ID code: '1ATO' 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' A A 4 alpha beta 104 126 110 107 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' C A 6 alpha beta 168 188 174 171 204 C1' U A 7 alpha beta 199 219 205 202 234 C1' C A 8 alpha beta 229 249 235 232 265 C1' C A 9 alpha beta 260 280 266 263 296 C1' U A 10 alpha beta 291 311 297 294 326 C1' C A 11 alpha beta 321 341 327 324 357 C1' G A 12 alpha beta 352 375 358 355 391 C1' C A 13 alpha beta 386 406 392 389 422 C1' G A 14 alpha beta 417 440 423 420 456 C1' G A 15 alpha beta 451 474 457 454 490 C1' U A 16 alpha beta 485 505 491 488 520 C1' G A 17 alpha beta 515 538 521 518 554 C1' C A 18 alpha beta 549 569 555 552 585 C1' C A 19 alpha beta 580 601 586 583 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 109 105 124 108 140 C2' C A 5 OK OK 142 138 155 141 171 C2' C A 6 OK OK 173 169 186 172 202 C2' U A 7 OK OK 204 200 217 203 232 C2' C A 8 OK OK 234 230 247 233 263 C2' C A 9 OK OK 265 261 278 264 294 C2' U A 10 OK OK 296 292 309 295 324 C2' C A 11 OK OK 326 322 339 325 355 C2' G A 12 OK OK 357 353 373 356 389 C2' C A 13 OK OK 391 387 404 390 420 C2' G A 14 OK OK 422 418 438 421 454 C2' G A 15 OK OK 456 452 472 455 488 C2' U A 16 OK OK 490 486 503 489 518 C2' G A 17 OK OK 520 516 536 519 552 C2' C A 18 OK OK 554 550 567 553 583 C2' C A 19 OK OK 585 581 599 584 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 103 123 106 107 138 C3' C A 5 OK OK 136 154 139 140 169 C3' C A 6 OK OK 167 185 170 171 200 C3' U A 7 OK OK 198 216 201 202 230 C3' C A 8 OK OK 228 246 231 232 261 C3' C A 9 OK OK 259 277 262 263 292 C3' U A 10 OK OK 290 308 293 294 322 C3' C A 11 OK OK 320 338 323 324 353 C3' G A 12 OK OK 351 372 354 355 387 C3' C A 13 OK OK 385 403 388 389 418 C3' G A 14 OK OK 416 437 419 420 452 C3' G A 15 OK OK 450 471 453 454 486 C3' U A 16 OK OK 484 502 487 488 516 C3' G A 17 OK OK 514 535 517 518 550 C3' C A 18 OK OK 548 566 551 552 581 C3' C A 19 OK OK 579 597 582 583 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 105 122 102 104 136 C4' C A 5 OK OK 138 153 135 137 167 C4' C A 6 OK OK 169 184 166 168 198 C4' U A 7 OK OK 200 215 197 199 228 C4' C A 8 OK OK 230 245 227 229 259 C4' C A 9 OK OK 261 276 258 260 290 C4' U A 10 OK OK 292 307 289 291 320 C4' C A 11 OK OK 322 337 319 321 351 C4' G A 12 OK OK 353 371 350 352 385 C4' C A 13 OK OK 387 402 384 386 416 C4' G A 14 OK OK 418 436 415 417 450 C4' G A 15 OK OK 452 470 449 451 484 C4' U A 16 OK OK 486 501 483 485 514 C4' G A 17 OK OK 516 534 513 515 548 C4' C A 18 OK OK 550 565 547 549 579 C4' C A 19 OK OK 581 596 578 580 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 101 120 121 103 135 C5' C A 5 OK OK 134 151 152 136 166 C5' C A 6 OK OK 165 182 183 167 197 C5' U A 7 OK OK 196 213 214 198 227 C5' C A 8 OK OK 226 243 244 228 258 C5' C A 9 OK OK 257 274 275 259 289 C5' U A 10 OK OK 288 305 306 290 319 C5' C A 11 OK OK 318 335 336 320 350 C5' G A 12 OK OK 349 369 370 351 384 C5' C A 13 OK OK 383 400 401 385 415 C5' G A 14 OK OK 414 434 435 416 449 C5' G A 15 OK OK 448 468 469 450 483 C5' U A 16 OK OK 482 499 500 484 513 C5' G A 17 OK OK 512 532 533 514 547 C5' C A 18 OK OK 546 563 564 548 578 C5' C A 19 OK OK 577 594 595 579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 99 100 101 131 P C A 5 distorted distorted 106 132 133 134 162 P C A 6 distorted distorted 139 163 164 165 193 P U A 7 distorted distorted 170 194 195 196 223 P C A 8 distorted distorted 201 224 225 226 254 P C A 9 distorted distorted 231 255 256 257 285 P U A 10 distorted distorted 262 286 287 288 315 P C A 11 distorted distorted 293 316 317 318 346 P G A 12 distorted distorted 323 347 348 349 380 P C A 13 distorted distorted 354 381 382 383 411 P G A 14 distorted distorted 388 412 413 414 445 P G A 15 distorted distorted 419 446 447 448 479 P U A 16 distorted distorted 453 480 481 482 509 P G A 17 distorted distorted 487 510 511 512 543 P C A 18 distorted distorted 517 544 545 546 574 P C A 19 distorted distorted 551 575 576 577 ---------------------------------------------------------------------------------