ID code: '1EVW' 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' T E 2 beta 4 9 7 28 C1' G E 3 beta 24 29 27 50 C1' G E 4 beta 46 51 49 72 C1' C E 5 beta 68 73 71 91 C1' T E 6 beta 87 92 90 111 C1' A E 7 beta 107 112 110 132 C1' C E 8 beta 128 133 131 151 C1' C E 9 beta 147 152 150 172 C1' G O 13 beta 168 173 171 194 C1' G O 14 beta 190 195 193 216 C1' T O 15 beta 212 217 215 236 C1' A O 16 beta 232 237 235 257 C1' G O 17 beta 253 258 256 279 C1' C O 18 beta 275 280 278 298 C1' C O 19 beta 294 299 297 317 C1' A O 20 beta 313 318 316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T E 2 8 5 27 C2' G E 3 28 25 49 C2' G E 4 50 47 71 C2' C E 5 72 69 90 C2' T E 6 91 88 110 C2' A E 7 111 108 131 C2' C E 8 132 129 150 C2' C E 9 151 148 171 C2' G O 13 172 169 193 C2' G O 14 194 191 215 C2' T O 15 216 213 235 C2' A O 16 236 233 256 C2' G O 17 257 254 278 C2' C O 18 279 276 297 C2' C O 19 298 295 316 C2' A O 20 317 314 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T E 2 OK 3 6 7 25 C3' G E 3 OK 23 26 27 47 C3' G E 4 OK 45 48 49 69 C3' C E 5 OK 67 70 71 88 C3' T E 6 OK 86 89 90 108 C3' A E 7 OK 106 109 110 129 C3' C E 8 OK 127 130 131 148 C3' C E 9 OK 146 149 150 169 C3' G O 13 OK 167 170 171 191 C3' G O 14 OK 189 192 193 213 C3' T O 15 OK 211 214 215 233 C3' A O 16 OK 231 234 235 254 C3' G O 17 OK 252 255 256 276 C3' C O 18 OK 274 277 278 295 C3' C O 19 OK 293 296 297 314 C3' A O 20 OK 312 315 316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T E 2 OK 5 2 4 23 C4' G E 3 OK 25 22 24 45 C4' G E 4 OK 47 44 46 67 C4' C E 5 OK 69 66 68 86 C4' T E 6 OK 88 85 87 106 C4' A E 7 OK 108 105 107 127 C4' C E 8 OK 129 126 128 146 C4' C E 9 OK 148 145 147 167 C4' G O 13 OK 169 166 168 189 C4' G O 14 OK 191 188 190 211 C4' T O 15 OK 213 210 212 231 C4' A O 16 OK 233 230 232 252 C4' G O 17 OK 254 251 253 274 C4' C O 18 OK 276 273 275 293 C4' C O 19 OK 295 292 294 312 C4' A O 20 OK 314 311 313 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T E 2 1 3 22 C5' G E 3 21 23 44 C5' G E 4 43 45 66 C5' C E 5 65 67 85 C5' T E 6 84 86 105 C5' A E 7 104 106 126 C5' C E 8 125 127 145 C5' C E 9 144 146 166 C5' G O 13 165 167 188 C5' G O 14 187 189 210 C5' T O 15 209 211 230 C5' A O 16 229 231 251 C5' G O 17 250 252 273 C5' C O 18 272 274 292 C5' C O 19 291 293 311 C5' A O 20 310 312 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G E 3 distorted distorted 6 19 20 21 40 P G E 4 distorted distorted 26 41 42 43 62 P C E 5 distorted distorted 48 63 64 65 81 P T E 6 distorted distorted 70 82 83 84 101 P A E 7 distorted distorted 89 102 103 104 122 P C E 8 distorted distorted 109 123 124 125 141 P C E 9 distorted distorted 130 142 143 144 162 P G O 13 distorted distorted 163 164 165 184 P G O 14 distorted distorted 170 185 186 187 206 P T O 15 distorted distorted 192 207 208 209 226 P A O 16 distorted distorted 214 227 228 229 247 P G O 17 distorted distorted 234 248 249 250 269 P C O 18 distorted distorted 255 270 271 272 288 P C O 19 distorted distorted 277 289 290 291 307 P A O 20 distorted distorted 296 308 309 310 ---------------------------------------------------------------------------------