Protein secondary structure and environment assignment from atomic coordinates
SSEnvID is a program to recognize secondary structural elements in proteins from their atomic coordinates. It performs the same task as DSSP by Kabsch and Sander (1983) or STRIDE by Frishman & Argos (1995) with analyzing both hydrogen bond and mainchain dihedral angles, as well some probabilistic measures. SSEnvID also computes accessible surface area, polarity and environment classes as defined by Bowie, Luthy, Eisenberg (1991). SSEnvID's new feature is the probability (quality) of secondary structure assignment for each amino acids.
SSEnvID computes 3D protein characteristics which are used in structure prediction by measuring the compatibility between protein sequences and known protein structures.
SSEnvID output:
SSENVID - Protein secondary structure and environment assignment
from atomic coordinates (Softberry Inc., 2001)
Name of PDB file: file.pdb
Ch - Chain
ResN - PDB resnumber
Nam - Amino acid sequence in three letter code
Ab - Area Buried
Fp - Fraction Polar
SS - Secondary structure assignment (E-beta sheet, H,G,I-helices, T-turn)
PDBSS- Original PDB secondary structure assignment (if provided)
Env - Side-Chain Environment Class
Phi - Phi torsional angles
Psi - Psi torsional angles
PrHel- Probability of helix
PrBet- Probability of beta bridge
Ch ResN Nam Ab Fp SS PDBSS Env Phi Psi PrHel PrBet
B 260 LEU 67.7 0.62 C C P2 ? 127.6 0.00 0.00
B 261 PRO 16.6 0.88 C C E -78.3 -23.5 0.00 0.00
B 262 ASN 70.0 0.54 C C P1 -93.6 3.5 0.01 0.13
B 263 GLN 89.0 0.58 C C P2 -42.8 121.5 0.13 0.00
B 264 GLN 127.8 0.24 C C B1 -107.0 -31.4 0.33 0.00
B 265 PHE 179.6 0.35 C C B2 -97.4 135.7 0.35 0.00
B 266 GLY 25.7 0.60 C C E 82.8 13.8 0.35 0.00
B 267 VAL 112.0 0.55 C C P1 -115.9 131.5 0.35 0.00
B 268 SER 46.7 0.55 C C P1 -56.0 150.3 0.13 0.00
B 269 LEU 146.0 0.27 H H B1 -59.6 -28.1 0.97 0.01
B 270 GLN 43.7 0.81 H H P2 -69.5 -46.7 0.98 0.01
B 271 HIS 60.6 0.76 H H P2 -70.5 -29.9 1.00 0.00
B 272 LEU 145.2 0.38 H H B2 -64.2 -40.2 1.00 0.00
B 273 GLN 76.3 0.68 H H P2 -76.3 -30.5 1.00 0.01
B 274 GLU 49.2 0.70 H H P2 -63.8 -34.8 1.00 0.01
B 275 LYS 116.1 0.59 T C B3 -95.9 15.3 0.25 0.00
B 276 ASN 79.5 0.70 C C P2 -117.9 124.0 0.26 0.00
B 277 PRO 37.7 0.90 C C E -61.1 -27.5 0.26 0.00
B 278 GLU 46.4 0.76 C C P2 -94.8 161.2 0.26 0.00
B 279 GLN 15.3 0.75 C C E -88.7 92.5 0.26 0.00
B 280 GLU 95.6 0.65 C C P2 -119.1 90.1 0.26 0.00
B 281 PRO 39.4 0.57 C C E -66.9 1.4 0.13 0.00
B 282 ILE 130.2 0.28 C C B1 -129.1 116.5 0.13 0.00
B 283 PRO 114.3 0.26 C C B1 -57.8 153.7 0.13 0.00
B 284 ILE 110.8 0.70 H H P2 -57.9 -40.5 0.99 0.09
B 285 VAL 130.0 0.18 H H B1 -61.5 -39.2 0.99 0.09
B 286 LEU 149.0 0.18 H H B1 -74.4 -42.5 0.99 0.09
B 287 ARG 125.8 0.53 H H B3 -56.0 -50.5 0.99 0.07
B 288 GLU 95.3 0.51 H H P1 -70.2 -47.9 0.99 0.09
B 289 THR 113.0 0.19 H H P1 -62.3 -40.9 0.99 0.09
B 290 VAL 126.6 0.20 H H B1 -64.9 -49.6 0.99 0.09
B 291 ALA 11.9 0.70 H H E -54.5 -44.4 0.99 0.07
B 292 TYR 162.0 0.47 H H B3 -68.5 -45.3 0.99 0.17
B 293 LEU 153.4 0.18 H H B1 -60.0 -46.4 0.99 0.16
B 294 GLN 84.9 0.49 H H P1 -77.1 14.1 0.96 0.01
B 295 ALA 26.5 0.76 H H E -125.2 -13.3 0.96 0.17
B 296 HIS 70.8 0.66 H H P2 -139.3 -13.4 0.96 0.12
B 297 ALA 69.3 0.30 C C P1 -125.9 18.6 0.27 0.16
B 298 LEU 106.2 0.58 T C P2 -62.5 -15.5 0.27 0.01
B 299 THR 49.2 0.64 T C P2 -128.5 24.3 0.27 0.00
B 300 THR 88.2 0.47 C C P1 -81.7 121.5 0.25 0.00
B 301 GLU 56.9 0.75 T C P2 -53.2 116.2 0.25 0.16
B 302 GLY 32.4 0.34 T C E 66.9 40.3 0.25 0.07
B 303 ILE 156.9 0.31 T C B1 -68.4 126.8 0.23 0.00
B 304 PHE 189.0 0.08 T C B1 88.0 -4.6 0.23 0.00
B 305 ALA 38.6 0.43 T C E -106.8 -22.1 0.23 0.00
B 306 ARG 10.7 0.79 C C E -97.2 148.1 0.23 0.00
B 307 SER 3.1 0.82 C C E -86.6 170.0 0.13 0.00
B 308 ALA 64.3 0.46 C C P1 -131.8 171.0 0.13 0.00
B 309 ASN 16.5 0.72 C C E -57.6 111.1 0.33 0.00
B 310 THR 11.6 0.88 H H E -52.3 -45.7 0.99 0.01
B 311 GLN 38.0 0.81 H H E -66.3 -30.7 0.99 0.01
B 312 VAL 97.9 0.50 H H P1 -71.0 -32.7 0.99 0.01
B 313 VAL 111.1 0.35 H H P1 -71.4 -34.5 1.00 0.01
B 314 ARG 50.0 0.68 H H P2 -68.6 -28.3 1.00 0.01
B 315 GLU 65.8 0.63 H H P2 -70.8 -41.3 1.00 0.01
B 316 VAL 128.9 0.17 H H B1 -73.0 -32.4 1.00 0.01
B 317 GLN 121.2 0.34 H H B2 -65.4 -42.1 1.00 0.01
B 318 GLN 48.9 0.60 H H P2 -60.0 -44.6 1.00 0.09
B 319 LYS 138.4 0.49 H H B3 -59.4 -43.0 1.00 0.15
B 320 TYR 195.9 0.23 H H B1 -67.5 -38.0 0.98 0.14
B 321 ASN 107.2 0.45 H H P1 -75.9 -15.6 0.97 0.01
B 322 MET 111.1 0.57 T C P2 -94.3 -5.0 0.66 0.13
B 323 GLY 17.3 0.78 T C E 74.8 14.9 0.13 0.15
B 324 LEU 69.8 0.47 C C P1 -80.5 156.9 0.13 0.00
B 325 PRO 0.0 0.82 C C E -71.9 143.0 0.13 0.00
B 326 VAL 129.2 0.37 C C B2 -125.9 124.6 0.01 0.00
B 327 ASP 31.9 0.73 C C E -122.6 113.4 0.10 0.00
B 328 PHE 184.5 0.24 T C B1 -72.9 0.6 0.12 0.00
B 329 ASP 38.0 0.78 T C E -78.2 -39.7 0.12 0.00
B 330 GLN 62.8 0.71 C C P2 -52.8 -37.5 0.13 0.00
B 331 TYR 186.7 0.46 C C B3 -86.7 128.0 0.13 0.00
B 332 ASN 0.0 0.97 C C E -92.1 76.9 0.13 0.00
B 333 GLU 98.2 0.58 C C P2 -170.8 122.4 0.33 0.00
B 334 LEU 96.0 0.58 C C P2 -81.0 -15.2 0.75 0.00
B 335 HIS 150.8 0.50 H H B3 -83.6 -14.9 0.85 0.01
B 336 LEU 153.1 0.18 H H B1 -62.1 -54.3 0.99 0.09
B 337 PRO 123.0 0.24 H H B1 -65.5 -26.7 0.99 0.09
B 338 ALA 71.0 0.27 H H P1 -69.3 -43.2 0.99 0.01
B 339 VAL 105.9 0.41 H H P1 -70.4 -33.5 0.99 0.01
B 340 ILE 157.0 0.17 H H B1 -72.7 -35.3 0.99 0.09
B 341 LEU 153.1 0.13 H H B1 -61.4 -52.7 0.99 0.09
B 342 LYS 156.6 0.41 H H B2 -61.0 -40.4 1.00 0.01
B 343 THR 100.7 0.58 H H P2 -61.2 -37.0 1.00 0.01
B 344 PHE 186.9 0.18 H H B1 -61.6 -49.5 1.00 0.07
B 345 LEU 152.5 0.12 H H B1 -62.9 -39.0 1.00 0.01
B 346 ARG 70.2 0.68 H H P2 -67.6 -31.6 0.99 0.01
B 347 GLU 68.7 0.67 T C P2 -87.2 -3.1 0.49 0.01
B 348 LEU 149.8 0.41 C C B2 -62.7 133.5 0.13 0.00
B 349 PRO 73.5 0.62 C C P2 -52.6 -20.9 0.13 0.00
B 350 GLU 20.6 0.59 C C E -146.5 134.1 0.13 0.00
B 351 PRO 123.0 0.33 C C B2 -41.3 142.0 0.13 0.00
B 352 LEU 154.0 0.15 T C B1 -57.8 -33.7 0.26 0.16
B 353 LEU 150.8 0.13 T C B1 -83.1 -12.3 0.30 0.09
B 354 THR 88.2 0.35 C C P1 71.2 148.5 0.53 0.00
B 355 PHE 128.3 0.54 G H B3 -59.4 -18.6 0.97 0.00
B 356 ASP 0.0 0.85 G H E -73.3 -21.9 0.97 0.00
B 357 LEU 149.1 0.28 G H B1 -90.0 -1.4 0.97 0.00
B 358 TYR 150.2 0.28 H H B1 -54.1 -49.8 0.99 0.09
B 359 PRO 32.3 0.72 H H E -59.6 -44.2 0.99 0.09
B 360 HIS 123.2 0.34 H H B2 -57.6 -42.3 0.99 0.00
B 361 VAL 130.0 0.14 H H B1 -66.8 -54.0 0.99 0.00
B 362 VAL 72.6 0.49 H H P1 -63.0 -30.0 0.99 0.09
B 363 GLY 19.7 0.82 T C E -107.0 23.8 0.45 0.09
B 364 PHE 184.6 0.24 G H B1 -57.2 -49.0 0.99 0.00
B 365 LEU 69.8 0.64 G H P2 -67.7 -4.3 0.99 0.00
B 366 ASN 0.0 0.85 G H E -90.2 -7.1 0.99 0.00
B 367 ILE 101.6 0.51 C C P1 -87.8 131.6 0.26 0.00
B 368 ASP 0.0 0.84 C C E -56.5 136.7 0.26 0.16
B 369 GLU 0.0 0.88 G H E -44.0 -42.9 0.97 0.22
B 370 SER 0.3 0.83 G H E -65.5 -22.1 0.97 0.00
B 371 GLN 39.9 0.75 G H E -103.9 6.3 0.97 0.16
B 372 ARG 149.5 0.42 H H B2 -69.5 -42.3 0.97 0.22
B 373 VAL 90.4 0.45 H H P1 -67.7 -56.0 0.99 0.01
B 374 PRO 62.3 0.65 H H P2 -64.4 -30.0 0.99 0.01
B 375 ALA 46.8 0.48 H H P1 -66.8 -42.5 0.99 0.01
B 376 THR 113.0 0.15 H H P1 -70.0 -33.7 0.99 0.09
B 377 LEU 69.5 0.59 H H P2 -59.9 -42.0 0.99 0.01
B 378 GLN 0.0 0.78 H H E -71.4 -28.2 0.96 0.01
B 379 VAL 107.5 0.38 H H P1 -72.5 -44.8 0.96 0.01
B 380 LEU 152.9 0.19 H H B1 -61.6 -25.5 0.97 0.01
B 381 GLN 22.9 0.72 H H E -68.9 -21.1 0.97 0.01
B 382 THR 48.1 0.70 H H P2 -87.6 -9.3 0.97 0.00
B 383 LEU 152.0 0.33 C C B2 -70.9 145.4 0.13 0.00
B 384 PRO 54.6 0.69 C C P2 -63.1 142.8 0.13 0.00
B 385 GLU 31.1 0.77 H H E -48.1 -41.9 0.99 0.01
B 386 GLU 105.5 0.47 H H P1 -68.5 -33.9 0.99 0.01
B 387 ASN 113.8 0.24 H H P1 -69.6 -36.0 0.99 0.01
B 388 TYR 173.7 0.43 H H B2 -68.2 -48.4 0.99 0.01
B 389 GLN 98.2 0.52 H H P1 -63.3 -42.2 0.99 0.01
B 390 VAL 129.9 0.17 H H B1 -63.2 -39.3 0.99 0.01
B 391 LEU 154.0 0.11 H H B1 -69.1 -41.3 0.99 0.09
B 392 ARG 121.8 0.52 H H B3 -62.4 -44.1 0.99 0.09
B 393 PHE 100.0 0.47 H H P1 -62.9 -53.5 0.99 0.01
B 394 LEU 149.3 0.10 H H B1 -57.5 -58.1 1.00 0.09
B 395 THR 110.0 0.22 H H P1 -56.1 -35.9 1.00 0.09
B 396 ALA 41.2 0.74 H H P2 -64.2 -36.5 1.00 0.09
B 397 PHE 182.4 0.27 H H B1 -73.9 -40.1 1.00 0.14
B 398 LEU 149.0 0.08 H H B1 -64.9 -36.6 0.99 0.01
B 399 VAL 83.6 0.63 H H P2 -67.2 -18.3 0.99 0.01
B 400 GLN 49.5 0.62 H H P2 -76.6 -40.3 0.99 0.14
B 401 ILE 156.7 0.24 H H B1 -63.0 -43.7 0.99 0.01
B 402 SER 70.2 0.55 H H P1 -68.9 -28.6 0.96 0.01
B 403 ALA 13.4 0.85 H H E -59.6 -24.2 0.96 0.01
B 404 HIS 99.1 0.60 H H P2 -107.2 24.3 0.96 0.01
B 405 SER 65.9 0.60 H H P2 -59.7 -20.1 0.99 0.15
B 406 ASP 0.0 0.94 H H E -70.0 -25.1 0.99 0.00
B 407 GLN 31.8 0.73 H H E -101.9 -45.0 0.99 0.00
B 408 ASN 123.0 0.43 H H B2 -84.5 -18.0 0.99 0.07
B 409 LYS 22.7 0.87 C C E 76.9 2.0 0.10 0.16
B 410 MET 162.3 0.42 C C B2 -96.8 88.9 0.01 0.01
B 411 THR 45.3 0.80 C C P2 -76.2 175.6 0.08 0.01
B 412 ASN 81.7 0.57 H H P2 -61.1 -34.7 0.99 0.09
B 413 THR 48.7 0.64 H H P2 -64.4 -46.6 0.99 0.01
B 414 ASN 57.6 0.55 H H P1 -68.5 -32.7 0.99 0.01
B 415 LEU 153.5 0.25 H H B1 -73.4 -39.4 0.99 0.09
B 416 ALA 69.8 0.31 H H P1 -60.5 -37.3 0.99 0.09
B 417 VAL 43.9 0.69 H H P2 -60.1 -52.2 0.99 0.01
B 418 VAL 93.2 0.47 H H P1 -78.8 -21.7 0.99 0.01
B 419 PHE 184.7 0.11 H H B1 -93.8 -34.4 0.99 0.09
B 420 GLY 40.0 0.41 H H E -36.9 -60.7 0.99 0.14
B 421 PRO 81.4 0.60 H H P2 -64.4 -11.0 0.99 0.01
B 422 ASN 120.4 0.32 H H B1 -91.3 -13.9 0.99 0.00
B 423 LEU 146.2 0.23 H H B1 -99.7 -18.3 0.90 0.16
B 424 LEU 154.0 0.22 C C B1 -165.8 143.5 0.12 0.00
B 425 TRP 198.2 0.51 C C B3 -156.5 172.3 0.04 0.00
B 426 ALA 62.5 0.41 C C P1 -105.4 170.4 0.13 0.00
B 427 LYS 0.0 0.65 C C E -65.2 -19.4 0.13 0.00
B 428 ASP 55.7 0.50 C C P1 -129.9 144.6 0.13 0.00
B 429 ALA 0.0 0.85 H H E -57.1 -43.6 0.99 0.01
B 430 ALA 12.9 0.67 H H E -58.7 -45.1 0.99 0.01
B 431 ILE 58.3 0.58 H H P2 -63.7 -39.7 0.99 0.01
B 432 THR 92.8 0.42 H H P1 -63.4 -45.3 0.99 0.09
B 433 LEU 29.0 0.70 H H E -56.0 -38.1 0.98 0.11
B 434 LYS 12.2 0.80 H H E -68.0 -30.6 0.97 0.01
B 435 ALA 66.7 0.33 H H P1 -101.2 5.5 0.89 0.09
B 436 ILE 120.2 0.45 H H B2 -60.9 -35.7 0.99 0.11
B 437 ASN 0.0 0.80 H H E -70.4 -45.5 0.99 0.01
B 438 PRO 96.5 0.50 H H P1 -63.1 -33.0 0.99 0.01
B 439 ILE 154.6 0.35 H H B2 -65.8 -45.6 0.99 0.01
B 440 ASN 97.0 0.47 H H P1 -71.1 -27.9 1.00 0.01
B 441 THR 47.6 0.47 H H P1 -70.5 -39.0 1.00 0.01
B 442 PHE 188.2 0.18 H H B1 -71.2 -33.4 1.00 0.01
B 443 THR 111.1 0.26 H H P1 -67.0 -45.2 1.00 0.11
B 444 LYS 80.1 0.70 H H P2 -62.9 -33.7 1.00 0.01
B 445 PHE 143.5 0.36 H H B2 -69.0 -30.1 1.00 0.01
B 446 LEU 152.6 0.13 H H B1 -70.6 -36.8 1.00 0.11
B 447 LEU 152.8 0.27 H H B1 -77.8 -43.6 1.00 0.01
B 448 ASP 60.8 0.61 H H P2 -63.0 -31.3 0.98 0.01
B 449 HIS 107.1 0.55 T C P1 -119.6 27.1 0.38 0.01
B 450 GLN 115.1 0.43 H H B2 -47.8 -46.4 1.00 0.09
B 451 GLY 4.8 0.84 H H E -67.1 -25.4 1.00 0.00
B 452 GLU 21.9 0.62 H H E -88.3 -21.2 1.00 0.00
B 453 LEU 152.7 0.24 H H B1 -96.8 -34.3 1.00 0.09
B 454 PHE 189.0 0.33 C C B1 -120.0 134.1 0.00 0.00
B 455 PRO 11.4 0.83 C C E -70.1 ? 0.00 0.00