ID code: '1Z30' 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' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' G A 8 alpha beta 229 252 235 232 268 C1' U A 9 alpha beta 263 283 269 266 298 C1' U A 10 alpha beta 293 313 299 296 328 C1' A A 11 alpha beta 323 345 329 326 361 C1' G A 12 alpha beta 356 379 362 359 395 C1' A A 13 alpha beta 390 412 396 393 428 C1' A A 14 alpha beta 423 445 429 426 461 C1' C A 15 alpha beta 456 476 462 459 492 C1' G A 16 alpha beta 487 510 493 490 526 C1' U A 17 alpha beta 521 541 527 524 556 C1' C A 18 alpha beta 551 571 557 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' U A 6 OK OK 173 169 186 172 201 C2' C A 7 OK OK 203 199 216 202 232 C2' G A 8 OK OK 234 230 250 233 266 C2' U A 9 OK OK 268 264 281 267 296 C2' U A 10 OK OK 298 294 311 297 326 C2' A A 11 OK OK 328 324 343 327 359 C2' G A 12 OK OK 361 357 377 360 393 C2' A A 13 OK OK 395 391 410 394 426 C2' A A 14 OK OK 428 424 443 427 459 C2' C A 15 OK OK 461 457 474 460 490 C2' G A 16 OK OK 492 488 508 491 524 C2' U A 17 OK OK 526 522 539 525 554 C2' C A 18 OK OK 556 552 569 555 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' U A 6 OK OK 167 185 170 171 199 C3' C A 7 OK OK 197 215 200 201 230 C3' G A 8 OK OK 228 249 231 232 264 C3' U A 9 OK OK 262 280 265 266 294 C3' U A 10 OK OK 292 310 295 296 324 C3' A A 11 OK OK 322 342 325 326 357 C3' G A 12 OK OK 355 376 358 359 391 C3' A A 13 OK OK 389 409 392 393 424 C3' A A 14 OK OK 422 442 425 426 457 C3' C A 15 OK OK 455 473 458 459 488 C3' G A 16 OK OK 486 507 489 490 522 C3' U A 17 OK OK 520 538 523 524 552 C3' C A 18 OK OK 550 568 553 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' U A 6 OK OK 169 184 166 168 197 C4' C A 7 OK OK 199 214 196 198 228 C4' G A 8 OK OK 230 248 227 229 262 C4' U A 9 OK OK 264 279 261 263 292 C4' U A 10 OK OK 294 309 291 293 322 C4' A A 11 OK OK 324 341 321 323 355 C4' G A 12 OK OK 357 375 354 356 389 C4' A A 13 OK OK 391 408 388 390 422 C4' A A 14 OK OK 424 441 421 423 455 C4' C A 15 OK OK 457 472 454 456 486 C4' G A 16 OK OK 488 506 485 487 520 C4' U A 17 OK OK 522 537 519 521 550 C4' C A 18 OK OK 552 567 549 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' U A 6 OK OK 165 182 183 167 196 C5' C A 7 OK OK 195 212 213 197 227 C5' G A 8 OK OK 226 246 247 228 261 C5' U A 9 OK OK 260 277 278 262 291 C5' U A 10 OK OK 290 307 308 292 321 C5' A A 11 OK OK 320 339 340 322 354 C5' G A 12 OK OK 353 373 374 355 388 C5' A A 13 OK OK 387 406 407 389 421 C5' A A 14 OK OK 420 439 440 422 454 C5' C A 15 OK OK 453 470 471 455 485 C5' G A 16 OK OK 484 504 505 486 519 C5' U A 17 OK OK 518 535 536 520 549 C5' C A 18 OK OK 548 565 566 550 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P U A 6 distorted distorted 140 163 164 165 192 P C A 7 distorted distorted 170 193 194 195 223 P G A 8 distorted distorted 200 224 225 226 257 P U A 9 distorted distorted 231 258 259 260 287 P U A 10 distorted distorted 265 288 289 290 317 P A A 11 distorted distorted 295 318 319 320 350 P G A 12 distorted distorted 325 351 352 353 384 P A A 13 distorted distorted 358 385 386 387 417 P A A 14 distorted distorted 392 418 419 420 450 P C A 15 distorted distorted 425 451 452 453 481 P G A 16 distorted distorted 458 482 483 484 515 P U A 17 distorted distorted 489 516 517 518 545 P C A 18 distorted distorted 523 546 547 548 ---------------------------------------------------------------------------------