ID code: '1OUP' 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' G C 1 beta 4 9 7 30 C1' C C 2 beta 26 31 29 49 C1' G C 3 beta 45 50 48 71 C1' A C 4 beta 67 72 70 92 C1' T C 5 beta 88 93 91 112 C1' C C 6 beta 108 113 111 131 C1' G C 7 beta 127 132 130 153 C1' C C 8 beta 149 154 152 170 C1' G D 9 beta 166 171 169 192 C1' C D 10 beta 188 193 191 211 C1' G D 11 beta 207 212 210 233 C1' A D 12 beta 229 234 232 254 C1' T D 13 beta 250 255 253 274 C1' C D 14 beta 270 275 273 293 C1' G D 15 beta 289 294 292 315 C1' C D 16 beta 311 316 314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 8 5 29 C2' C C 2 30 27 48 C2' G C 3 49 46 70 C2' A C 4 71 68 91 C2' T C 5 92 89 111 C2' C C 6 112 109 130 C2' G C 7 131 128 152 C2' C C 8 153 150 169 C2' G D 9 170 167 191 C2' C D 10 192 189 210 C2' G D 11 211 208 232 C2' A D 12 233 230 253 C2' T D 13 254 251 273 C2' C D 14 274 271 292 C2' G D 15 293 290 314 C2' C D 16 315 312 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 27 C3' C C 2 OK 25 28 29 46 C3' G C 3 OK 44 47 48 68 C3' A C 4 OK 66 69 70 89 C3' T C 5 OK 87 90 91 109 C3' C C 6 OK 107 110 111 128 C3' G C 7 OK 126 129 130 150 C3' C C 8 OK 148 151 152 167 C3' G D 9 OK 165 168 169 189 C3' C D 10 OK 187 190 191 208 C3' G D 11 OK 206 209 210 230 C3' A D 12 OK 228 231 232 251 C3' T D 13 OK 249 252 253 271 C3' C D 14 OK 269 272 273 290 C3' G D 15 OK 288 291 292 312 C3' C D 16 OK 310 313 314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 25 C4' C C 2 OK 27 24 26 44 C4' G C 3 OK 46 43 45 66 C4' A C 4 OK 68 65 67 87 C4' T C 5 OK 89 86 88 107 C4' C C 6 OK 109 106 108 126 C4' G C 7 OK 128 125 127 148 C4' C C 8 OK 150 147 149 165 C4' G D 9 OK 167 164 166 187 C4' C D 10 OK 189 186 188 206 C4' G D 11 OK 208 205 207 228 C4' A D 12 OK 230 227 229 249 C4' T D 13 OK 251 248 250 269 C4' C D 14 OK 271 268 270 288 C4' G D 15 OK 290 287 289 310 C4' C D 16 OK 312 309 311 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 24 C5' C C 2 23 25 43 C5' G C 3 42 44 65 C5' A C 4 64 66 86 C5' T C 5 85 87 106 C5' C C 6 105 107 125 C5' G C 7 124 126 147 C5' C C 8 146 148 164 C5' G D 9 163 165 186 C5' C D 10 185 187 205 C5' G D 11 204 206 227 C5' A D 12 226 228 248 C5' T D 13 247 249 268 C5' C D 14 267 269 287 C5' G D 15 286 288 309 C5' C D 16 308 310 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C C 2 distorted distorted 6 21 22 23 39 P G C 3 distorted distorted 28 40 41 42 61 P A C 4 distorted distorted 47 62 63 64 82 P T C 5 distorted distorted 69 83 84 85 102 P C C 6 distorted distorted 90 103 104 105 121 P G C 7 distorted distorted 110 122 123 124 143 P C C 8 distorted distorted 129 144 145 146 182 P C D 10 distorted distorted 168 183 184 185 201 P G D 11 distorted distorted 190 202 203 204 223 P A D 12 distorted distorted 209 224 225 226 244 P T D 13 distorted distorted 231 245 246 247 264 P C D 14 distorted distorted 252 265 266 267 283 P G D 15 distorted distorted 272 284 285 286 305 P C D 16 distorted distorted 291 306 307 308 ---------------------------------------------------------------------------------