 
PFRMAT TS 
TARGET T0046 
AUTHOR 4662-5570-8620 
REMARK 
METHOD The three-dimensional structure of proteins is predicted 
METHOD from their sequence alone. 
METHOD The method is based on the electrostatic screening model for the stability 
METHOD of the protein main-chain conformation (1,2). 
METHOD Accoding to the electrostatic screening model 
METHOD the stability of a main-chain conformational state of an amino acid in a protein 
METHOD depends primarily on the strengths of local and short-range nonlocal main-chain 
METHOD electrostatic interactions. 
METHOD The strength of local and nonlocal electrostatic interactions 
METHOD is related to the electrostatic screening with solvent and protein groups. 
METHOD The local main-chain electrostatic interactions are 
METHOD primarily due to the interaction of the main-chain CO and NH groups within an amino acid. 
METHOD The nonlocal main-chain 
METHOD electrostatic interactions are predominantly due to the main-chain hydrogen bonding. 
METHOD The free energy of a protein as a function of its conformation 
METHOD is obtained from the potentials of mean force analysis of 
METHOD high resolution x-ray protein structures (3). 
METHOD The free energy function is simple and contains only 44 fitted coefficients (4). 
METHOD The minimization of the free energy 
METHOD is performed by the torsion (5) and cartesian space (6) Monte Carlo simulations. 
METHOD In the first phase of the minimization procedure 
METHOD only the short-range interactions are activated. 
METHOD Short-range interactions are interactions between amino 
METHOD acids less than four residues apart in the sequence. 
METHOD The $\beta$-strands are formed during the initial phase. 
METHOD The long-range interactions are activated in later phases in which 
METHOD $\beta$-strands interact with each other in a specific order (6). 
METHOD 
METHOD References: 
METHOD 1. F. Avbelj and J. Moult, Biochemistry, 34, 755-764 (1995). 
METHOD 2. F. Avbelj and L. Fele, J. Mol. Biol., 279, 665-684 (1998). 
METHOD 3. F. Avbelj, Biochemistry, 31, 6290-6297 (1992). 
METHOD 4. F. Avbelj and L. Fele, Proteins: Struc., Funct., Genet., 31, 74-96 (1998). 
METHOD 5. F. Avbelj and J. Moult, Proteins: Struc., Funct., Genet., 23, 129-141, (1995). 
METHOD 6. F. Avbelj in preparation. 
REMARK 
MODEL 3 
REMARK 
REMARK T0046 Fragments cont. 
REMARK 
PARENT N/A 
ATOM    355  N   GLU    39      14.551  -3.022 -24.070  1.00  0.00 
ATOM    356  HN  GLU    39      14.956  -2.578 -23.271  1.00  0.00 
ATOM    357  CA  GLU    39      15.127  -4.024 -24.707  1.00  0.00 
ATOM    358  C   GLU    39      14.647  -5.402 -23.953  1.00  0.00 
ATOM    359  O   GLU    39      14.735  -5.387 -22.806  1.00  0.00 
ATOM    360  CB  GLU    39      16.730  -4.188 -24.127  1.00  0.00 
ATOM    361  CG  GLU    39      17.714  -4.748 -25.158  1.00  0.00 
ATOM    362  CD  GLU    39      19.079  -5.014 -24.522  1.00  0.00 
ATOM    363  OE1 GLU    39      19.765  -4.055 -24.076  1.00  0.00 
ATOM    364  OE2 GLU    39      19.522  -6.192 -24.448  1.00  0.00 
ATOM    365  N   LEU    40      14.036  -6.340 -24.759  1.00  0.00 
ATOM    366  HN  LEU    40      13.848  -6.105 -25.713  1.00  0.00 
ATOM    367  CA  LEU    40      13.661  -7.635 -24.283  1.00  0.00 
ATOM    368  C   LEU    40      14.669  -8.166 -22.999  1.00  0.00 
ATOM    369  O   LEU    40      14.003  -8.505 -21.966  1.00  0.00 
ATOM    370  CB  LEU    40      13.894  -8.629 -25.458  1.00  0.00 
ATOM    371  CG  LEU    40      13.510 -10.078 -25.159  1.00  0.00 
ATOM    372  CD1 LEU    40      12.069 -10.284 -24.722  1.00  0.00 
ATOM    373  CD2 LEU    40      13.867 -10.907 -26.408  1.00  0.00 
ATOM    374  N   ASP    41      16.102  -7.979 -23.213  1.00  0.00 
ATOM    375  HN  ASP    41      16.504  -7.600 -24.046  1.00  0.00 
ATOM    376  CA  ASP    41      16.884  -8.425 -22.032  1.00  0.00 
ATOM    377  C   ASP    41      16.826  -7.386 -21.009  1.00  0.00 
ATOM    378  O   ASP    41      17.816  -6.438 -21.202  1.00  0.00 
ATOM    379  CB  ASP    41      18.319  -8.583 -22.592  1.00  0.00 
ATOM    380  CG  ASP    41      18.410  -9.702 -23.630  1.00  0.00 
ATOM    381  OD1 ASP    41      17.612 -10.673 -23.581  1.00  0.00 
ATOM    382  OD2 ASP    41      19.283  -9.651 -24.538  1.00  0.00 
ATOM    383  N   MET    42      15.867  -7.459 -20.298  1.00  0.00 
ATOM    384  HN  MET    42      15.154  -8.138 -20.476  1.00  0.00 
ATOM    385  CA  MET    42      15.765  -6.651 -19.300  1.00  0.00 
ATOM    386  C   MET    42      16.903  -6.631 -18.374  1.00  0.00 
ATOM    387  O   MET    42      18.231  -6.822 -18.599  1.00  0.00 
ATOM    388  CB  MET    42      14.550  -7.012 -18.281  1.00  0.00 
ATOM    389  CG  MET    42      13.271  -7.456 -19.079  1.00  0.00 
ATOM    390  SD  MET    42      12.148  -8.283 -18.040  1.00  0.00 
ATOM    391  CE  MET    42      12.410  -9.872 -18.487  1.00  0.00 
ATOM    392  N   THR    43      16.830  -6.473 -17.124  1.00  0.00 
ATOM    393  HN  THR    43      15.905  -6.404 -16.750  1.00  0.00 
ATOM    394  CA  THR    43      17.948  -6.374 -16.120  1.00  0.00 
ATOM    395  C   THR    43      17.563  -6.587 -14.793  1.00  0.00 
ATOM    396  O   THR    43      16.627  -5.896 -14.451  1.00  0.00 
ATOM    397  CB  THR    43      18.674  -5.002 -16.289  1.00  0.00 
ATOM    398  OG1 THR    43      19.641  -5.071 -15.233  1.00  0.00 
ATOM    399  HG1 THR    43      19.500  -5.908 -14.705  1.00  0.00 
ATOM    400  CG2 THR    43      17.742  -3.830 -16.090  1.00  0.00 
ATOM    401  N   ASP    44      18.071  -7.523 -14.201  1.00  0.00 
ATOM    402  HN  ASP    44      18.710  -8.075 -14.737  1.00  0.00 
ATOM    403  CA  ASP    44      17.859  -7.997 -12.677  1.00  0.00 
ATOM    404  C   ASP    44      19.175  -7.565 -11.699  1.00  0.00 
ATOM    405  O   ASP    44      20.577  -7.567 -11.989  1.00  0.00 
ATOM    406  CB  ASP    44      17.584  -9.499 -12.574  1.00  0.00 
ATOM    407  CG  ASP    44      18.611 -10.300 -13.380  1.00  0.00 
ATOM    408  OD1 ASP    44      18.758 -10.078 -14.610  1.00  0.00 
ATOM    409  OD2 ASP    44      19.305 -11.184 -12.809  1.00  0.00 
ATOM    410  N   PHE    45      18.883  -7.149 -10.432  1.00  0.00 
ATOM    411  HN  PHE    45      17.925  -7.047 -10.163  1.00  0.00 
ATOM    412  CA  PHE    45      19.913  -6.854  -9.475  1.00  0.00 
ATOM    413  C   PHE    45      19.865  -7.864  -8.354  1.00  0.00 
ATOM    414  O   PHE    45      18.673  -8.031  -7.966  1.00  0.00 
ATOM    415  CB  PHE    45      19.738  -5.435  -8.864  1.00  0.00 
ATOM    416  CG  PHE    45      19.686  -4.362  -9.869  1.00  0.00 
ATOM    417  CD1 PHE    45      20.805  -3.707 -10.329  1.00  0.00 
ATOM    418  CE1 PHE    45      20.746  -2.710 -11.264  1.00  0.00 
ATOM    419  CZ  PHE    45      19.507  -2.342 -11.772  1.00  0.00 
ATOM    420  CE2 PHE    45      18.356  -2.970 -11.341  1.00  0.00 
ATOM    421  CD2 PHE    45      18.478  -3.966 -10.400  1.00  0.00 
ATOM    422  N   VAL    46      21.023  -8.334  -7.969  1.00  0.00 
ATOM    423  HN  VAL    46      21.877  -8.017  -8.381  1.00  0.00 
ATOM    424  CA  VAL    46      21.015  -9.299  -6.956  1.00  0.00 
ATOM    425  C   VAL    46      21.805  -8.592  -5.669  1.00  0.00 
ATOM    426  O   VAL    46      22.804  -8.255  -5.627  1.00  0.00 
ATOM    427  CB  VAL    46      22.138 -10.553  -7.242  1.00  0.00 
ATOM    428  CG1 VAL    46      21.965 -11.655  -6.211  1.00  0.00 
ATOM    429  CG2 VAL    46      21.836 -11.055  -8.637  1.00  0.00 
ATOM    430  N   PHE    47      21.215  -8.280  -4.658  1.00  0.00 
ATOM    431  HN  PHE    47      20.224  -8.415  -4.650  1.00  0.00 
ATOM    432  CA  PHE    47      21.844  -7.701  -3.399  1.00  0.00 
ATOM    433  C   PHE    47      22.040  -8.824  -2.459  1.00  0.00 
ATOM    434  O   PHE    47      21.309  -9.734  -2.360  1.00  0.00 
ATOM    435  CB  PHE    47      21.339  -6.498  -2.929  1.00  0.00 
ATOM    436  CG  PHE    47      20.150  -6.701  -2.089  1.00  0.00 
ATOM    437  CD1 PHE    47      20.215  -6.945  -0.737  1.00  0.00 
ATOM    438  CE1 PHE    47      19.101  -7.133   0.035  1.00  0.00 
ATOM    439  CZ  PHE    47      17.852  -7.075  -0.567  1.00  0.00 
ATOM    440  CE2 PHE    47      17.734  -6.833  -1.921  1.00  0.00 
ATOM    441  CD2 PHE    47      18.889  -6.652  -2.648  1.00  0.00 
ATOM    442  N   GLN    48      23.190  -8.611  -1.612  1.00  0.00 
ATOM    443  HN  GLN    48      23.741  -7.801  -1.812  1.00  0.00 
ATOM    444  CA  GLN    48      23.608  -9.376  -0.584  1.00  0.00 
ATOM    445  C   GLN    48      24.578  -8.770   0.380  1.00  0.00 
ATOM    446  O   GLN    48      25.274  -7.781  -0.193  1.00  0.00 
ATOM    447  CB  GLN    48      24.061 -10.680  -0.989  1.00  0.00 
ATOM    448  CG  GLN    48      23.978 -11.736   0.116  1.00  0.00 
ATOM    449  CD  GLN    48      24.576 -13.065  -0.350  1.00  0.00 
ATOM    450  OE1 GLN    48      23.972 -13.819  -1.097  1.00  0.00 
ATOM    451  NE2 GLN    48      25.791 -13.308   0.127  1.00  0.00 
ATOM    452  HE21GLN    48      26.230 -12.647   0.736  1.00  0.00 
ATOM    453  HE22GLN    48      26.267 -14.152  -0.122  1.00  0.00 
ATOM    454  N   ALA    49      24.544  -9.173   1.729  1.00  0.00 
ATOM    455  HN  ALA    49      23.753  -9.738   1.964  1.00  0.00 
ATOM    456  CA  ALA    49      25.479  -8.912   2.888  1.00  0.00 
ATOM    457  C   ALA    49      25.617  -9.710   3.997  1.00  0.00 
ATOM    458  O   ALA    49      24.574 -10.249   4.257  1.00  0.00 
ATOM    459  CB  ALA    49      25.751  -7.513   3.064  1.00  0.00 
ATOM    460  N   ALA    50      26.966  -9.886   4.455  1.00  0.00 
ATOM    461  HN  ALA    50      27.732  -9.536   3.916  1.00  0.00 
ATOM    462  CA  ALA    50      27.198 -10.552   5.664  1.00  0.00 
ATOM    463  C   ALA    50      26.557  -9.948   6.871  1.00  0.00 
ATOM    464  O   ALA    50      26.076 -10.723   7.811  1.00  0.00 
ATOM    465  CB  ALA    50      28.681 -10.624   6.008  1.00  0.00 
ATOM    466  N   VAL    51      26.666  -8.417   6.984  1.00  0.00 
ATOM    467  HN  VAL    51      27.174  -7.948   6.262  1.00  0.00 
ATOM    468  CA  VAL    51      26.101  -7.580   8.042  1.00  0.00 
ATOM    469  C   VAL    51      24.940  -6.816   7.549  1.00  0.00 
ATOM    470  O   VAL    51      24.954  -6.103   6.767  1.00  0.00 
ATOM    471  CB  VAL    51      27.169  -6.592   8.580  1.00  0.00 
ATOM    472  CG1 VAL    51      26.774  -6.151   9.978  1.00  0.00 
ATOM    473  CG2 VAL    51      28.555  -7.196   8.568  1.00  0.00 
ATOM    474  N   PRO    52      23.744  -6.877   8.082  1.00  0.00 
ATOM    475  CA  PRO    52      22.346  -6.071   7.597  1.00  0.00 
ATOM    476  CD  PRO    52      23.542  -7.161   9.524  1.00  0.00 
ATOM    477  C   PRO    52      22.549  -4.802   7.163  1.00  0.00 
ATOM    478  O   PRO    52      21.954  -4.340   6.364  1.00  0.00 
ATOM    479  CB  PRO    52      21.428  -6.407   8.683  1.00  0.00 
ATOM    480  CG  PRO    52      22.336  -6.235   9.913  1.00  0.00 
ATOM    481  N   LYS    53      23.632  -4.032   7.919  1.00  0.00 
ATOM    482  HN  LYS    53      24.133  -4.510   8.641  1.00  0.00 
ATOM    483  CA  LYS    53      23.974  -2.651   7.650  1.00  0.00 
ATOM    484  C   LYS    53      24.531  -2.518   6.239  1.00  0.00 
ATOM    485  O   LYS    53      24.116  -1.641   5.485  1.00  0.00 
ATOM    486  CB  LYS    53      25.030  -2.145   8.635  1.00  0.00 
ATOM    487  CG  LYS    53      25.341  -0.677   8.342  1.00  0.00 
ATOM    488  CD  LYS    53      26.595  -0.222   9.092  1.00  0.00 
ATOM    489  CE  LYS    53      26.506  -0.584  10.577  1.00  0.00 
ATOM    490  NZ  LYS    53      27.686  -0.082  11.317  1.00  0.00 
ATOM    491  HZ1 LYS    53      28.390   0.205  10.667  1.00  0.00 
ATOM    492  HZ2 LYS    53      27.417   0.697  11.883  1.00  0.00 
ATOM    493  HZ3 LYS    53      28.048  -0.809  11.900  1.00  0.00 
ATOM    494  N   THR    54      25.501  -3.202   5.980  1.00  0.00 
ATOM    495  HN  THR    54      25.910  -3.723   6.729  1.00  0.00 
ATOM    496  CA  THR    54      26.094  -3.320   4.713  1.00  0.00 
ATOM    497  C   THR    54      25.387  -4.372   3.761  1.00  0.00 
ATOM    498  O   THR    54      24.652  -5.083   4.316  1.00  0.00 
ATOM    499  CB  THR    54      27.586  -3.726   4.649  1.00  0.00 
ATOM    500  OG1 THR    54      27.682  -4.961   5.365  1.00  0.00 
ATOM    501  HG1 THR    54      27.372  -5.711   4.780  1.00  0.00 
ATOM    502  CG2 THR    54      28.361  -2.633   5.354  1.00  0.00 
ATOM    503  N   PHE    55      25.677  -4.107   2.449  1.00  0.00 
ATOM    504  HN  PHE    55      26.304  -3.339   2.319  1.00  0.00 
ATOM    505  CA  PHE    55      25.259  -4.713   1.248  1.00  0.00 
ATOM    506  C   PHE    55      26.151  -4.865   0.285  1.00  0.00 
ATOM    507  O   PHE    55      27.300  -4.006   0.447  1.00  0.00 
ATOM    508  CB  PHE    55      23.963  -4.292   0.786  1.00  0.00 
ATOM    509  CG  PHE    55      22.842  -4.602   1.688  1.00  0.00 
ATOM    510  CD1 PHE    55      22.301  -5.862   1.808  1.00  0.00 
ATOM    511  CE1 PHE    55      21.259  -6.138   2.651  1.00  0.00 
ATOM    512  CZ  PHE    55      20.726  -5.111   3.418  1.00  0.00 
ATOM    513  CE2 PHE    55      21.235  -3.832   3.331  1.00  0.00 
ATOM    514  CD2 PHE    55      22.283  -3.611   2.466  1.00  0.00 
ATOM    515  N   GLN    56      25.973  -5.653  -0.614  1.00  0.00 
ATOM    516  HN  GLN    56      25.182  -6.253  -0.493  1.00  0.00 
ATOM    517  CA  GLN    56      26.701  -5.866  -1.811  1.00  0.00 
ATOM    518  C   GLN    56      25.945  -6.240  -3.029  1.00  0.00 
ATOM    519  O   GLN    56      24.712  -6.799  -2.692  1.00  0.00 
ATOM    520  CB  GLN    56      27.636  -7.240  -1.464  1.00  0.00 
ATOM    521  CG  GLN    56      28.758  -6.858  -0.496  1.00  0.00 
ATOM    522  CD  GLN    56      29.588  -8.085  -0.107  1.00  0.00 
ATOM    523  OE1 GLN    56      29.072  -9.104   0.314  1.00  0.00 
ATOM    524  NE2 GLN    56      30.898  -7.924  -0.273  1.00  0.00 
ATOM    525  HE21GLN    56      31.255  -7.058  -0.624  1.00  0.00 
ATOM    526  HE22GLN    56      31.526  -8.669  -0.047  1.00  0.00 
ATOM    527  N   LEU    57      26.479  -6.135  -4.363  1.00  0.00 
ATOM    528  HN  LEU    57      27.411  -5.821  -4.545  1.00  0.00 
ATOM    529  CA  LEU    57      25.660  -6.479  -5.315  1.00  0.00 
ATOM    530  C   LEU    57      26.236  -7.712  -6.035  1.00  0.00 
ATOM    531  O   LEU    57      27.514  -7.561  -6.509  1.00  0.00 
ATOM    532  CB  LEU    57      25.588  -5.362  -6.344  1.00  0.00 
ATOM    533  CG  LEU    57      24.467  -4.345  -6.118  1.00  0.00 
ATOM    534  CD1 LEU    57      24.473  -3.161  -7.067  1.00  0.00 
ATOM    535  CD2 LEU    57      23.139  -5.124  -6.166  1.00  0.00 
ATOM    536  N   GLN    58      25.639  -8.691  -6.064  1.00  0.00 
ATOM    537  HN  GLN    58      24.746  -8.710  -5.614  1.00  0.00 
ATOM    538  CA  GLN    58      26.122  -9.964  -6.746  1.00  0.00 
ATOM    539  C   GLN    58      26.134  -9.655  -8.304  1.00  0.00 
ATOM    540  O   GLN    58      26.999 -10.022  -8.850  1.00  0.00 
ATOM    541  CB  GLN    58      25.355 -11.144  -6.486  1.00  0.00 
ATOM    542  CG  GLN    58      25.235 -11.400  -4.982  1.00  0.00 
ATOM    543  CD  GLN    58      25.102 -12.894  -4.689  1.00  0.00 
ATOM    544  OE1 GLN    58      24.275 -13.593  -5.251  1.00  0.00 
ATOM    545  NE2 GLN    58      25.962 -13.347  -3.779  1.00  0.00 
ATOM    546  HE21GLN    58      26.616 -12.721  -3.354  1.00  0.00 
ATOM    547  HE22GLN    58      25.954 -14.313  -3.520  1.00  0.00 
ATOM    548  N   LEU    59      25.112  -8.996  -8.948  1.00  0.00 
ATOM    549  HN  LEU    59      24.343  -8.608  -8.440  1.00  0.00 
ATOM    550  CA  LEU    59      25.192  -8.888 -10.366  1.00  0.00 
ATOM    551  C   LEU    59      25.263  -7.246 -10.689  1.00  0.00 
ATOM    552  O   LEU    59      24.967  -6.329  -9.735  1.00  0.00 
ATOM    553  CB  LEU    59      23.670  -9.102 -10.931  1.00  0.00 
ATOM    554  CG  LEU    59      23.591 -10.059 -12.121  1.00  0.00 
ATOM    555  CD1 LEU    59      24.250 -11.412 -11.902  1.00  0.00 
ATOM    556  CD2 LEU    59      22.104 -10.190 -12.498  1.00  0.00 
TER 
END 
