 
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 
REMARK 
REMARK T0059 Fragments 
REMARK 
ATOM      1  CA  MET     1      -0.035   0.033  -0.284  1.00  0.00 
ATOM      2  C   MET     1       1.558  -0.004  -0.173  1.00  0.00 
ATOM      3  O   MET     1       2.189   0.959  -0.096  1.00  0.00 
ATOM      4  N   SER     2       2.150  -1.200  -0.063  1.00  0.00 
ATOM      5  HN  SER     2       1.643  -2.057  -0.159  1.00  0.00 
ATOM      6  CA  SER     2       3.646  -1.168   0.218  1.00  0.00 
ATOM      7  C   SER     2       4.317  -1.759  -1.065  1.00  0.00 
ATOM      8  O   SER     2       5.469  -1.541  -1.145  1.00  0.00 
ATOM      9  CB  SER     2       3.986  -1.958   1.358  1.00  0.00 
ATOM     10  OG  SER     2       3.347  -3.197   1.388  1.00  0.00 
ATOM     11  HG  SER     2       3.777  -3.778   2.079  1.00  0.00 
ATOM     12  N   ILE     3       3.306  -2.434  -1.900  1.00  0.00 
ATOM     13  HN  ILE     3       2.332  -2.383  -1.678  1.00  0.00 
ATOM     14  CA  ILE     3       3.796  -3.204  -3.101  1.00  0.00 
ATOM     15  C   ILE     3       4.632  -1.982  -3.880  1.00  0.00 
ATOM     16  O   ILE     3       5.650  -2.058  -4.225  1.00  0.00 
ATOM     17  CB  ILE     3       2.554  -3.318  -4.146  1.00  0.00 
ATOM     18  CG2 ILE     3       2.911  -4.287  -5.260  1.00  0.00 
ATOM     19  CG1 ILE     3       1.451  -3.926  -3.298  1.00  0.00 
ATOM     20  CD1 ILE     3       1.852  -5.178  -2.514  1.00  0.00 
ATOM     21  N   GLY     4       4.129  -0.916  -4.244  1.00  0.00 
ATOM     22  HN  GLY     4       3.163  -0.681  -4.133  1.00  0.00 
ATOM     23  CA  GLY     4       5.057  -0.102  -4.815  1.00  0.00 
ATOM     24  C   GLY     4       5.173  -0.225  -6.293  1.00  0.00 
ATOM     25  O   GLY     4       6.071   0.224  -6.680  1.00  0.00 
ATOM     26  N   VAL     5       4.119  -0.907  -6.949  1.00  0.00 
ATOM     27  HN  VAL     5       3.420  -1.354  -6.391  1.00  0.00 
ATOM     28  CA  VAL     5       4.018  -0.980  -8.259  1.00  0.00 
ATOM     29  C   VAL     5       4.253   0.481  -8.703  1.00  0.00 
ATOM     30  O   VAL     5       5.125   0.857  -9.682  1.00  0.00 
ATOM     31  CB  VAL     5       2.369  -1.315  -8.742  1.00  0.00 
ATOM     32  CG1 VAL     5       1.853  -2.560  -8.042  1.00  0.00 
ATOM     33  CG2 VAL     5       1.503  -0.116  -8.430  1.00  0.00 
ATOM     34  N   PRO     6       3.747   1.683  -8.049  1.00  0.00 
ATOM     35  CA  PRO     6       4.157   3.236  -8.371  1.00  0.00 
ATOM     36  CD  PRO     6       3.457   1.716  -6.529  1.00  0.00 
ATOM     37  C   PRO     6       5.540   3.469  -8.299  1.00  0.00 
ATOM     38  O   PRO     6       6.058   4.257  -8.953  1.00  0.00 
ATOM     39  CB  PRO     6       3.550   4.076  -7.267  1.00  0.00 
ATOM     40  CG  PRO     6       3.524   3.151  -6.040  1.00  0.00 
ATOM     41  N   ILE     7       6.392   2.786  -7.386  1.00  0.00 
ATOM     42  HN  ILE     7       5.973   2.034  -6.877  1.00  0.00 
ATOM     43  CA  ILE     7       7.636   3.013  -7.131  1.00  0.00 
ATOM     44  C   ILE     7       8.520   2.843  -8.431  1.00  0.00 
ATOM     45  O   ILE     7       9.288   3.560  -8.732  1.00  0.00 
ATOM     46  CB  ILE     7       8.385   1.828  -6.248  1.00  0.00 
ATOM     47  CG2 ILE     7       9.901   1.795  -6.365  1.00  0.00 
ATOM     48  CG1 ILE     7       8.006   2.146  -4.812  1.00  0.00 
ATOM     49  CD1 ILE     7       8.231   3.599  -4.389  1.00  0.00 
ATOM     50  N   LYS     8       8.531   1.676  -9.230  1.00  0.00 
ATOM     51  HN  LYS     8       7.978   0.920  -8.879  1.00  0.00 
ATOM     52  CA  LYS     8       9.214   1.405 -10.471  1.00  0.00 
ATOM     53  C   LYS     8       8.928   2.761 -11.439  1.00  0.00 
ATOM     54  O   LYS     8       9.659   3.388 -11.930  1.00  0.00 
ATOM     55  CB  LYS     8       8.451   0.247 -11.248  1.00  0.00 
ATOM     56  CG  LYS     8       9.433  -0.657 -11.996  1.00  0.00 
ATOM     57  CD  LYS     8       8.979  -0.884 -13.440  1.00  0.00 
ATOM     58  CE  LYS     8       9.707  -2.076 -14.062  1.00  0.00 
ATOM     59  NZ  LYS     8      10.040  -1.813 -15.480  1.00  0.00 
ATOM     60  HZ1 LYS     8      10.084  -0.826 -15.635  1.00  0.00 
ATOM     61  HZ2 LYS     8      10.926  -2.224 -15.696  1.00  0.00 
ATOM     62  HZ3 LYS     8       9.335  -2.211 -16.067  1.00  0.00 
ATOM     63  N   VAL     9       7.455   3.022 -11.339  1.00  0.00 
ATOM     64  HN  VAL     9       6.917   2.492 -10.683  1.00  0.00 
ATOM     65  CA  VAL     9       6.699   4.129 -12.252  1.00  0.00 
ATOM     66  C   VAL     9       7.639   5.301 -12.036  1.00  0.00 
ATOM     67  O   VAL     9       7.950   6.148 -12.733  1.00  0.00 
ATOM     68  CB  VAL     9       5.360   4.786 -11.665  1.00  0.00 
ATOM     69  CG1 VAL     9       4.924   6.027 -12.425  1.00  0.00 
ATOM     70  CG2 VAL     9       4.321   3.692 -11.767  1.00  0.00 
ATOM     71  N   LEU    10       8.038   5.453 -10.792  1.00  0.00 
ATOM     72  HN  LEU    10       7.787   4.759 -10.117  1.00  0.00 
ATOM     73  CA  LEU    10       8.723   6.439 -10.421  1.00  0.00 
ATOM     74  C   LEU    10      10.148   6.560 -10.972  1.00  0.00 
ATOM     75  O   LEU    10      10.635   7.407 -11.588  1.00  0.00 
ATOM     76  CB  LEU    10       9.067   6.479  -8.813  1.00  0.00 
ATOM     77  CG  LEU    10       8.068   7.107  -7.840  1.00  0.00 
ATOM     78  CD1 LEU    10       6.607   6.801  -8.131  1.00  0.00 
ATOM     79  CD2 LEU    10       8.485   6.672  -6.423  1.00  0.00 
ATOM     80  N   HIS    11      10.861   5.250 -10.747  1.00  0.00 
ATOM     81  HN  HIS    11      10.337   4.489 -10.364  1.00  0.00 
ATOM     82  CA  HIS    11      12.352   5.013 -11.073  1.00  0.00 
ATOM     83  C   HIS    11      12.573   5.586 -12.357  1.00  0.00 
ATOM     84  O   HIS    11      13.361   6.249 -12.646  1.00  0.00 
ATOM     85  CB  HIS    11      12.434   3.338 -11.305  1.00  0.00 
ATOM     86  CG  HIS    11      13.751   2.893 -11.299  1.00  0.00 
ATOM     87  ND1 HIS    11      14.663   3.052 -10.262  1.00  0.00 
ATOM     88  HD1 HIS    11      14.486   3.506  -9.389  1.00  0.00 
ATOM     89  CE1 HIS    11      15.863   2.470 -10.652  1.00  0.00 
ATOM     90  NE2 HIS    11      15.696   1.953 -11.932  1.00  0.00 
ATOM     91  HE2 HIS    11      16.392   1.478 -12.470  1.00  0.00 
ATOM     92  CD2 HIS    11      14.389   2.213 -12.332  1.00  0.00 
ATOM     93  N   GLU    12      11.472   5.143 -13.278  1.00  0.00 
ATOM     94  HN  GLU    12      10.705   4.608 -12.924  1.00  0.00 
ATOM     95  CA  GLU    12      11.526   5.479 -14.617  1.00  0.00 
ATOM     96  C   GLU    12      11.442   7.182 -14.649  1.00  0.00 
ATOM     97  O   GLU    12      11.872   7.779 -15.569  1.00  0.00 
ATOM     98  CB  GLU    12      10.078   5.219 -15.320  1.00  0.00 
ATOM     99  CG  GLU    12      10.327   5.561 -16.788  1.00  0.00 
ATOM    100  CD  GLU    12      11.213   4.506 -17.455  1.00  0.00 
ATOM    101  OE1 GLU    12      10.685   3.534 -18.061  1.00  0.00 
ATOM    102  OE2 GLU    12      12.467   4.606 -17.397  1.00  0.00 
ATOM    103  N   ALA    13      10.803   7.873 -13.836  1.00  0.00 
ATOM    104  HN  ALA    13      10.257   7.349 -13.182  1.00  0.00 
ATOM    105  CA  ALA    13      10.711   9.428 -13.665  1.00  0.00 
ATOM    106  C   ALA    13      11.699  10.040 -12.572  1.00  0.00 
ATOM    107  O   ALA    13      11.551  10.151 -11.386  1.00  0.00 
ATOM    108  CB  ALA    13       9.397  10.048 -13.214  1.00  0.00 
ATOM    109  N   GLU    14      13.069  10.583 -12.898  1.00  0.00 
ATOM    110  HN  GLU    14      13.350  10.625 -13.857  1.00  0.00 
ATOM    111  CA  GLU    14      14.009  11.052 -11.871  1.00  0.00 
ATOM    112  C   GLU    14      13.491  11.862 -10.841  1.00  0.00 
ATOM    113  O   GLU    14      14.042  12.011  -9.789  1.00  0.00 
ATOM    114  CB  GLU    14      15.005  12.119 -12.792  1.00  0.00 
ATOM    115  CG  GLU    14      15.994  11.387 -13.701  1.00  0.00 
ATOM    116  CD  GLU    14      17.058  12.347 -14.240  1.00  0.00 
ATOM    117  OE1 GLU    14      18.266  12.202 -13.908  1.00  0.00 
ATOM    118  OE2 GLU    14      16.727  13.283 -15.015  1.00  0.00 
ATOM    119  N   GLY    15      12.490  12.685 -10.853  1.00  0.00 
ATOM    120  HN  GLY    15      12.050  12.879 -11.730  1.00  0.00 
ATOM    121  CA  GLY    15      11.921  13.404  -9.553  1.00  0.00 
ATOM    122  C   GLY    15      12.218  14.842  -9.573  1.00  0.00 
ATOM    123  O   GLY    15      11.886  15.613  -8.596  1.00  0.00 
ATOM    124  N   HIS    16      12.850  15.211 -10.437  1.00  0.00 
ATOM    125  HN  HIS    16      13.099  14.635 -11.216  1.00  0.00 
ATOM    126  CA  HIS    16      13.293  16.685 -10.303  1.00  0.00 
ATOM    127  C   HIS    16      12.385  17.632 -11.220  1.00  0.00 
ATOM    128  O   HIS    16      11.975  18.548 -10.693  1.00  0.00 
ATOM    129  CB  HIS    16      14.767  16.959 -10.784  1.00  0.00 
ATOM    130  CG  HIS    16      15.765  16.259 -10.113  1.00  0.00 
ATOM    131  ND1 HIS    16      16.145  14.945 -10.356  1.00  0.00 
ATOM    132  HD1 HIS    16      15.750  14.336 -11.044  1.00  0.00 
ATOM    133  CE1 HIS    16      17.172  14.626  -9.474  1.00  0.00 
ATOM    134  NE2 HIS    16      17.423  15.743  -8.684  1.00  0.00 
ATOM    135  HE2 HIS    16      18.108  15.808  -7.959  1.00  0.00 
ATOM    136  CD2 HIS    16      16.554  16.752  -9.080  1.00  0.00 
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 
TER 
END 
