ID code: '1SLP' 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' U A 8 alpha beta 4 24 10 7 40 C1' U A 9 alpha beta 35 55 41 38 70 C1' A A 10 alpha beta 65 87 71 68 103 C1' C A 11 alpha beta 98 118 104 101 134 C1' C A 12 alpha beta 129 149 135 132 165 C1' C A 13 alpha beta 160 180 166 163 196 C1' A A 14 alpha beta 191 213 197 194 229 C1' A A 15 alpha beta 224 246 230 227 262 C1' G A 16 alpha beta 257 280 263 260 296 C1' U A 17 alpha beta 291 311 297 294 326 C1' U A 18 alpha beta 321 341 327 324 356 C1' U A 19 alpha beta 351 371 357 354 386 C1' G A 20 alpha beta 381 404 387 384 420 C1' A A 21 alpha beta 415 437 421 418 453 C1' G A 22 alpha beta 448 471 454 451 487 C1' G A 23 alpha beta 482 505 488 485 521 C1' U A 24 alpha beta 516 536 522 519 551 C1' A A 25 alpha beta 546 568 552 549 584 C1' A A 26 alpha beta 579 602 585 582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 8 OK OK 9 5 22 8 38 C2' U A 9 OK OK 40 36 53 39 68 C2' A A 10 OK OK 70 66 85 69 101 C2' C A 11 OK OK 103 99 116 102 132 C2' C A 12 OK OK 134 130 147 133 163 C2' C A 13 OK OK 165 161 178 164 194 C2' A A 14 OK OK 196 192 211 195 227 C2' A A 15 OK OK 229 225 244 228 260 C2' G A 16 OK OK 262 258 278 261 294 C2' U A 17 OK OK 296 292 309 295 324 C2' U A 18 OK OK 326 322 339 325 354 C2' U A 19 OK OK 356 352 369 355 384 C2' G A 20 OK OK 386 382 402 385 418 C2' A A 21 OK OK 420 416 435 419 451 C2' G A 22 OK OK 453 449 469 452 485 C2' G A 23 OK OK 487 483 503 486 519 C2' U A 24 OK OK 521 517 534 520 549 C2' A A 25 OK OK 551 547 566 550 582 C2' A A 26 OK OK 584 580 600 583 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 8 OK OK 3 21 6 7 36 C3' U A 9 OK OK 34 52 37 38 66 C3' A A 10 OK OK 64 84 67 68 99 C3' C A 11 OK OK 97 115 100 101 130 C3' C A 12 OK OK 128 146 131 132 161 C3' C A 13 OK OK 159 177 162 163 192 C3' A A 14 OK OK 190 210 193 194 225 C3' A A 15 OK OK 223 243 226 227 258 C3' G A 16 OK OK 256 277 259 260 292 C3' U A 17 OK OK 290 308 293 294 322 C3' U A 18 OK OK 320 338 323 324 352 C3' U A 19 OK OK 350 368 353 354 382 C3' G A 20 OK OK 380 401 383 384 416 C3' A A 21 OK OK 414 434 417 418 449 C3' G A 22 OK OK 447 468 450 451 483 C3' G A 23 OK OK 481 502 484 485 517 C3' U A 24 OK OK 515 533 518 519 547 C3' A A 25 OK OK 545 565 548 549 580 C3' A A 26 OK OK 578 598 581 582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 8 OK OK 5 20 2 4 34 C4' U A 9 OK OK 36 51 33 35 64 C4' A A 10 OK OK 66 83 63 65 97 C4' C A 11 OK OK 99 114 96 98 128 C4' C A 12 OK OK 130 145 127 129 159 C4' C A 13 OK OK 161 176 158 160 190 C4' A A 14 OK OK 192 209 189 191 223 C4' A A 15 OK OK 225 242 222 224 256 C4' G A 16 OK OK 258 276 255 257 290 C4' U A 17 OK OK 292 307 289 291 320 C4' U A 18 OK OK 322 337 319 321 350 C4' U A 19 OK OK 352 367 349 351 380 C4' G A 20 OK OK 382 400 379 381 414 C4' A A 21 OK OK 416 433 413 415 447 C4' G A 22 OK OK 449 467 446 448 481 C4' G A 23 OK OK 483 501 480 482 515 C4' U A 24 OK OK 517 532 514 516 545 C4' A A 25 OK OK 547 564 544 546 578 C4' A A 26 OK OK 580 597 577 579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 8 OK OK 1 18 19 3 33 C5' U A 9 OK OK 32 49 50 34 63 C5' A A 10 OK OK 62 81 82 64 96 C5' C A 11 OK OK 95 112 113 97 127 C5' C A 12 OK OK 126 143 144 128 158 C5' C A 13 OK OK 157 174 175 159 189 C5' A A 14 OK OK 188 207 208 190 222 C5' A A 15 OK OK 221 240 241 223 255 C5' G A 16 OK OK 254 274 275 256 289 C5' U A 17 OK OK 288 305 306 290 319 C5' U A 18 OK OK 318 335 336 320 349 C5' U A 19 OK OK 348 365 366 350 379 C5' G A 20 OK OK 378 398 399 380 413 C5' A A 21 OK OK 412 431 432 414 446 C5' G A 22 OK OK 445 465 466 447 480 C5' G A 23 OK OK 479 499 500 481 514 C5' U A 24 OK OK 513 530 531 515 544 C5' A A 25 OK OK 543 562 563 545 577 C5' A A 26 OK OK 576 595 596 578 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 9 distorted distorted 6 30 31 32 59 P A A 10 distorted distorted 37 60 61 62 92 P C A 11 distorted distorted 67 93 94 95 123 P C A 12 distorted distorted 100 124 125 126 154 P C A 13 distorted distorted 131 155 156 157 185 P A A 14 distorted distorted 162 186 187 188 218 P A A 15 distorted distorted 193 219 220 221 251 P G A 16 distorted distorted 226 252 253 254 285 P U A 17 distorted distorted 259 286 287 288 315 P U A 18 distorted distorted 293 316 317 318 345 P U A 19 distorted distorted 323 346 347 348 375 P G A 20 distorted distorted 353 376 377 378 409 P A A 21 distorted distorted 383 410 411 412 442 P G A 22 distorted distorted 417 443 444 445 476 P G A 23 distorted distorted 450 477 478 479 510 P U A 24 distorted distorted 484 511 512 513 540 P A A 25 distorted distorted 518 541 542 543 573 P A A 26 distorted distorted 548 574 575 576 ---------------------------------------------------------------------------------