ID code: '1ESY' 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 A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' C A 6 alpha beta 173 193 179 176 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' U A 10 alpha beta 302 322 308 305 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' A A 12 alpha beta 366 388 372 369 404 C1' G A 13 alpha beta 399 422 405 402 438 C1' U A 14 alpha beta 433 453 439 436 468 C1' A A 15 alpha beta 463 485 469 466 501 C1' C A 16 alpha beta 496 516 502 499 532 C1' G A 17 alpha beta 527 550 533 530 566 C1' C A 18 alpha beta 561 581 567 564 597 C1' C A 19 alpha beta 592 612 598 595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' C A 6 OK OK 178 174 191 177 207 C2' U A 7 OK OK 209 205 222 208 237 C2' G A 8 OK OK 239 235 255 238 271 C2' G A 9 OK OK 273 269 289 272 305 C2' U A 10 OK OK 307 303 320 306 335 C2' G A 11 OK OK 337 333 353 336 369 C2' A A 12 OK OK 371 367 386 370 402 C2' G A 13 OK OK 404 400 420 403 436 C2' U A 14 OK OK 438 434 451 437 466 C2' A A 15 OK OK 468 464 483 467 499 C2' C A 16 OK OK 501 497 514 500 530 C2' G A 17 OK OK 532 528 548 531 564 C2' C A 18 OK OK 566 562 579 565 595 C2' C A 19 OK OK 597 593 610 596 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' C A 6 OK OK 172 190 175 176 205 C3' U A 7 OK OK 203 221 206 207 235 C3' G A 8 OK OK 233 254 236 237 269 C3' G A 9 OK OK 267 288 270 271 303 C3' U A 10 OK OK 301 319 304 305 333 C3' G A 11 OK OK 331 352 334 335 367 C3' A A 12 OK OK 365 385 368 369 400 C3' G A 13 OK OK 398 419 401 402 434 C3' U A 14 OK OK 432 450 435 436 464 C3' A A 15 OK OK 462 482 465 466 497 C3' C A 16 OK OK 495 513 498 499 528 C3' G A 17 OK OK 526 547 529 530 562 C3' C A 18 OK OK 560 578 563 564 593 C3' C A 19 OK OK 591 609 594 595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' C A 6 OK OK 174 189 171 173 203 C4' U A 7 OK OK 205 220 202 204 233 C4' G A 8 OK OK 235 253 232 234 267 C4' G A 9 OK OK 269 287 266 268 301 C4' U A 10 OK OK 303 318 300 302 331 C4' G A 11 OK OK 333 351 330 332 365 C4' A A 12 OK OK 367 384 364 366 398 C4' G A 13 OK OK 400 418 397 399 432 C4' U A 14 OK OK 434 449 431 433 462 C4' A A 15 OK OK 464 481 461 463 495 C4' C A 16 OK OK 497 512 494 496 526 C4' G A 17 OK OK 528 546 525 527 560 C4' C A 18 OK OK 562 577 559 561 591 C4' C A 19 OK OK 593 608 590 592 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' C A 6 OK OK 170 187 188 172 202 C5' U A 7 OK OK 201 218 219 203 232 C5' G A 8 OK OK 231 251 252 233 266 C5' G A 9 OK OK 265 285 286 267 300 C5' U A 10 OK OK 299 316 317 301 330 C5' G A 11 OK OK 329 349 350 331 364 C5' A A 12 OK OK 363 382 383 365 397 C5' G A 13 OK OK 396 416 417 398 431 C5' U A 14 OK OK 430 447 448 432 461 C5' A A 15 OK OK 460 479 480 462 494 C5' C A 16 OK OK 493 510 511 495 525 C5' G A 17 OK OK 524 544 545 526 559 C5' C A 18 OK OK 558 575 576 560 590 C5' C A 19 OK OK 589 606 607 591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P G A 4 distorted distorted 77 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P C A 6 distorted distorted 142 168 169 170 198 P U A 7 distorted distorted 175 199 200 201 228 P G A 8 distorted distorted 206 229 230 231 262 P G A 9 distorted distorted 236 263 264 265 296 P U A 10 distorted distorted 270 297 298 299 326 P G A 11 distorted distorted 304 327 328 329 360 P A A 12 distorted distorted 334 361 362 363 393 P G A 13 distorted distorted 368 394 395 396 427 P U A 14 distorted distorted 401 428 429 430 457 P A A 15 distorted distorted 435 458 459 460 490 P C A 16 distorted distorted 465 491 492 493 521 P G A 17 distorted distorted 498 522 523 524 555 P C A 18 distorted distorted 529 556 557 558 586 P C A 19 distorted distorted 563 587 588 589 ---------------------------------------------------------------------------------