 
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 2 
REMARK 
REMARK T0046 Fragments 
REMARK 
PARENT N/A 
REMARK 
REMARK T0046 Fragments 
REMARK 
ATOM      4  N   PRO     2       2.121  -1.191   0.000  1.00  0.00 
ATOM      5  CA  PRO     2       3.643  -1.308   0.000  1.00  0.00 
ATOM      6  CD  PRO     2       1.581  -2.531  -0.336  1.00  0.00 
ATOM      7  C   PRO     2       4.317  -0.754  -1.253  1.00  0.00 
ATOM      8  O   PRO     2       5.438  -0.201  -1.123  1.00  0.00 
ATOM      9  CB  PRO     2       3.956  -2.794   0.109  1.00  0.00 
ATOM     10  CG  PRO     2       2.779  -3.395  -0.679  1.00  0.00 
ATOM     11  N   SER     3       3.465  -0.745  -2.392  1.00  0.00 
ATOM     12  HN  SER     3       2.490  -0.951  -2.312  1.00  0.00 
ATOM     13  CA  SER     3       4.042  -0.437  -3.626  1.00  0.00 
ATOM     14  C   SER     3       4.290   1.097  -3.894  1.00  0.00 
ATOM     15  O   SER     3       3.470   1.878  -3.658  1.00  0.00 
ATOM     16  CB  SER     3       3.227  -0.930  -4.779  1.00  0.00 
ATOM     17  OG  SER     3       2.060  -0.194  -4.968  1.00  0.00 
ATOM     18  HG  SER     3       1.940  -0.003  -5.942  1.00  0.00 
ATOM     19  N   ILE     4       5.451   1.635  -4.286  1.00  0.00 
ATOM     20  HN  ILE     4       6.234   1.020  -4.381  1.00  0.00 
ATOM     21  CA  ILE     4       5.670   3.060  -4.589  1.00  0.00 
ATOM     22  C   ILE     4       6.076   3.366  -5.840  1.00  0.00 
ATOM     23  O   ILE     4       6.928   2.753  -6.141  1.00  0.00 
ATOM     24  CB  ILE     4       6.206   3.961  -3.431  1.00  0.00 
ATOM     25  CG2 ILE     4       5.350   3.997  -2.174  1.00  0.00 
ATOM     26  CG1 ILE     4       7.515   3.258  -3.116  1.00  0.00 
ATOM     27  CD1 ILE     4       8.424   3.996  -2.131  1.00  0.00 
ATOM     28  N   THR     5       5.402   4.397  -6.296  1.00  0.00 
ATOM     29  HN  THR     5       4.656   4.686  -5.696  1.00  0.00 
ATOM     30  CA  THR     5       5.537   5.275  -7.611  1.00  0.00 
ATOM     31  C   THR     5       6.671   6.422  -7.519  1.00  0.00 
ATOM     32  O   THR     5       7.034   6.677  -6.231  1.00  0.00 
ATOM     33  CB  THR     5       4.362   5.252  -8.348  1.00  0.00 
ATOM     34  OG1 THR     5       3.997   6.619  -8.130  1.00  0.00 
ATOM     35  HG1 THR     5       3.031   6.670  -7.877  1.00  0.00 
ATOM     36  CG2 THR     5       3.224   4.325  -7.979  1.00  0.00 
ATOM     37  N   ALA     6       6.925   7.009  -8.722  1.00  0.00 
ATOM     38  HN  ALA     6       6.336   6.703  -9.470  1.00  0.00 
ATOM     39  CA  ALA     6       7.875   7.969  -9.081  1.00  0.00 
ATOM     40  C   ALA     6       8.132   8.461 -10.649  1.00  0.00 
ATOM     41  O   ALA     6       8.411   7.496 -11.347  1.00  0.00 
ATOM     42  CB  ALA     6       9.326   7.653  -8.745  1.00  0.00 
ATOM     43  N   TYR     7       8.080   9.721 -10.680  1.00  0.00 
ATOM     44  HN  TYR     7       8.060  10.172  -9.788  1.00  0.00 
ATOM     45  CA  TYR     7       8.042  10.687 -11.929  1.00  0.00 
ATOM     46  C   TYR     7       9.239  11.402 -12.422  1.00  0.00 
ATOM     47  O   TYR     7       9.637  12.706 -12.050  1.00  0.00 
ATOM     48  CB  TYR     7       6.853  11.677 -12.090  1.00  0.00 
ATOM     49  CG  TYR     7       6.053  11.609 -13.369  1.00  0.00 
ATOM     50  CD1 TYR     7       6.678  11.716 -14.606  1.00  0.00 
ATOM     51  CE1 TYR     7       5.969  11.658 -15.789  1.00  0.00 
ATOM     52  CZ  TYR     7       4.596  11.490 -15.753  1.00  0.00 
ATOM     53  OH  TYR     7       3.846  11.426 -16.912  1.00  0.00 
ATOM     54  HH  TYR     7       4.294  11.502 -17.803  1.00  0.00 
ATOM     55  CE2 TYR     7       3.952  11.380 -14.536  1.00  0.00 
ATOM     56  CD2 TYR     7       4.683  11.439 -13.357  1.00  0.00 
ATOM     57  N   SER     8       9.999  10.837 -13.258  1.00  0.00 
ATOM     58  HN  SER     8       9.782   9.952 -13.671  1.00  0.00 
ATOM     59  CA  SER     8      11.058  11.477 -13.534  1.00  0.00 
ATOM     60  C   SER     8      10.652  12.518 -14.729  1.00  0.00 
ATOM     61  O   SER     8       9.594  12.355 -15.591  1.00  0.00 
ATOM     62  CB  SER     8      12.202  10.778 -14.311  1.00  0.00 
ATOM     63  OG  SER     8      13.018   9.953 -13.539  1.00  0.00 
ATOM     64  HG  SER     8      13.671   9.481 -14.131  1.00  0.00 
ATOM     65  N   LYS     9      11.480  13.298 -14.788  1.00  0.00 
ATOM     66  HN  LYS     9      12.209  13.208 -14.110  1.00  0.00 
ATOM     67  CA  LYS     9      11.633  14.530 -15.822  1.00  0.00 
ATOM     68  C   LYS     9      13.006  14.830 -15.908  1.00  0.00 
ATOM     69  O   LYS     9      13.614  14.548 -14.953  1.00  0.00 
ATOM     70  CB  LYS     9      10.680  15.530 -15.428  1.00  0.00 
ATOM     71  CG  LYS     9      10.912  16.194 -14.068  1.00  0.00 
ATOM     72  CD  LYS     9       9.846  17.255 -13.787  1.00  0.00 
ATOM     73  CE  LYS     9      10.453  18.658 -13.800  1.00  0.00 
ATOM     74  NZ  LYS     9       9.396  19.694 -13.759  1.00  0.00 
ATOM     75  HZ1 LYS     9       8.759  19.551 -14.516  1.00  0.00 
ATOM     76  HZ2 LYS     9       8.902  19.632 -12.892  1.00  0.00 
ATOM     77  HZ3 LYS     9       9.813  20.599 -13.841  1.00  0.00 
ATOM     78  N   ASN    10      13.300  15.505 -17.072  1.00  0.00 
ATOM     79  HN  ASN    10      12.553  15.614 -17.728  1.00  0.00 
ATOM     80  CA  ASN    10      14.581  16.074 -17.445  1.00  0.00 
ATOM     81  C   ASN    10      15.739  15.127 -17.079  1.00  0.00 
ATOM     82  O   ASN    10      16.522  15.599 -16.489  1.00  0.00 
ATOM     83  CB  ASN    10      14.805  17.403 -16.719  1.00  0.00 
ATOM     84  CG  ASN    10      15.378  18.443 -17.668  1.00  0.00 
ATOM     85  OD1 ASN    10      15.088  19.633 -17.557  1.00  0.00 
ATOM     86  ND2 ASN    10      16.192  17.975 -18.597  1.00  0.00 
ATOM     87  HD21ASN    10      16.392  16.996 -18.640  1.00  0.00 
ATOM     88  HD22ASN    10      16.608  18.600 -19.258  1.00  0.00 
ATOM     89  N   GLY    11      15.767  13.938 -17.482  1.00  0.00 
ATOM     90  HN  GLY    11      15.015  13.584 -18.037  1.00  0.00 
ATOM     91  CA  GLY    11      16.884  13.075 -17.147  1.00  0.00 
ATOM     92  C   GLY    11      17.195  13.032 -15.561  1.00  0.00 
ATOM     93  O   GLY    11      18.477  12.788 -15.272  1.00  0.00 
ATOM     94  N   LEU    12      16.256  13.245 -14.709  1.00  0.00 
ATOM     95  HN  LEU    12      15.326  13.378 -15.051  1.00  0.00 
ATOM     96  CA  LEU    12      16.451  13.295 -13.444  1.00  0.00 
ATOM     97  C   LEU    12      16.478  11.834 -12.762  1.00  0.00 
ATOM     98  O   LEU    12      15.774  10.836 -13.023  1.00  0.00 
ATOM     99  CB  LEU    12      15.351  14.010 -12.601  1.00  0.00 
ATOM    100  CG  LEU    12      15.703  15.382 -12.021  1.00  0.00 
ATOM    101  CD1 LEU    12      14.781  15.870 -10.916  1.00  0.00 
ATOM    102  CD2 LEU    12      17.172  15.318 -11.567  1.00  0.00 
ATOM    103  N   LYS    13      17.175  11.733 -11.728  1.00  0.00 
ATOM    104  HN  LYS    13      17.608  12.539 -11.326  1.00  0.00 
ATOM    105  CA  LYS    13      17.360  10.297 -11.064  1.00  0.00 
ATOM    106  C   LYS    13      16.200  10.019 -10.259  1.00  0.00 
ATOM    107  O   LYS    13      15.689  10.915  -9.692  1.00  0.00 
ATOM    108  CB  LYS    13      18.609  10.159 -10.191  1.00  0.00 
ATOM    109  CG  LYS    13      18.543  11.164  -9.041  1.00  0.00 
ATOM    110  CD  LYS    13      19.589  10.847  -7.972  1.00  0.00 
ATOM    111  CE  LYS    13      21.000  10.884  -8.559  1.00  0.00 
ATOM    112  NZ  LYS    13      22.003  11.177  -7.509  1.00  0.00 
ATOM    113  HZ1 LYS    13      22.365  10.319  -7.144  1.00  0.00 
ATOM    114  HZ2 LYS    13      22.750  11.713  -7.902  1.00  0.00 
ATOM    115  HZ3 LYS    13      21.571  11.696  -6.772  1.00  0.00 
ATOM    116  N   ILE    14      15.567   8.694 -10.167  1.00  0.00 
ATOM    117  HN  ILE    14      15.871   7.957 -10.771  1.00  0.00 
ATOM    118  CA  ILE    14      14.546   8.455  -9.245  1.00  0.00 
ATOM    119  C   ILE    14      14.953   7.725  -8.103  1.00  0.00 
ATOM    120  O   ILE    14      16.183   6.983  -8.181  1.00  0.00 
ATOM    121  CB  ILE    14      13.238   8.064  -9.668  1.00  0.00 
ATOM    122  CG2 ILE    14      12.692   8.966 -10.763  1.00  0.00 
ATOM    123  CG1 ILE    14      13.416   6.663 -10.227  1.00  0.00 
ATOM    124  CD1 ILE    14      12.719   5.555  -9.431  1.00  0.00 
ATOM    125  N   GLU    15      14.159   7.743  -7.047  1.00  0.00 
ATOM    126  HN  GLU    15      13.277   8.212  -7.087  1.00  0.00 
ATOM    127  CA  GLU    15      14.583   7.068  -5.813  1.00  0.00 
ATOM    128  C   GLU    15      13.600   5.948  -5.463  1.00  0.00 
ATOM    129  O   GLU    15      12.400   6.035  -5.764  1.00  0.00 
ATOM    130  CB  GLU    15      14.632   8.050  -4.640  1.00  0.00 
ATOM    131  CG  GLU    15      15.818   9.006  -4.774  1.00  0.00 
ATOM    132  CD  GLU    15      15.929   9.919  -3.552  1.00  0.00 
ATOM    133  OE1 GLU    15      16.045   9.421  -2.401  1.00  0.00 
ATOM    134  OE2 GLU    15      15.906  11.171  -3.696  1.00  0.00 
ATOM    135  N   PHE    16      14.143   4.817  -4.962  1.00  0.00 
ATOM    136  HN  PHE    16      15.138   4.724  -4.993  1.00  0.00 
ATOM    137  CA  PHE    16      13.400   3.759  -4.398  1.00  0.00 
ATOM    138  C   PHE    16      13.636   3.514  -2.805  1.00  0.00 
ATOM    139  O   PHE    16      14.853   3.161  -2.174  1.00  0.00 
ATOM    140  CB  PHE    16      13.818   2.226  -4.921  1.00  0.00 
ATOM    141  CG  PHE    16      13.333   1.104  -4.099  1.00  0.00 
ATOM    142  CD1 PHE    16      12.020   0.968  -3.714  1.00  0.00 
ATOM    143  CE1 PHE    16      11.581  -0.079  -2.949  1.00  0.00 
ATOM    144  CZ  PHE    16      12.493  -1.042  -2.543  1.00  0.00 
ATOM    145  CE2 PHE    16      13.822  -0.948  -2.907  1.00  0.00 
ATOM    146  CD2 PHE    16      14.208   0.125  -3.677  1.00  0.00 
ATOM    147  N   THR    17      12.380   3.579  -2.097  1.00  0.00 
ATOM    148  HN  THR    17      11.569   3.817  -2.632  1.00  0.00 
ATOM    149  CA  THR    17      12.190   3.337  -0.714  1.00  0.00 
ATOM    150  C   THR    17      11.473   2.022  -0.343  1.00  0.00 
ATOM    151  O   THR    17      10.413   1.799  -1.088  1.00  0.00 
ATOM    152  CB  THR    17      11.433   4.545  -0.069  1.00  0.00 
ATOM    153  OG1 THR    17      12.149   5.742  -0.395  1.00  0.00 
ATOM    154  HG1 THR    17      13.124   5.535  -0.480  1.00  0.00 
ATOM    155  CG2 THR    17      11.280   4.400   1.430  1.00  0.00 
ATOM    156  N   PHE    18      11.848   1.355   0.662  1.00  0.00 
ATOM    157  HN  PHE    18      12.689   1.612   1.138  1.00  0.00 
ATOM    158  CA  PHE    18      11.066   0.206   1.143  1.00  0.00 
ATOM    159  C   PHE    18      11.088   0.270   2.659  1.00  0.00 
ATOM    160  O   PHE    18      12.250   0.542   3.109  1.00  0.00 
ATOM    161  CB  PHE    18      12.048  -1.118   1.220  1.00  0.00 
ATOM    162  CG  PHE    18      11.243  -2.349   1.183  1.00  0.00 
ATOM    163  CD1 PHE    18       9.868  -2.350   1.245  1.00  0.00 
ATOM    164  CE1 PHE    18       9.128  -3.502   1.211  1.00  0.00 
ATOM    165  CZ  PHE    18       9.788  -4.719   1.110  1.00  0.00 
ATOM    166  CE2 PHE    18      11.166  -4.768   1.046  1.00  0.00 
ATOM    167  CD2 PHE    18      11.857  -3.579   1.084  1.00  0.00 
ATOM    168  N   GLU    19       9.942   0.095   3.184  1.00  0.00 
ATOM    169  HN  GLU    19       9.143   0.065   2.584  1.00  0.00 
ATOM    170  CA  GLU    19       9.737  -0.065   4.631  1.00  0.00 
ATOM    171  C   GLU    19      10.659  -0.795   5.343  1.00  0.00 
ATOM    172  O   GLU    19      11.357  -0.295   6.455  1.00  0.00 
ATOM    173  CB  GLU    19       8.260  -0.288   4.959  1.00  0.00 
ATOM    174  CG  GLU    19       7.296   0.897   4.889  1.00  0.00 
ATOM    175  CD  GLU    19       5.902   0.502   5.383  1.00  0.00 
ATOM    176  OE1 GLU    19       5.590  -0.714   5.481  1.00  0.00 
ATOM    177  OE2 GLU    19       5.068   1.395   5.693  1.00  0.00 
ATOM    178  N   ARG    20      10.913  -2.247   4.920  1.00  0.00 
ATOM    179  HN  ARG    20      10.366  -2.632   4.177  1.00  0.00 
ATOM    180  CA  ARG    20      11.813  -3.002   5.489  1.00  0.00 
ATOM    181  C   ARG    20      12.051  -4.019   4.546  1.00  0.00 
ATOM    182  O   ARG    20      10.919  -4.493   4.000  1.00  0.00 
ATOM    183  CB  ARG    20      11.259  -3.649   6.884  1.00  0.00 
ATOM    184  CG  ARG    20      10.763  -2.675   7.744  1.00  0.00 
ATOM    185  CD  ARG    20       9.682  -3.252   8.660  1.00  0.00 
ATOM    186  NE  ARG    20       9.814  -2.952   9.937  1.00  0.00 
ATOM    187  HE  ARG    20      10.279  -2.098  10.171  1.00  0.00 
ATOM    188  CZ  ARG    20       9.362  -3.723  10.948  1.00  0.00 
ATOM    189  NH1 ARG    20       9.550  -3.322  12.192  1.00  0.00 
ATOM    190  HH11ARG    20       9.221  -3.882  12.953  1.00  0.00 
ATOM    191  HH12ARG    20      10.021  -2.459  12.373  1.00  0.00 
ATOM    192  NH2 ARG    20       8.745  -4.853  10.663  1.00  0.00 
ATOM    193  HH21ARG    20       8.404  -5.436  11.400  1.00  0.00 
ATOM    194  HH22ARG    20       8.618  -5.127   9.710  1.00  0.00 
TER 
END 
