ID code: '1Q75' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' C A 5 alpha beta 134 154 140 137 170 C1' U A 6 alpha beta 165 185 171 168 200 C1' C A 7 alpha beta 195 215 201 198 231 C1' A A 8 alpha beta 226 248 232 229 264 C1' G A 9 alpha beta 259 282 265 262 298 C1' U A 10 alpha beta 293 313 299 296 328 C1' G A 11 alpha beta 323 346 329 326 362 C1' A A 12 alpha beta 357 379 363 360 395 C1' G A 13 alpha beta 390 413 396 393 429 C1' C A 14 alpha beta 424 444 430 427 460 C1' C A 15 alpha beta 455 476 461 458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' C A 5 OK OK 139 135 152 138 168 C2' U A 6 OK OK 170 166 183 169 198 C2' C A 7 OK OK 200 196 213 199 229 C2' A A 8 OK OK 231 227 246 230 262 C2' G A 9 OK OK 264 260 280 263 296 C2' U A 10 OK OK 298 294 311 297 326 C2' G A 11 OK OK 328 324 344 327 360 C2' A A 12 OK OK 362 358 377 361 393 C2' G A 13 OK OK 395 391 411 394 427 C2' C A 14 OK OK 429 425 442 428 458 C2' C A 15 OK OK 460 456 474 459 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' C A 5 OK OK 133 151 136 137 166 C3' U A 6 OK OK 164 182 167 168 196 C3' C A 7 OK OK 194 212 197 198 227 C3' A A 8 OK OK 225 245 228 229 260 C3' G A 9 OK OK 258 279 261 262 294 C3' U A 10 OK OK 292 310 295 296 324 C3' G A 11 OK OK 322 343 325 326 358 C3' A A 12 OK OK 356 376 359 360 391 C3' G A 13 OK OK 389 410 392 393 425 C3' C A 14 OK OK 423 441 426 427 456 C3' C A 15 OK OK 454 472 457 458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' C A 5 OK OK 135 150 132 134 164 C4' U A 6 OK OK 166 181 163 165 194 C4' C A 7 OK OK 196 211 193 195 225 C4' A A 8 OK OK 227 244 224 226 258 C4' G A 9 OK OK 260 278 257 259 292 C4' U A 10 OK OK 294 309 291 293 322 C4' G A 11 OK OK 324 342 321 323 356 C4' A A 12 OK OK 358 375 355 357 389 C4' G A 13 OK OK 391 409 388 390 423 C4' C A 14 OK OK 425 440 422 424 454 C4' C A 15 OK OK 456 471 453 455 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' C A 5 OK OK 131 148 149 133 163 C5' U A 6 OK OK 162 179 180 164 193 C5' C A 7 OK OK 192 209 210 194 224 C5' A A 8 OK OK 223 242 243 225 257 C5' G A 9 OK OK 256 276 277 258 291 C5' U A 10 OK OK 290 307 308 292 321 C5' G A 11 OK OK 320 340 341 322 355 C5' A A 12 OK OK 354 373 374 356 388 C5' G A 13 OK OK 387 407 408 389 422 C5' C A 14 OK OK 421 438 439 423 453 C5' C A 15 OK OK 452 469 470 454 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P C A 5 distorted distorted 106 129 130 131 159 P U A 6 distorted distorted 136 160 161 162 189 P C A 7 distorted distorted 167 190 191 192 220 P A A 8 distorted distorted 197 221 222 223 253 P G A 9 distorted distorted 228 254 255 256 287 P U A 10 distorted distorted 261 288 289 290 317 P G A 11 distorted distorted 295 318 319 320 351 P A A 12 distorted distorted 325 352 353 354 384 P G A 13 distorted distorted 359 385 386 387 418 P C A 14 distorted distorted 392 419 420 421 449 P C A 15 distorted distorted 426 450 451 452 ---------------------------------------------------------------------------------