ID code: '1FEQ' 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 27 alpha beta 4 27 10 7 44 C1' C A 28 alpha beta 39 59 45 42 75 C1' A A 29 alpha beta 70 92 76 73 108 C1' G A 30 alpha beta 103 126 109 106 142 C1' A A 31 alpha beta 137 159 143 140 175 C1' C A 32 alpha beta 170 190 176 173 206 C1' U A 33 alpha beta 201 221 207 204 236 C1' U A 34 alpha beta 231 251 237 234 266 C1' U A 35 alpha beta 261 281 267 264 296 C1' U A 36 alpha beta 291 311 297 294 326 C1' T6A A 37 alpha beta 321 353 327 324 375 C1' A A 38 alpha beta 370 393 376 373 409 C1' U A 39 alpha beta 404 424 410 407 439 C1' C A 40 alpha beta 434 454 440 437 470 C1' U A 41 alpha beta 465 485 471 468 500 C1' G A 42 alpha beta 495 518 501 498 534 C1' C A 43 alpha beta 529 550 535 532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 27 OK OK 9 5 25 8 42 C2' C A 28 OK OK 44 40 57 43 73 C2' A A 29 OK OK 75 71 90 74 106 C2' G A 30 OK OK 108 104 124 107 140 C2' A A 31 OK OK 142 138 157 141 173 C2' C A 32 OK OK 175 171 188 174 204 C2' U A 33 OK OK 206 202 219 205 234 C2' U A 34 OK OK 236 232 249 235 264 C2' U A 35 OK OK 266 262 279 265 294 C2' U A 36 OK OK 296 292 309 295 324 C2' T6A A 37 OK OK 326 322 351 325 373 C2' A A 38 OK OK 375 371 391 374 407 C2' U A 39 OK OK 409 405 422 408 437 C2' C A 40 OK OK 439 435 452 438 468 C2' U A 41 OK OK 470 466 483 469 498 C2' G A 42 OK OK 500 496 516 499 532 C2' C A 43 OK OK 534 530 548 533 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 27 OK OK 3 24 6 7 40 C3' C A 28 OK OK 38 56 41 42 71 C3' A A 29 OK OK 69 89 72 73 104 C3' G A 30 OK OK 102 123 105 106 138 C3' A A 31 OK OK 136 156 139 140 171 C3' C A 32 OK OK 169 187 172 173 202 C3' U A 33 OK OK 200 218 203 204 232 C3' U A 34 OK OK 230 248 233 234 262 C3' U A 35 OK OK 260 278 263 264 292 C3' U A 36 OK OK 290 308 293 294 322 C3' T6A A 37 OK OK 320 350 323 324 371 C3' A A 38 OK OK 369 390 372 373 405 C3' U A 39 OK OK 403 421 406 407 435 C3' C A 40 OK OK 433 451 436 437 466 C3' U A 41 OK OK 464 482 467 468 496 C3' G A 42 OK OK 494 515 497 498 530 C3' C A 43 OK OK 528 546 531 532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 27 OK OK 5 23 2 4 38 C4' C A 28 OK OK 40 55 37 39 69 C4' A A 29 OK OK 71 88 68 70 102 C4' G A 30 OK OK 104 122 101 103 136 C4' A A 31 OK OK 138 155 135 137 169 C4' C A 32 OK OK 171 186 168 170 200 C4' U A 33 OK OK 202 217 199 201 230 C4' U A 34 OK OK 232 247 229 231 260 C4' U A 35 OK OK 262 277 259 261 290 C4' U A 36 OK OK 292 307 289 291 320 C4' T6A A 37 OK OK 322 349 319 321 369 C4' A A 38 OK OK 371 389 368 370 403 C4' U A 39 OK OK 405 420 402 404 433 C4' C A 40 OK OK 435 450 432 434 464 C4' U A 41 OK OK 466 481 463 465 494 C4' G A 42 OK OK 496 514 493 495 528 C4' C A 43 OK OK 530 545 527 529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 27 OK OK 1 21 22 3 37 C5' C A 28 OK OK 36 53 54 38 68 C5' A A 29 OK OK 67 86 87 69 101 C5' G A 30 OK OK 100 120 121 102 135 C5' A A 31 OK OK 134 153 154 136 168 C5' C A 32 OK OK 167 184 185 169 199 C5' U A 33 OK OK 198 215 216 200 229 C5' U A 34 OK OK 228 245 246 230 259 C5' U A 35 OK OK 258 275 276 260 289 C5' U A 36 OK OK 288 305 306 290 319 C5' T6A A 37 OK OK 318 347 348 320 368 C5' A A 38 OK OK 367 387 388 369 402 C5' U A 39 OK OK 401 418 419 403 432 C5' C A 40 OK OK 431 448 449 433 463 C5' U A 41 OK OK 462 479 480 464 493 C5' G A 42 OK OK 492 512 513 494 527 C5' C A 43 OK OK 526 543 544 528 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 28 distorted distorted 6 34 35 36 64 P A A 29 distorted distorted 41 65 66 67 97 P G A 30 distorted distorted 72 98 99 100 131 P A A 31 distorted distorted 105 132 133 134 164 P C A 32 distorted distorted 139 165 166 167 195 P U A 33 distorted distorted 172 196 197 198 225 P U A 34 distorted distorted 203 226 227 228 255 P U A 35 distorted distorted 233 256 257 258 285 P U A 36 distorted distorted 263 286 287 288 315 P T6A A 37 distorted distorted 293 316 317 318 364 P A A 38 distorted distorted 323 365 366 367 398 P U A 39 distorted distorted 372 399 400 401 428 P C A 40 distorted distorted 406 429 430 431 459 P U A 41 distorted distorted 436 460 461 462 489 P G A 42 distorted distorted 467 490 491 492 523 P C A 43 distorted distorted 497 524 525 526 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