ID code: '1N3E' 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' --------------------------------------------------------------------------------- 12 C1' G D 415 beta 8 13 11 34 C1' A D 416 beta 30 35 33 55 C1' C D 417 beta 51 56 54 74 C1' G D 418 beta 70 75 73 96 C1' T D 419 beta 92 97 95 116 C1' T D 420 beta 112 117 115 136 C1' T D 421 beta 132 137 135 156 C1' T D 422 beta 152 157 155 176 C1' C D 423 beta 172 177 175 195 C1' G D 424 beta 191 196 194 215 C1' C E 451 beta 211 216 214 234 C1' G E 452 beta 230 235 233 256 C1' A E 453 beta 252 257 255 277 C1' A E 454 beta 273 278 276 298 C1' A E 455 beta 294 299 297 319 C1' A E 456 beta 315 320 318 340 C1' C E 457 beta 336 341 339 359 C1' G E 458 beta 355 360 358 381 C1' T E 459 beta 377 382 380 401 C1' C E 460 beta 397 402 400 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G D 415 12 9 33 C2' A D 416 34 31 54 C2' C D 417 55 52 73 C2' G D 418 74 71 95 C2' T D 419 96 93 115 C2' T D 420 116 113 135 C2' T D 421 136 133 155 C2' T D 422 156 153 175 C2' C D 423 176 173 194 C2' G D 424 195 192 214 C2' C E 451 215 212 233 C2' G E 452 234 231 255 C2' A E 453 256 253 276 C2' A E 454 277 274 297 C2' A E 455 298 295 318 C2' A E 456 319 316 339 C2' C E 457 340 337 358 C2' G E 458 359 356 380 C2' T E 459 381 378 400 C2' C E 460 401 398 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G D 415 OK 7 10 11 31 C3' A D 416 OK 29 32 33 52 C3' C D 417 OK 50 53 54 71 C3' G D 418 OK 69 72 73 93 C3' T D 419 OK 91 94 95 113 C3' T D 420 OK 111 114 115 133 C3' T D 421 OK 131 134 135 153 C3' T D 422 OK 151 154 155 173 C3' C D 423 OK 171 174 175 192 C3' G D 424 OK 190 193 194 212 C3' C E 451 OK 210 213 214 231 C3' G E 452 OK 229 232 233 253 C3' A E 453 OK 251 254 255 274 C3' A E 454 OK 272 275 276 295 C3' A E 455 OK 293 296 297 316 C3' A E 456 OK 314 317 318 337 C3' C E 457 OK 335 338 339 356 C3' G E 458 OK 354 357 358 378 C3' T E 459 OK 376 379 380 398 C3' C E 460 OK 396 399 400 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G D 415 OK 9 6 8 29 C4' A D 416 OK 31 28 30 50 C4' C D 417 OK 52 49 51 69 C4' G D 418 OK 71 68 70 91 C4' T D 419 OK 93 90 92 111 C4' T D 420 OK 113 110 112 131 C4' T D 421 OK 133 130 132 151 C4' T D 422 OK 153 150 152 171 C4' C D 423 OK 173 170 172 190 C4' G D 424 OK 192 189 191 210 C4' C E 451 OK 212 209 211 229 C4' G E 452 OK 231 228 230 251 C4' A E 453 OK 253 250 252 272 C4' A E 454 OK 274 271 273 293 C4' A E 455 OK 295 292 294 314 C4' A E 456 OK 316 313 315 335 C4' C E 457 OK 337 334 336 354 C4' G E 458 OK 356 353 355 376 C4' T E 459 OK 378 375 377 396 C4' C E 460 OK 398 395 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G D 415 5 7 28 C5' A D 416 27 29 49 C5' C D 417 48 50 68 C5' G D 418 67 69 90 C5' T D 419 89 91 110 C5' T D 420 109 111 130 C5' T D 421 129 131 150 C5' T D 422 149 151 170 C5' C D 423 169 171 189 C5' G D 424 188 190 209 C5' C E 451 208 210 228 C5' G E 452 227 229 250 C5' A E 453 249 251 271 C5' A E 454 270 272 292 C5' A E 455 291 293 313 C5' A E 456 312 314 334 C5' C E 457 333 335 353 C5' G E 458 352 354 375 C5' T E 459 374 376 395 C5' C E 460 394 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G D 415 OK OK 3 4 5 24 P A D 416 distorted distorted 10 25 26 27 45 P C D 417 distorted distorted 32 46 47 48 64 P G D 418 distorted distorted 53 65 66 67 86 P T D 419 distorted distorted 72 87 88 89 106 P T D 420 distorted distorted 94 107 108 109 126 P T D 421 distorted distorted 114 127 128 129 146 P T D 422 distorted distorted 134 147 148 149 166 P C D 423 distorted distorted 154 167 168 169 185 P G D 424 distorted distorted 174 186 187 188 224 P G E 452 distorted distorted 213 225 226 227 246 P A E 453 distorted distorted 232 247 248 249 267 P A E 454 distorted distorted 254 268 269 270 288 P A E 455 distorted distorted 275 289 290 291 309 P A E 456 distorted distorted 296 310 311 312 330 P C E 457 distorted distorted 317 331 332 333 349 P G E 458 distorted distorted 338 350 351 352 371 P T E 459 distorted distorted 357 372 373 374 391 P C E 460 distorted distorted 379 392 393 394 ---------------------------------------------------------------------------------