ID code: '1CQT' 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' --------------------------------------------------------------------------------- 11 C1' G M 202 beta 7 12 10 33 C1' T M 203 beta 29 34 32 53 C1' A M 204 beta 49 54 52 74 C1' T M 205 beta 70 75 73 94 C1' G M 206 beta 90 95 93 116 C1' C M 207 beta 112 117 115 135 C1' A M 208 beta 131 136 134 156 C1' A M 209 beta 152 157 155 177 C1' A M 210 beta 173 178 176 198 C1' T M 211 beta 194 199 197 218 C1' A M 212 beta 214 219 217 239 C1' A M 213 beta 235 240 238 260 C1' G M 214 beta 256 261 259 282 C1' G M 215 beta 278 283 281 305 C1' C N 217 beta 301 306 304 324 C1' C N 218 beta 320 325 323 343 C1' T N 219 beta 339 344 342 363 C1' T N 220 beta 359 364 362 383 C1' A N 221 beta 379 384 382 404 C1' T N 222 beta 400 405 403 424 C1' T N 223 beta 420 425 423 444 C1' T N 224 beta 440 445 443 464 C1' G N 225 beta 460 465 463 486 C1' C N 226 beta 482 487 485 505 C1' A N 227 beta 501 506 504 526 C1' T N 228 beta 522 527 525 546 C1' A N 229 beta 542 547 545 567 C1' C N 230 beta 563 568 566 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G M 202 11 8 32 C2' T M 203 33 30 52 C2' A M 204 53 50 73 C2' T M 205 74 71 93 C2' G M 206 94 91 115 C2' C M 207 116 113 134 C2' A M 208 135 132 155 C2' A M 209 156 153 176 C2' A M 210 177 174 197 C2' T M 211 198 195 217 C2' A M 212 218 215 238 C2' A M 213 239 236 259 C2' G M 214 260 257 281 C2' G M 215 282 279 304 C2' C N 217 305 302 323 C2' C N 218 324 321 342 C2' T N 219 343 340 362 C2' T N 220 363 360 382 C2' A N 221 383 380 403 C2' T N 222 404 401 423 C2' T N 223 424 421 443 C2' T N 224 444 441 463 C2' G N 225 464 461 485 C2' C N 226 486 483 504 C2' A N 227 505 502 525 C2' T N 228 526 523 545 C2' A N 229 546 543 566 C2' C N 230 567 564 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G M 202 OK 6 9 10 30 C3' T M 203 OK 28 31 32 50 C3' A M 204 OK 48 51 52 71 C3' T M 205 OK 69 72 73 91 C3' G M 206 OK 89 92 93 113 C3' C M 207 OK 111 114 115 132 C3' A M 208 OK 130 133 134 153 C3' A M 209 OK 151 154 155 174 C3' A M 210 OK 172 175 176 195 C3' T M 211 OK 193 196 197 215 C3' A M 212 OK 213 216 217 236 C3' A M 213 OK 234 237 238 257 C3' G M 214 OK 255 258 259 279 C3' G M 215 OK 277 280 281 302 C3' C N 217 OK 300 303 304 321 C3' C N 218 OK 319 322 323 340 C3' T N 219 OK 338 341 342 360 C3' T N 220 OK 358 361 362 380 C3' A N 221 OK 378 381 382 401 C3' T N 222 OK 399 402 403 421 C3' T N 223 OK 419 422 423 441 C3' T N 224 OK 439 442 443 461 C3' G N 225 OK 459 462 463 483 C3' C N 226 OK 481 484 485 502 C3' A N 227 OK 500 503 504 523 C3' T N 228 OK 521 524 525 543 C3' A N 229 OK 541 544 545 564 C3' C N 230 OK 562 565 566 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G M 202 OK 8 5 7 28 C4' T M 203 OK 30 27 29 48 C4' A M 204 OK 50 47 49 69 C4' T M 205 OK 71 68 70 89 C4' G M 206 OK 91 88 90 111 C4' C M 207 OK 113 110 112 130 C4' A M 208 OK 132 129 131 151 C4' A M 209 OK 153 150 152 172 C4' A M 210 OK 174 171 173 193 C4' T M 211 OK 195 192 194 213 C4' A M 212 OK 215 212 214 234 C4' A M 213 OK 236 233 235 255 C4' G M 214 OK 257 254 256 277 C4' G M 215 OK 279 276 278 300 C4' C N 217 OK 302 299 301 319 C4' C N 218 OK 321 318 320 338 C4' T N 219 OK 340 337 339 358 C4' T N 220 OK 360 357 359 378 C4' A N 221 OK 380 377 379 399 C4' T N 222 OK 401 398 400 419 C4' T N 223 OK 421 418 420 439 C4' T N 224 OK 441 438 440 459 C4' G N 225 OK 461 458 460 481 C4' C N 226 OK 483 480 482 500 C4' A N 227 OK 502 499 501 521 C4' T N 228 OK 523 520 522 541 C4' A N 229 OK 543 540 542 562 C4' C N 230 OK 564 561 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G M 202 4 6 27 C5' T M 203 26 28 47 C5' A M 204 46 48 68 C5' T M 205 67 69 88 C5' G M 206 87 89 110 C5' C M 207 109 111 129 C5' A M 208 128 130 150 C5' A M 209 149 151 171 C5' A M 210 170 172 192 C5' T M 211 191 193 212 C5' A M 212 211 213 233 C5' A M 213 232 234 254 C5' G M 214 253 255 276 C5' G M 215 275 277 299 C5' C N 217 298 300 318 C5' C N 218 317 319 337 C5' T N 219 336 338 357 C5' T N 220 356 358 377 C5' A N 221 376 378 398 C5' T N 222 397 399 418 C5' T N 223 417 419 438 C5' T N 224 437 439 458 C5' G N 225 457 459 480 C5' C N 226 479 481 499 C5' A N 227 498 500 520 C5' T N 228 519 521 540 C5' A N 229 539 541 561 C5' C N 230 560 562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G M 202 distorted distorted 2 3 4 23 P T M 203 distorted distorted 9 24 25 26 43 P A M 204 distorted distorted 31 44 45 46 64 P T M 205 distorted distorted 51 65 66 67 84 P G M 206 distorted distorted 72 85 86 87 106 P C M 207 distorted distorted 92 107 108 109 125 P A M 208 distorted distorted 114 126 127 128 146 P A M 209 distorted distorted 133 147 148 149 167 P A M 210 distorted distorted 154 168 169 170 188 P T M 211 distorted distorted 175 189 190 191 208 P A M 212 distorted distorted 196 209 210 211 229 P A M 213 distorted distorted 216 230 231 232 250 P G M 214 distorted distorted 237 251 252 253 272 P G M 215 distorted distorted 258 273 274 275 295 P C N 217 distorted distorted 296 297 298 314 P C N 218 distorted distorted 303 315 316 317 333 P T N 219 distorted distorted 322 334 335 336 353 P T N 220 distorted distorted 341 354 355 356 373 P A N 221 distorted distorted 361 374 375 376 394 P T N 222 distorted distorted 381 395 396 397 414 P T N 223 distorted distorted 402 415 416 417 434 P T N 224 distorted distorted 422 435 436 437 454 P G N 225 distorted distorted 442 455 456 457 476 P C N 226 distorted distorted 462 477 478 479 495 P A N 227 distorted distorted 484 496 497 498 516 P T N 228 distorted distorted 503 517 518 519 536 P A N 229 distorted distorted 524 537 538 539 557 P C N 230 distorted distorted 544 558 559 560 ---------------------------------------------------------------------------------