beta 297 302 300 320 C1' DT C 847 beta 316 321 319 3299 C1' TTP A 505 beta 3295 3300 3298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DA B 7 11 8 31 C2' DG B 8 32 29 53 C2' DG B 9 54 51 75 C2' DA B 10 76 73 96 C2' DC B 11 97 94 115 C2' DC B 12 116 113 134 C2' DOC B 13 133 135 150 C2' DT C 839 151 148 176 C2' EFG C 840 174 178 195 C2' DG C 841 196 193 217 C2' DG C 842 218 215 239 C2' DG C 843 240 237 261 C2' DT C 844 262 259 281 C2' DC C 845 282 279 300 C2' DC C 846 301 298 319 C2' DT C 847 320 317 3298 C2' TTP A 505 3299 3296 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DA B 7 OK 6 9 10 29 C3' DG B 8 OK 27 30 31 51 C3' DG B 9 OK 49 52 53 73 C3' DA B 10 OK 71 74 75 94 C3' DC B 11 OK 92 95 96 113 C3' DC B 12 OK 111 114 115 135 C3' DOC B 13 136 134 148 C3' DT C 839 OK 146 149 150 178 C3' EFG C 840 OK 180 179 176 193 C3' DG C 841 OK 191 194 195 215 C3' DG C 842 OK 213 216 217 237 C3' DG C 843 OK 235 238 239 259 C3' DT C 844 OK 257 260 261 279 C3' DC C 845 OK 277 280 281 298 C3' DC C 846 OK 296 299 300 317 C3' DT C 847 OK 315 318 319 3296 C3' TTP A 505 OK 3294 3297 3298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DA B 7 OK 8 5 7 27 C4' DG B 8 OK 29 26 28 49 C4' DG B 9 OK 51 48 50 71 C4' DA B 10 OK 73 70 72 92 C4' DC B 11 OK 94 91 93 111 C4' DC B 12 OK 113 110 112 136 C4' DOC B 13 OK 135 138 137 146 C4' DT C 839 OK 148 145 147 180 C4' EFG C 840 OK 178 181 175 191 C4' DG C 841 OK 193 190 192 213 C4' DG C 842 OK 215 212 214 235 C4' DG C 843 OK 237 234 236 257 C4' DT C 844 OK 259 256 258 277 C4' DC C 845 OK 279 276 278 296 C4' DC C 846 OK 298 295 297 315 C4' DT C 847 OK 317 314 316 3294 C4' TTP A 505 OK 3296 3293 3295 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DA B 7 4 6 26 C5' DG B 8 25 27 48 C5' DG B 9 47 49 70 C5' DA B 10 69 71 91 C5' DC B 11 90 92 110 C5' DC B 12 109 111 138 C5' DOC B 13 139 136 145 C5' DT C 839 144 146 181 C5' EFG C 840 182 180 190 C5' DG C 841 189 191 212 C5' DG C 842 211 213 234 C5' DG C 843 233 235 256 C5' DT C 844 255 257 276 C5' DC C 845 275 277 295 C5' DC C 846 294 296 314 C5' DT C 847 313 315 3293 C5' TTP A 505 3292 3294 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DA B 7 distorted distorted 2 3 4 22 P DG B 8 distorted distorted 9 23 24 25 44 P DG B 9 distorted distorted 30 45 46 47 66 P DA B 10 distorted distorted 52 67 68 69 87 P DC B 11 distorted distorted 74 88 89 90 106 P DC B 12 distorted distorted 95 107 108 109 140 P DOC B 13 distorted distorted 114 141 142 139 183 P EFG C 840 distorted distorted 149 184 185 182 186 P DG C 841 distorted distorted 179 187 188 189 208 P DG C 842 distorted distorted 194 209 210 211 230 P DG C 843 distorted distorted 216 231 232 233 252 P DT C 844 distorted distorted 238 253 254 255 272 P DC C 845 distorted distorted 260 273 274 275 291 P DC C 846 distorted distorted 280 292 293 294 310 P DT C 847 distorted distorted 299 311 312 313 ---------------------------------------------------------------------------------