 
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 3 
REMARK 
REMARK T0059 Fragments 
REMARK 
PARENT N/A 
REMARK 
REMARK T0059 Fragments 
REMARK 
ATOM    137  N   ILE    17      12.431  17.164 -12.554  1.00  0.00 
ATOM    138  HN  ILE    17      13.055  16.424 -12.806  1.00  0.00 
ATOM    139  CA  ILE    17      11.628  17.722 -13.487  1.00  0.00 
ATOM    140  C   ILE    17      10.198  17.540 -12.982  1.00  0.00 
ATOM    141  O   ILE    17       9.367  18.204 -13.194  1.00  0.00 
ATOM    142  CB  ILE    17      11.515  16.820 -14.939  1.00  0.00 
ATOM    143  CG2 ILE    17      10.562  17.451 -15.941  1.00  0.00 
ATOM    144  CG1 ILE    17      12.913  16.793 -15.539  1.00  0.00 
ATOM    145  CD1 ILE    17      13.557  18.165 -15.738  1.00  0.00 
ATOM    146  N   VAL    18       9.837  16.433 -12.315  1.00  0.00 
ATOM    147  HN  VAL    18      10.587  15.828 -12.048  1.00  0.00 
ATOM    148  CA  VAL    18       8.446  15.969 -11.908  1.00  0.00 
ATOM    149  C   VAL    18       8.378  15.206 -10.475  1.00  0.00 
ATOM    150  O   VAL    18       9.563  14.524 -10.075  1.00  0.00 
ATOM    151  CB  VAL    18       7.703  15.507 -13.164  1.00  0.00 
ATOM    152  CG1 VAL    18       8.395  15.669 -14.505  1.00  0.00 
ATOM    153  CG2 VAL    18       7.412  14.052 -12.871  1.00  0.00 
ATOM    154  N   THR    19       7.497  15.279  -9.729  1.00  0.00 
ATOM    155  HN  THR    19       6.676  15.808  -9.942  1.00  0.00 
ATOM    156  CA  THR    19       7.650  14.493  -8.336  1.00  0.00 
ATOM    157  C   THR    19       6.469  13.530  -8.287  1.00  0.00 
ATOM    158  O   THR    19       5.737  13.076  -9.224  1.00  0.00 
ATOM    159  CB  THR    19       7.674  15.433  -7.283  1.00  0.00 
ATOM    160  OG1 THR    19       6.600  16.357  -7.484  1.00  0.00 
ATOM    161  HG1 THR    19       6.875  17.263  -7.162  1.00  0.00 
ATOM    162  CG2 THR    19       8.993  16.162  -7.138  1.00  0.00 
ATOM    163  N   CYS    20       6.267  13.230  -7.107  1.00  0.00 
ATOM    164  HN  CYS    20       6.769  13.688  -6.374  1.00  0.00 
ATOM    165  CA  CYS    20       5.258  12.169  -6.790  1.00  0.00 
ATOM    166  C   CYS    20       4.846  12.064  -5.475  1.00  0.00 
ATOM    167  O   CYS    20       5.726  12.249  -4.366  1.00  0.00 
ATOM    168  CB  CYS    20       5.440  10.955  -7.616  1.00  0.00 
ATOM    169  SG  CYS    20       7.064  10.114  -7.618  1.00  0.00 
ATOM    170  N   GLU    21       3.773  11.672  -5.135  1.00  0.00 
ATOM    171  HN  GLU    21       3.061  11.404  -5.785  1.00  0.00 
ATOM    172  CA  GLU    21       3.574  11.613  -3.580  1.00  0.00 
ATOM    173  C   GLU    21       3.110  10.289  -3.131  1.00  0.00 
ATOM    174  O   GLU    21       1.760   9.979  -3.499  1.00  0.00 
ATOM    175  CB  GLU    21       2.630  12.723  -3.090  1.00  0.00 
ATOM    176  CG  GLU    21       3.074  13.307  -1.747  1.00  0.00 
ATOM    177  CD  GLU    21       2.411  14.664  -1.492  1.00  0.00 
ATOM    178  OE1 GLU    21       1.601  15.136  -2.331  1.00  0.00 
ATOM    179  OE2 GLU    21       2.675  15.306  -0.441  1.00  0.00 
ATOM    180  N   THR    22       3.984   9.634  -2.701  1.00  0.00 
ATOM    181  HN  THR    22       4.904  10.004  -2.570  1.00  0.00 
ATOM    182  CA  THR    22       3.693   8.403  -2.404  1.00  0.00 
ATOM    183  C   THR    22       4.009   8.164  -0.778  1.00  0.00 
ATOM    184  O   THR    22       4.975   8.870  -0.294  1.00  0.00 
ATOM    185  CB  THR    22       4.882   7.398  -2.830  1.00  0.00 
ATOM    186  OG1 THR    22       5.337   7.885  -4.098  1.00  0.00 
ATOM    187  HG1 THR    22       5.096   7.229  -4.813  1.00  0.00 
ATOM    188  CG2 THR    22       4.597   5.913  -2.895  1.00  0.00 
ATOM    189  N   ASN    23       3.117   7.475  -0.248  1.00  0.00 
ATOM    190  HN  ASN    23       2.319   7.141  -0.750  1.00  0.00 
ATOM    191  CA  ASN    23       3.342   7.186   1.216  1.00  0.00 
ATOM    192  C   ASN    23       2.694   5.899   1.707  1.00  0.00 
ATOM    193  O   ASN    23       1.446   5.551   1.558  1.00  0.00 
ATOM    194  CB  ASN    23       3.148   8.333   2.248  1.00  0.00 
ATOM    195  CG  ASN    23       4.280   8.502   3.247  1.00  0.00 
ATOM    196  OD1 ASN    23       5.060   7.581   3.483  1.00  0.00 
ATOM    197  ND2 ASN    23       4.355   9.687   3.825  1.00  0.00 
ATOM    198  HD21ASN    23       3.692  10.399   3.594  1.00  0.00 
ATOM    199  HD22ASN    23       5.075   9.872   4.494  1.00  0.00 
ATOM    200  N   THR    24       3.640   5.028   2.527  1.00  0.00 
ATOM    201  HN  THR    24       4.563   5.403   2.613  1.00  0.00 
ATOM    202  CA  THR    24       3.449   3.708   3.233  1.00  0.00 
ATOM    203  C   THR    24       2.004   3.481   3.474  1.00  0.00 
ATOM    204  O   THR    24       1.453   2.403   3.999  1.00  0.00 
ATOM    205  CB  THR    24       4.221   3.452   4.551  1.00  0.00 
ATOM    206  OG1 THR    24       5.446   4.190   4.460  1.00  0.00 
ATOM    207  HG1 THR    24       6.004   4.011   5.270  1.00  0.00 
ATOM    208  CG2 THR    24       4.495   1.974   4.715  1.00  0.00 
ATOM    209  N   GLY    25       1.112   4.162   3.091  1.00  0.00 
ATOM    210  HN  GLY    25       1.315   4.979   2.552  1.00  0.00 
ATOM    211  CA  GLY    25      -0.182   3.851   3.372  1.00  0.00 
ATOM    212  C   GLY    25      -0.846   3.115   2.030  1.00  0.00 
ATOM    213  O   GLY    25      -0.311   2.306   1.571  1.00  0.00 
ATOM    214  N   GLU    26      -1.910   3.668   1.509  1.00  0.00 
ATOM    215  HN  GLU    26      -2.324   4.430   2.006  1.00  0.00 
ATOM    216  CA  GLU    26      -2.510   3.279   0.319  1.00  0.00 
ATOM    217  C   GLU    26      -2.621   4.309  -0.755  1.00  0.00 
ATOM    218  O   GLU    26      -3.194   3.844  -1.814  1.00  0.00 
ATOM    219  CB  GLU    26      -3.912   2.610   0.514  1.00  0.00 
ATOM    220  CG  GLU    26      -3.860   1.439   1.499  1.00  0.00 
ATOM    221  CD  GLU    26      -5.267   0.956   1.849  1.00  0.00 
ATOM    222  OE1 GLU    26      -6.249   1.736   1.733  1.00  0.00 
ATOM    223  OE2 GLU    26      -5.445  -0.224   2.255  1.00  0.00 
ATOM    224  N   VAL    27      -2.070   5.330  -0.569  1.00  0.00 
ATOM    225  HN  VAL    27      -1.469   5.338   0.230  1.00  0.00 
ATOM    226  CA  VAL    27      -2.117   6.671  -1.354  1.00  0.00 
ATOM    227  C   VAL    27      -1.064   6.694  -2.285  1.00  0.00 
ATOM    228  O   VAL    27       0.097   6.805  -2.098  1.00  0.00 
ATOM    229  CB  VAL    27      -1.895   7.766  -0.181  1.00  0.00 
ATOM    230  CG1 VAL    27      -1.790   9.130  -0.842  1.00  0.00 
ATOM    231  CG2 VAL    27      -2.911   7.781   0.939  1.00  0.00 
ATOM    232  N   TYR    28      -1.464   6.575  -3.416  1.00  0.00 
ATOM    233  HN  TYR    28      -2.444   6.441  -3.563  1.00  0.00 
ATOM    234  CA  TYR    28      -0.687   6.612  -4.446  1.00  0.00 
ATOM    235  C   TYR    28      -0.784   7.928  -5.396  1.00  0.00 
ATOM    236  O   TYR    28      -1.495   7.595  -6.575  1.00  0.00 
ATOM    237  CB  TYR    28      -1.202   5.432  -5.549  1.00  0.00 
ATOM    238  CG  TYR    28      -1.071   4.080  -4.888  1.00  0.00 
ATOM    239  CD1 TYR    28       0.164   3.441  -4.820  1.00  0.00 
ATOM    240  CE1 TYR    28       0.310   2.207  -4.220  1.00  0.00 
ATOM    241  CZ  TYR    28      -0.794   1.578  -3.668  1.00  0.00 
ATOM    242  OH  TYR    28      -0.691   0.343  -3.060  1.00  0.00 
ATOM    243  HH  TYR    28       0.195  -0.118  -3.011  1.00  0.00 
ATOM    244  CE2 TYR    28      -2.027   2.195  -3.724  1.00  0.00 
ATOM    245  CD2 TYR    28      -2.157   3.436  -4.332  1.00  0.00 
ATOM    246  N   ARG    29      -0.352   9.143  -4.922  1.00  0.00 
ATOM    247  HN  ARG    29       0.029   9.201  -3.999  1.00  0.00 
ATOM    248  CA  ARG    29      -0.439  10.357  -5.742  1.00  0.00 
ATOM    249  C   ARG    29       0.632  10.584  -6.731  1.00  0.00 
ATOM    250  O   ARG    29       1.917   9.992  -6.616  1.00  0.00 
ATOM    251  CB  ARG    29      -0.547  11.627  -4.808  1.00  0.00 
ATOM    252  CG  ARG    29      -1.710  12.336  -5.081  1.00  0.00 
ATOM    253  CD  ARG    29      -1.881  13.504  -4.107  1.00  0.00 
ATOM    254  NE  ARG    29      -2.562  14.531  -4.581  1.00  0.00 
ATOM    255  HE  ARG    29      -2.289  14.905  -5.467  1.00  0.00 
ATOM    256  CZ  ARG    29      -3.603  15.107  -3.945  1.00  0.00 
ATOM    257  NH1 ARG    29      -4.212  16.132  -4.513  1.00  0.00 
ATOM    258  HH11ARG    29      -4.985  16.571  -4.055  1.00  0.00 
ATOM    259  HH12ARG    29      -3.900  16.470  -5.401  1.00  0.00 
ATOM    260  NH2 ARG    29      -3.982  14.628  -2.775  1.00  0.00 
ATOM    261  HH21ARG    29      -4.752  15.043  -2.290  1.00  0.00 
ATOM    262  HH22ARG    29      -3.499  13.850  -2.373  1.00  0.00 
ATOM    263  N   GLY    30       0.578  11.610  -7.898  1.00  0.00 
ATOM    264  HN  GLY    30      -0.220  12.191  -8.061  1.00  0.00 
ATOM    265  CA  GLY    30       1.740  11.668  -8.719  1.00  0.00 
ATOM    266  C   GLY    30       1.622  12.939  -9.625  1.00  0.00 
ATOM    267  O   GLY    30       0.301  13.189  -9.813  1.00  0.00 
ATOM    268  N   LYS    31       2.696  13.492 -10.187  1.00  0.00 
ATOM    269  HN  LYS    31       3.606  13.128  -9.986  1.00  0.00 
ATOM    270  CA  LYS    31       2.568  14.493 -10.988  1.00  0.00 
ATOM    271  C   LYS    31       3.860  14.962 -11.924  1.00  0.00 
ATOM    272  O   LYS    31       5.132  14.951 -11.365  1.00  0.00 
ATOM    273  CB  LYS    31       1.891  15.797 -10.460  1.00  0.00 
ATOM    274  CG  LYS    31       0.825  16.078 -11.521  1.00  0.00 
ATOM    275  CD  LYS    31       0.390  17.544 -11.482  1.00  0.00 
ATOM    276  CE  LYS    31      -0.369  17.859 -10.193  1.00  0.00 
ATOM    277  NZ  LYS    31      -0.703  19.299 -10.112  1.00  0.00 
ATOM    278  HZ1 LYS    31      -1.259  19.467  -9.298  1.00  0.00 
ATOM    279  HZ2 LYS    31       0.140  19.834 -10.056  1.00  0.00 
ATOM    280  HZ3 LYS    31      -1.216  19.568 -10.927  1.00  0.00 
ATOM    281  N   LEU    32       3.790  15.392 -13.293  1.00  0.00 
ATOM    282  HN  LEU    32       2.904  15.509 -13.741  1.00  0.00 
ATOM    283  CA  LEU    32       4.867  15.623 -13.930  1.00  0.00 
ATOM    284  C   LEU    32       5.143  17.300 -14.234  1.00  0.00 
ATOM    285  O   LEU    32       4.323  18.352 -13.945  1.00  0.00 
ATOM    286  CB  LEU    32       4.716  15.120 -15.401  1.00  0.00 
ATOM    287  CG  LEU    32       5.936  14.342 -15.898  1.00  0.00 
ATOM    288  CD1 LEU    32       5.644  12.931 -16.380  1.00  0.00 
ATOM    289  CD2 LEU    32       6.607  15.202 -16.984  1.00  0.00 
ATOM    290  N   ILE    33       6.333  17.820 -15.016  1.00  0.00 
ATOM    291  HN  ILE    33       6.949  17.177 -15.471  1.00  0.00 
ATOM    292  CA  ILE    33       6.600  19.354 -15.113  1.00  0.00 
ATOM    293  C   ILE    33       6.797  19.589 -16.403  1.00  0.00 
ATOM    294  O   ILE    33       7.803  19.108 -17.172  1.00  0.00 
ATOM    295  CB  ILE    33       7.586  19.802 -14.190  1.00  0.00 
ATOM    296  CG2 ILE    33       7.828  21.278 -14.456  1.00  0.00 
ATOM    297  CG1 ILE    33       7.298  19.607 -12.712  1.00  0.00 
ATOM    298  CD1 ILE    33       7.827  20.716 -11.798  1.00  0.00 
ATOM    299  N   GLU    34       5.966  20.611 -16.949  1.00  0.00 
ATOM    300  HN  GLU    34       5.372  21.142 -16.345  1.00  0.00 
ATOM    301  CA  GLU    34       5.976  20.907 -18.479  1.00  0.00 
ATOM    302  C   GLU    34       7.317  21.133 -18.856  1.00  0.00 
ATOM    303  O   GLU    34       7.746  21.200 -19.892  1.00  0.00 
ATOM    304  CB  GLU    34       5.063  22.082 -18.721  1.00  0.00 
ATOM    305  CG  GLU    34       5.595  22.818 -19.951  1.00  0.00 
ATOM    306  CD  GLU    34       6.031  24.242 -19.592  1.00  0.00 
ATOM    307  OE1 GLU    34       5.237  25.008 -18.983  1.00  0.00 
ATOM    308  OE2 GLU    34       7.181  24.647 -19.908  1.00  0.00 
ATOM    309  N   ALA    35       8.002  21.376 -18.034  1.00  0.00 
ATOM    310  HN  ALA    35       7.561  21.554 -17.154  1.00  0.00 
ATOM    311  CA  ALA    35       9.528  21.484 -18.028  1.00  0.00 
ATOM    312  C   ALA    35      10.278  20.715 -18.768  1.00  0.00 
ATOM    313  O   ALA    35      11.662  21.024 -19.159  1.00  0.00 
ATOM    314  CB  ALA    35      10.180  21.715 -16.600  1.00  0.00 
TER 
END 
