 
PFRMAT TS 
TARGET T0059 
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 majority of alpha-helices and beta-strands are formed 
METHOD during the initial phase. 
METHOD The long-range interactions are activated in later phases in which 
METHOD alpha-helices and 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 2 
REMARK 
REMARK T0059 Fragments 
REMARK 
PARENT N/A 
ATOM    509  N   VAL    55      -0.645   1.071 -12.262  1.00  0.00 
ATOM    510  HN  VAL    55      -0.681   0.409 -13.011  1.00  0.00 
ATOM    511  CA  VAL    55      -0.668   2.407 -12.524  1.00  0.00 
ATOM    512  C   VAL    55      -1.942   2.880 -12.918  1.00  0.00 
ATOM    513  O   VAL    55      -2.604   2.006 -13.811  1.00  0.00 
ATOM    514  CB  VAL    55       0.539   3.001 -13.231  1.00  0.00 
ATOM    515  CG1 VAL    55       1.051   4.335 -12.714  1.00  0.00 
ATOM    516  CG2 VAL    55       1.594   1.926 -13.103  1.00  0.00 
ATOM    517  N   ALA    56      -2.291   3.886 -12.330  1.00  0.00 
ATOM    518  HN  ALA    56      -1.717   4.232 -11.588  1.00  0.00 
ATOM    519  CA  ALA    56      -3.488   4.593 -12.658  1.00  0.00 
ATOM    520  C   ALA    56      -3.305   5.223 -14.105  1.00  0.00 
ATOM    521  O   ALA    56      -2.112   5.804 -14.702  1.00  0.00 
ATOM    522  CB  ALA    56      -3.914   5.801 -11.868  1.00  0.00 
ATOM    523  N   GLN    57      -4.085   5.187 -14.950  1.00  0.00 
ATOM    524  HN  GLN    57      -4.871   4.599 -14.759  1.00  0.00 
ATOM    525  CA  GLN    57      -4.131   5.859 -16.275  1.00  0.00 
ATOM    526  C   GLN    57      -4.018   7.316 -16.130  1.00  0.00 
ATOM    527  O   GLN    57      -5.050   7.836 -15.516  1.00  0.00 
ATOM    528  CB  GLN    57      -5.253   5.400 -17.098  1.00  0.00 
ATOM    529  CG  GLN    57      -5.172   3.888 -17.321  1.00  0.00 
ATOM    530  CD  GLN    57      -6.439   3.366 -18.002  1.00  0.00 
ATOM    531  OE1 GLN    57      -6.465   2.293 -18.583  1.00  0.00 
ATOM    532  NE2 GLN    57      -7.484   4.182 -17.898  1.00  0.00 
ATOM    533  HE21GLN    57      -7.395   5.049 -17.407  1.00  0.00 
ATOM    534  HE22GLN    57      -8.359   3.929 -18.311  1.00  0.00 
ATOM    535  N   LEU    58      -3.198   7.900 -16.592  1.00  0.00 
ATOM    536  HN  LEU    58      -2.565   7.369 -17.155  1.00  0.00 
ATOM    537  CA  LEU    58      -2.897   9.341 -16.504  1.00  0.00 
ATOM    538  C   LEU    58      -2.726   9.954 -18.050  1.00  0.00 
ATOM    539  O   LEU    58      -2.452   9.301 -19.050  1.00  0.00 
ATOM    540  CB  LEU    58      -1.899   9.809 -15.742  1.00  0.00 
ATOM    541  CG  LEU    58      -1.978   9.568 -14.234  1.00  0.00 
ATOM    542  CD1 LEU    58      -3.350   9.790 -13.618  1.00  0.00 
ATOM    543  CD2 LEU    58      -1.445   8.146 -13.977  1.00  0.00 
ATOM    544  N   GLU    59      -2.980  11.053 -17.970  1.00  0.00 
ATOM    545  HN  GLU    59      -3.263  11.422 -17.085  1.00  0.00 
ATOM    546  CA  GLU    59      -2.908  11.941 -19.109  1.00  0.00 
ATOM    547  C   GLU    59      -2.551  13.267 -18.869  1.00  0.00 
ATOM    548  O   GLU    59      -2.432  13.614 -17.503  1.00  0.00 
ATOM    549  CB  GLU    59      -4.318  11.723 -19.935  1.00  0.00 
ATOM    550  CG  GLU    59      -5.514  12.216 -19.116  1.00  0.00 
ATOM    551  CD  GLU    59      -6.813  12.095 -19.916  1.00  0.00 
ATOM    552  OE1 GLU    59      -7.039  12.880 -20.875  1.00  0.00 
ATOM    553  OE2 GLU    59      -7.658  11.210 -19.614  1.00  0.00 
ATOM    554  N   GLN    60      -2.245  13.762 -19.849  1.00  0.00 
ATOM    555  HN  GLN    60      -2.279  13.241 -20.702  1.00  0.00 
ATOM    556  CA  GLN    60      -1.813  15.125 -19.865  1.00  0.00 
ATOM    557  C   GLN    60      -3.283  15.944 -20.134  1.00  0.00 
ATOM    558  O   GLN    60      -4.122  15.325 -20.301  1.00  0.00 
ATOM    559  CB  GLN    60      -1.148  15.432 -21.276  1.00  0.00 
ATOM    560  CG  GLN    60      -2.089  15.044 -22.417  1.00  0.00 
ATOM    561  CD  GLN    60      -1.454  15.343 -23.777  1.00  0.00 
ATOM    562  OE1 GLN    60      -0.833  16.370 -23.989  1.00  0.00 
ATOM    563  NE2 GLN    60      -1.644  14.387 -24.685  1.00  0.00 
ATOM    564  HE21GLN    60      -2.164  13.567 -24.446  1.00  0.00 
ATOM    565  HE22GLN    60      -1.266  14.489 -25.605  1.00  0.00 
ATOM    566  N   VAL    61      -2.986  17.111 -20.066  1.00  0.00 
ATOM    567  HN  VAL    61      -2.071  17.392 -19.777  1.00  0.00 
ATOM    568  CA  VAL    61      -3.863  17.971 -20.370  1.00  0.00 
ATOM    569  C   VAL    61      -3.328  19.000 -21.604  1.00  0.00 
ATOM    570  O   VAL    61      -3.548  18.576 -22.919  1.00  0.00 
ATOM    571  CB  VAL    61      -4.087  19.113 -19.114  1.00  0.00 
ATOM    572  CG1 VAL    61      -5.269  20.043 -19.315  1.00  0.00 
ATOM    573  CG2 VAL    61      -4.247  18.288 -17.856  1.00  0.00 
ATOM    574  N   TYR    62      -2.582  20.159 -21.057  1.00  0.00 
ATOM    575  HN  TYR    62      -2.595  20.226 -20.059  1.00  0.00 
ATOM    576  CA  TYR    62      -1.826  21.227 -21.729  1.00  0.00 
ATOM    577  C   TYR    62      -1.416  20.879 -23.028  1.00  0.00 
ATOM    578  O   TYR    62      -0.715  20.001 -23.233  1.00  0.00 
ATOM    579  CB  TYR    62      -0.512  21.855 -20.954  1.00  0.00 
ATOM    580  CG  TYR    62      -0.161  23.225 -21.480  1.00  0.00 
ATOM    581  CD1 TYR    62      -0.807  24.358 -20.998  1.00  0.00 
ATOM    582  CE1 TYR    62      -0.503  25.622 -21.463  1.00  0.00 
ATOM    583  CZ  TYR    62       0.471  25.776 -22.435  1.00  0.00 
ATOM    584  OH  TYR    62       0.806  27.021 -22.929  1.00  0.00 
ATOM    585  HH  TYR    62       1.513  27.107 -23.631  1.00  0.00 
ATOM    586  CE2 TYR    62       1.125  24.665 -22.929  1.00  0.00 
ATOM    587  CD2 TYR    62       0.807  23.401 -22.450  1.00  0.00 
ATOM    588  N   ILE    63      -1.671  21.693 -24.107  1.00  0.00 
ATOM    589  HN  ILE    63      -2.146  22.547 -23.893  1.00  0.00 
ATOM    590  CA  ILE    63      -1.331  21.484 -25.612  1.00  0.00 
ATOM    591  C   ILE    63       0.209  20.942 -25.523  1.00  0.00 
ATOM    592  O   ILE    63       0.729  20.434 -26.266  1.00  0.00 
ATOM    593  CB  ILE    63      -1.566  22.756 -26.352  1.00  0.00 
ATOM    594  CG2 ILE    63      -3.064  23.002 -26.271  1.00  0.00 
ATOM    595  CG1 ILE    63      -0.835  23.986 -25.838  1.00  0.00 
ATOM    596  CD1 ILE    63      -1.295  25.312 -26.447  1.00  0.00 
ATOM    597  N   ARG    64       1.021  21.197 -24.613  1.00  0.00 
ATOM    598  HN  ARG    64       0.727  21.688 -23.793  1.00  0.00 
ATOM    599  CA  ARG    64       2.353  20.785 -24.756  1.00  0.00 
ATOM    600  C   ARG    64       2.433  19.447 -24.265  1.00  0.00 
ATOM    601  O   ARG    64       3.227  18.651 -24.459  1.00  0.00 
ATOM    602  CB  ARG    64       3.276  21.774 -24.327  1.00  0.00 
ATOM    603  CG  ARG    64       3.439  22.689 -25.360  1.00  0.00 
ATOM    604  CD  ARG    64       4.153  22.049 -26.553  1.00  0.00 
ATOM    605  NE  ARG    64       4.349  22.853 -27.581  1.00  0.00 
ATOM    606  HE  ARG    64       4.052  23.804 -27.496  1.00  0.00 
ATOM    607  CZ  ARG    64       4.927  22.470 -28.742  1.00  0.00 
ATOM    608  NH1 ARG    64       5.071  23.360 -29.707  1.00  0.00 
ATOM    609  HH11ARG    64       5.496  23.095 -30.572  1.00  0.00 
ATOM    610  HH12ARG    64       4.755  24.299 -29.572  1.00  0.00 
ATOM    611  NH2 ARG    64       5.326  21.219 -28.874  1.00  0.00 
ATOM    612  HH21ARG    64       5.755  20.918 -29.726  1.00  0.00 
ATOM    613  HH22ARG    64       5.199  20.572 -28.122  1.00  0.00 
ATOM    614  N   GLY    65       1.560  18.788 -23.364  1.00  0.00 
ATOM    615  HN  GLY    65       0.815  19.282 -22.916  1.00  0.00 
ATOM    616  CA  GLY    65       1.750  17.553 -23.142  1.00  0.00 
ATOM    617  C   GLY    65       2.988  17.469 -22.008  1.00  0.00 
ATOM    618  O   GLY    65       3.539  16.476 -21.801  1.00  0.00 
ATOM    619  N   SER    66       3.399  18.524 -21.338  1.00  0.00 
ATOM    620  HN  SER    66       3.007  19.429 -21.504  1.00  0.00 
ATOM    621  CA  SER    66       4.494  18.316 -20.299  1.00  0.00 
ATOM    622  C   SER    66       4.110  17.744 -19.011  1.00  0.00 
ATOM    623  O   SER    66       4.712  16.774 -18.225  1.00  0.00 
ATOM    624  CB  SER    66       5.488  19.468 -20.078  1.00  0.00 
ATOM    625  OG  SER    66       5.794  19.995 -21.332  1.00  0.00 
ATOM    626  HG  SER    66       6.770  20.210 -21.375  1.00  0.00 
ATOM    627  N   LYS    67       2.919  18.314 -18.236  1.00  0.00 
ATOM    628  HN  LYS    67       2.479  19.163 -18.529  1.00  0.00 
ATOM    629  CA  LYS    67       2.437  17.588 -17.054  1.00  0.00 
ATOM    630  C   LYS    67       1.867  16.366 -17.223  1.00  0.00 
ATOM    631  O   LYS    67       0.922  16.239 -17.704  1.00  0.00 
ATOM    632  CB  LYS    67       1.642  18.592 -16.160  1.00  0.00 
ATOM    633  CG  LYS    67       2.292  19.962 -15.966  1.00  0.00 
ATOM    634  CD  LYS    67       1.739  20.663 -14.723  1.00  0.00 
ATOM    635  CE  LYS    67       1.735  22.182 -14.906  1.00  0.00 
ATOM    636  NZ  LYS    67       1.969  22.545 -16.322  1.00  0.00 
ATOM    637  HZ1 LYS    67       2.808  23.084 -16.394  1.00  0.00 
ATOM    638  HZ2 LYS    67       2.060  21.713 -16.869  1.00  0.00 
ATOM    639  HZ3 LYS    67       1.197  23.083 -16.660  1.00  0.00 
ATOM    640  N   ILE    68       2.430  15.347 -16.695  1.00  0.00 
ATOM    641  HN  ILE    68       3.343  15.419 -16.294  1.00  0.00 
ATOM    642  CA  ILE    68       1.637  13.942 -16.689  1.00  0.00 
ATOM    643  C   ILE    68       1.275  13.781 -15.286  1.00  0.00 
ATOM    644  O   ILE    68       2.152  14.003 -14.187  1.00  0.00 
ATOM    645  CB  ILE    68       2.361  12.951 -17.358  1.00  0.00 
ATOM    646  CG2 ILE    68       1.392  11.794 -17.533  1.00  0.00 
ATOM    647  CG1 ILE    68       2.894  13.357 -18.722  1.00  0.00 
ATOM    648  CD1 ILE    68       1.838  13.876 -19.700  1.00  0.00 
ATOM    649  N   ARG    69       0.202  13.587 -14.967  1.00  0.00 
ATOM    650  HN  ARG    69      -0.478  13.662 -15.696  1.00  0.00 
ATOM    651  CA  ARG    69      -0.367  13.222 -13.567  1.00  0.00 
ATOM    652  C   ARG    69       0.111  11.692 -13.440  1.00  0.00 
ATOM    653  O   ARG    69       0.243  10.860 -14.450  1.00  0.00 
ATOM    654  CB  ARG    69      -1.793  13.270 -13.571  1.00  0.00 
ATOM    655  CG  ARG    69      -2.440  14.006 -12.586  1.00  0.00 
ATOM    656  CD  ARG    69      -3.831  14.444 -13.053  1.00  0.00 
ATOM    657  NE  ARG    69      -4.609  14.935 -12.107  1.00  0.00 
ATOM    658  HE  ARG    69      -4.187  15.181 -11.234  1.00  0.00 
ATOM    659  CZ  ARG    69      -5.938  15.126 -12.243  1.00  0.00 
ATOM    660  NH1 ARG    69      -6.621  15.623 -11.230  1.00  0.00 
ATOM    661  HH11ARG    69      -7.606  15.770 -11.316  1.00  0.00 
ATOM    662  HH12ARG    69      -6.153  15.853 -10.376  1.00  0.00 
ATOM    663  NH2 ARG    69      -6.516  14.808 -13.388  1.00  0.00 
ATOM    664  HH21ARG    69      -7.500  14.943 -13.506  1.00  0.00 
ATOM    665  HH22ARG    69      -5.970  14.432 -14.137  1.00  0.00 
ATOM    666  N   PHE    70       0.639  11.133 -12.163  1.00  0.00 
ATOM    667  HN  PHE    70       0.772  11.798 -11.428  1.00  0.00 
ATOM    668  CA  PHE    70       1.004   9.704 -11.816  1.00  0.00 
ATOM    669  C   PHE    70       0.029   9.171 -10.869  1.00  0.00 
ATOM    670  O   PHE    70      -0.099   9.534  -9.510  1.00  0.00 
ATOM    671  CB  PHE    70       2.476   9.717 -11.180  1.00  0.00 
ATOM    672  CG  PHE    70       3.584  10.013 -12.103  1.00  0.00 
ATOM    673  CD1 PHE    70       4.046   9.115 -13.036  1.00  0.00 
ATOM    674  CE1 PHE    70       5.076   9.402 -13.888  1.00  0.00 
ATOM    675  CZ  PHE    70       5.683  10.648 -13.814  1.00  0.00 
ATOM    676  CE2 PHE    70       5.254  11.583 -12.893  1.00  0.00 
ATOM    677  CD2 PHE    70       4.215  11.239 -12.062  1.00  0.00 
ATOM    678  N   LEU    71      -0.763   8.435 -11.141  1.00  0.00 
ATOM    679  HN  LEU    71      -0.790   8.070 -12.072  1.00  0.00 
ATOM    680  CA  LEU    71      -1.669   8.032 -10.264  1.00  0.00 
ATOM    681  C   LEU    71      -1.491   6.344 -10.285  1.00  0.00 
ATOM    682  O   LEU    71      -1.564   5.533 -11.413  1.00  0.00 
ATOM    683  CB  LEU    71      -3.114   8.049 -10.988  1.00  0.00 
ATOM    684  CG  LEU    71      -3.991   8.942 -10.108  1.00  0.00 
ATOM    685  CD1 LEU    71      -5.488   8.757 -10.296  1.00  0.00 
ATOM    686  CD2 LEU    71      -3.555   8.702  -8.651  1.00  0.00 
ATOM    687  N   ILE    72      -1.220   5.775  -9.335  1.00  0.00 
ATOM    688  HN  ILE    72      -1.178   6.280  -8.473  1.00  0.00 
ATOM    689  CA  ILE    72      -0.935   4.365  -9.318  1.00  0.00 
ATOM    690  C   ILE    72      -1.988   3.721  -8.350  1.00  0.00 
ATOM    691  O   ILE    72      -2.597   4.270  -7.364  1.00  0.00 
ATOM    692  CB  ILE    72       0.347   4.205  -8.209  1.00  0.00 
ATOM    693  CG2 ILE    72       0.931   2.806  -8.112  1.00  0.00 
ATOM    694  CG1 ILE    72       1.425   5.160  -8.694  1.00  0.00 
ATOM    695  CD1 ILE    72       1.541   6.463  -7.899  1.00  0.00 
ATOM    696  N   LEU    73      -2.466   2.671  -8.541  1.00  0.00 
ATOM    697  HN  LEU    73      -2.076   2.139  -9.292  1.00  0.00 
ATOM    698  CA  LEU    73      -3.596   2.028  -7.791  1.00  0.00 
ATOM    699  C   LEU    73      -3.127   1.096  -6.675  1.00  0.00 
ATOM    700  O   LEU    73      -1.808   0.616  -6.444  1.00  0.00 
ATOM    701  CB  LEU    73      -4.556   1.403  -8.758  1.00  0.00 
ATOM    702  CG  LEU    73      -4.837   2.345  -9.931  1.00  0.00 
ATOM    703  CD1 LEU    73      -5.627   1.731 -11.073  1.00  0.00 
ATOM    704  CD2 LEU    73      -5.527   3.593  -9.349  1.00  0.00 
ATOM    705  N   PRO    74      -4.047   0.509  -5.752  1.00  0.00 
ATOM    706  CA  PRO    74      -3.622  -0.353  -4.480  1.00  0.00 
ATOM    707  CD  PRO    74      -5.569   0.153  -5.826  1.00  0.00 
ATOM    708  C   PRO    74      -3.079  -1.701  -4.954  1.00  0.00 
ATOM    709  O   PRO    74      -3.431  -1.933  -6.067  1.00  0.00 
ATOM    710  CB  PRO    74      -4.783  -0.598  -3.528  1.00  0.00 
ATOM    711  CG  PRO    74      -5.963  -0.625  -4.512  1.00  0.00 
ATOM    712  N   ASP    75      -2.350  -2.248  -4.217  1.00  0.00 
ATOM    713  HN  ASP    75      -2.110  -1.837  -3.338  1.00  0.00 
ATOM    714  CA  ASP    75      -1.771  -3.608  -4.629  1.00  0.00 
TER 
END 
