ID code: '1LV5' 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 E 20 beta 4 9 7 30 C1' G E 21 beta 26 31 29 52 C1' A E 22 beta 48 53 51 73 C1' T E 23 beta 69 74 72 93 C1' C E 24 beta 89 94 92 112 C1' A E 25 beta 108 113 111 133 C1' G E 26 beta 129 134 132 155 C1' C E 27 beta 151 156 154 174 C1' G E 28 beta 170 175 173 195 C1' A E 29 beta 192 196 194 217 C1' T F 4 beta 213 218 216 237 C1' C F 5 beta 233 238 236 256 C1' G F 6 beta 252 257 255 278 C1' C F 7 beta 274 279 277 297 C1' T F 8 beta 293 298 296 317 C1' G F 9 beta 313 318 316 339 C1' A F 10 beta 335 340 338 360 C1' T F 11 beta 356 361 359 380 C1' C F 12 beta 376 381 379 399 C1' C F 13 beta 395 400 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G E 20 8 5 29 C2' G E 21 30 27 51 C2' A E 22 52 49 72 C2' T E 23 73 70 92 C2' C E 24 93 90 111 C2' A E 25 112 109 132 C2' G E 26 133 130 154 C2' C E 27 155 152 173 C2' G E 28 174 171 194 C2' A E 29 195 193 216 C2' T F 4 217 214 236 C2' C F 5 237 234 255 C2' G F 6 256 253 277 C2' C F 7 278 275 296 C2' T F 8 297 294 316 C2' G F 9 317 314 338 C2' A F 10 339 336 359 C2' T F 11 360 357 379 C2' C F 12 380 377 398 C2' C F 13 399 396 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G E 20 OK 3 6 7 27 C3' G E 21 OK 25 28 29 49 C3' A E 22 OK 47 50 51 70 C3' T E 23 OK 68 71 72 90 C3' C E 24 OK 88 91 92 109 C3' A E 25 OK 107 110 111 130 C3' G E 26 OK 128 131 132 152 C3' C E 27 OK 150 153 154 171 C3' G E 28 OK 169 172 173 193 C3' A E 29 191 194 214 C3' T F 4 OK 212 215 216 234 C3' C F 5 OK 232 235 236 253 C3' G F 6 OK 251 254 255 275 C3' C F 7 OK 273 276 277 294 C3' T F 8 OK 292 295 296 314 C3' G F 9 OK 312 315 316 336 C3' A F 10 OK 334 337 338 357 C3' T F 11 OK 355 358 359 377 C3' C F 12 OK 375 378 379 396 C3' C F 13 OK 394 397 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G E 20 OK 5 2 4 25 C4' G E 21 OK 27 24 26 47 C4' A E 22 OK 49 46 48 68 C4' T E 23 OK 70 67 69 88 C4' C E 24 OK 90 87 89 107 C4' A E 25 OK 109 106 108 128 C4' G E 26 OK 130 127 129 150 C4' C E 27 OK 152 149 151 169 C4' G E 28 OK 171 168 170 191 C4' A E 29 OK 193 190 192 212 C4' T F 4 OK 214 211 213 232 C4' C F 5 OK 234 231 233 251 C4' G F 6 OK 253 250 252 273 C4' C F 7 OK 275 272 274 292 C4' T F 8 OK 294 291 293 312 C4' G F 9 OK 314 311 313 334 C4' A F 10 OK 336 333 335 355 C4' T F 11 OK 357 354 356 375 C4' C F 12 OK 377 374 376 394 C4' C F 13 OK 396 393 395 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G E 20 1 3 24 C5' G E 21 23 25 46 C5' A E 22 45 47 67 C5' T E 23 66 68 87 C5' C E 24 86 88 106 C5' A E 25 105 107 127 C5' G E 26 126 128 149 C5' C E 27 148 150 168 C5' G E 28 167 169 190 C5' A E 29 189 191 211 C5' T F 4 210 212 231 C5' C F 5 230 232 250 C5' G F 6 249 251 272 C5' C F 7 271 273 291 C5' T F 8 290 292 311 C5' G F 9 310 312 333 C5' A F 10 332 334 354 C5' T F 11 353 355 374 C5' C F 12 373 375 393 C5' C F 13 392 394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G E 21 distorted distorted 6 21 22 23 42 P A E 22 distorted distorted 28 43 44 45 63 P T E 23 distorted distorted 50 64 65 66 83 P C E 24 distorted distorted 71 84 85 86 102 P A E 25 distorted distorted 91 103 104 105 123 P G E 26 distorted distorted 110 124 125 126 145 P C E 27 distorted distorted 131 146 147 148 164 P G E 28 distorted distorted 153 165 166 167 186 P A E 29 distorted distorted 172 187 188 189 207 P T F 4 distorted distorted 208 209 210 227 P C F 5 distorted distorted 215 228 229 230 246 P G F 6 distorted distorted 235 247 248 249 268 P C F 7 distorted distorted 254 269 270 271 287 P T F 8 distorted distorted 276 288 289 290 307 P G F 9 distorted distorted 295 308 309 310 329 P A F 10 distorted distorted 315 330 331 332 350 P T F 11 distorted distorted 337 351 352 353 370 P C F 12 distorted distorted 358 371 372 373 389 P C F 13 distorted distorted 378 390 391 392 ---------------------------------------------------------------------------------