ID code: '2TOB' 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' A A 4 alpha beta 4 26 10 7 43 C1' C A 5 alpha beta 38 58 44 41 74 C1' U A 6 alpha beta 69 89 75 72 104 C1' U A 7 alpha beta 99 119 105 102 134 C1' G A 8 alpha beta 129 152 135 132 168 C1' G A 9 alpha beta 163 186 169 166 202 C1' U A 10 alpha beta 197 217 203 200 232 C1' U A 11 alpha beta 227 247 233 230 262 C1' U A 12 alpha beta 257 277 263 260 292 C1' A A 13 alpha beta 287 309 293 290 325 C1' G A 14 alpha beta 320 343 326 323 359 C1' G A 15 alpha beta 354 377 360 357 393 C1' U A 16 alpha beta 388 408 394 391 423 C1' A A 17 alpha beta 418 440 424 421 456 C1' A A 18 alpha beta 451 473 457 454 489 C1' U A 19 alpha beta 484 504 490 487 519 C1' G A 20 alpha beta 514 537 520 517 553 C1' A A 21 alpha beta 548 570 554 551 586 C1' G A 22 alpha beta 581 604 587 584 620 C1' U A 23 alpha beta 615 636 621 618 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A A 4 OK OK 9 5 24 8 41 C2' C A 5 OK OK 43 39 56 42 72 C2' U A 6 OK OK 74 70 87 73 102 C2' U A 7 OK OK 104 100 117 103 132 C2' G A 8 OK OK 134 130 150 133 166 C2' G A 9 OK OK 168 164 184 167 200 C2' U A 10 OK OK 202 198 215 201 230 C2' U A 11 OK OK 232 228 245 231 260 C2' U A 12 OK OK 262 258 275 261 290 C2' A A 13 OK OK 292 288 307 291 323 C2' G A 14 OK OK 325 321 341 324 357 C2' G A 15 OK OK 359 355 375 358 391 C2' U A 16 OK OK 393 389 406 392 421 C2' A A 17 OK OK 423 419 438 422 454 C2' A A 18 OK OK 456 452 471 455 487 C2' U A 19 OK OK 489 485 502 488 517 C2' G A 20 OK OK 519 515 535 518 551 C2' A A 21 OK OK 553 549 568 552 584 C2' G A 22 OK OK 586 582 602 585 618 C2' U A 23 OK OK 620 616 634 619 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A A 4 OK OK 3 23 6 7 39 C3' C A 5 OK OK 37 55 40 41 70 C3' U A 6 OK OK 68 86 71 72 100 C3' U A 7 OK OK 98 116 101 102 130 C3' G A 8 OK OK 128 149 131 132 164 C3' G A 9 OK OK 162 183 165 166 198 C3' U A 10 OK OK 196 214 199 200 228 C3' U A 11 OK OK 226 244 229 230 258 C3' U A 12 OK OK 256 274 259 260 288 C3' A A 13 OK OK 286 306 289 290 321 C3' G A 14 OK OK 319 340 322 323 355 C3' G A 15 OK OK 353 374 356 357 389 C3' U A 16 OK OK 387 405 390 391 419 C3' A A 17 OK OK 417 437 420 421 452 C3' A A 18 OK OK 450 470 453 454 485 C3' U A 19 OK OK 483 501 486 487 515 C3' G A 20 OK OK 513 534 516 517 549 C3' A A 21 OK OK 547 567 550 551 582 C3' G A 22 OK OK 580 601 583 584 616 C3' U A 23 OK OK 614 632 617 618 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A A 4 OK OK 5 22 2 4 37 C4' C A 5 OK OK 39 54 36 38 68 C4' U A 6 OK OK 70 85 67 69 98 C4' U A 7 OK OK 100 115 97 99 128 C4' G A 8 OK OK 130 148 127 129 162 C4' G A 9 OK OK 164 182 161 163 196 C4' U A 10 OK OK 198 213 195 197 226 C4' U A 11 OK OK 228 243 225 227 256 C4' U A 12 OK OK 258 273 255 257 286 C4' A A 13 OK OK 288 305 285 287 319 C4' G A 14 OK OK 321 339 318 320 353 C4' G A 15 OK OK 355 373 352 354 387 C4' U A 16 OK OK 389 404 386 388 417 C4' A A 17 OK OK 419 436 416 418 450 C4' A A 18 OK OK 452 469 449 451 483 C4' U A 19 OK OK 485 500 482 484 513 C4' G A 20 OK OK 515 533 512 514 547 C4' A A 21 OK OK 549 566 546 548 580 C4' G A 22 OK OK 582 600 579 581 614 C4' U A 23 OK OK 616 631 613 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A A 4 OK OK 1 20 21 3 36 C5' C A 5 OK OK 35 52 53 37 67 C5' U A 6 OK OK 66 83 84 68 97 C5' U A 7 OK OK 96 113 114 98 127 C5' G A 8 OK OK 126 146 147 128 161 C5' G A 9 OK OK 160 180 181 162 195 C5' U A 10 OK OK 194 211 212 196 225 C5' U A 11 OK OK 224 241 242 226 255 C5' U A 12 OK OK 254 271 272 256 285 C5' A A 13 OK OK 284 303 304 286 318 C5' G A 14 OK OK 317 337 338 319 352 C5' G A 15 OK OK 351 371 372 353 386 C5' U A 16 OK OK 385 402 403 387 416 C5' A A 17 OK OK 415 434 435 417 449 C5' A A 18 OK OK 448 467 468 450 482 C5' U A 19 OK OK 481 498 499 483 512 C5' G A 20 OK OK 511 531 532 513 546 C5' A A 21 OK OK 545 564 565 547 579 C5' G A 22 OK OK 578 598 599 580 613 C5' U A 23 OK OK 612 629 630 614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P C A 5 distorted distorted 6 33 34 35 63 P U A 6 distorted distorted 40 64 65 66 93 P U A 7 distorted distorted 71 94 95 96 123 P G A 8 distorted distorted 101 124 125 126 157 P G A 9 distorted distorted 131 158 159 160 191 P U A 10 distorted distorted 165 192 193 194 221 P U A 11 distorted distorted 199 222 223 224 251 P U A 12 distorted distorted 229 252 253 254 281 P A A 13 distorted distorted 259 282 283 284 314 P G A 14 distorted distorted 289 315 316 317 348 P G A 15 distorted distorted 322 349 350 351 382 P U A 16 distorted distorted 356 383 384 385 412 P A A 17 distorted distorted 390 413 414 415 445 P A A 18 distorted distorted 420 446 447 448 478 P U A 19 distorted distorted 453 479 480 481 508 P G A 20 distorted distorted 486 509 510 511 542 P A A 21 distorted distorted 516 543 544 545 575 P G A 22 distorted distorted 550 576 577 578 609 P U A 23 distorted distorted 583 610 611 612 ---------------------------------------------------------------------------------