 
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 
REMARK 
REMARK T0046 Fragments cont. 
REMARK 
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 
ATOM    195  N   SER    21      13.416  -4.266   4.264  1.00  0.00 
ATOM    196  HN  SER    21      14.104  -3.767   4.791  1.00  0.00 
ATOM    197  CA  SER    21      13.873  -5.200   3.256  1.00  0.00 
ATOM    198  C   SER    21      13.842  -6.627   3.758  1.00  0.00 
ATOM    199  O   SER    21      13.646  -6.875   4.954  1.00  0.00 
ATOM    200  CB  SER    21      15.309  -4.882   2.849  1.00  0.00 
ATOM    201  OG  SER    21      16.286  -5.421   3.682  1.00  0.00 
ATOM    202  HG  SER    21      17.172  -5.394   3.219  1.00  0.00 
ATOM    203  N   ASN    22      14.179  -7.626   3.066  1.00  0.00 
ATOM    204  HN  ASN    22      14.463  -7.462   2.121  1.00  0.00 
ATOM    205  CA  ASN    22      14.185  -9.114   3.583  1.00  0.00 
ATOM    206  C   ASN    22      15.614  -9.635   3.593  1.00  0.00 
ATOM    207  O   ASN    22      16.030  -9.660   2.579  1.00  0.00 
ATOM    208  CB  ASN    22      13.173  -9.767   2.819  1.00  0.00 
ATOM    209  CG  ASN    22      12.188 -10.550   3.672  1.00  0.00 
ATOM    210  OD1 ASN    22      10.981 -10.314   3.630  1.00  0.00 
ATOM    211  ND2 ASN    22      12.721 -11.482   4.440  1.00  0.00 
ATOM    212  HD21ASN    22      13.710 -11.630   4.433  1.00  0.00 
ATOM    213  HD22ASN    22      12.136 -12.040   5.028  1.00  0.00 
ATOM    214  N   THR    23      16.052  -9.775   5.007  1.00  0.00 
ATOM    215  HN  THR    23      15.351  -9.529   5.676  1.00  0.00 
ATOM    216  CA  THR    23      17.309 -10.203   5.600  1.00  0.00 
ATOM    217  C   THR    23      18.095 -11.343   5.022  1.00  0.00 
ATOM    218  O   THR    23      19.409 -11.371   4.680  1.00  0.00 
ATOM    219  CB  THR    23      17.003 -10.809   7.096  1.00  0.00 
ATOM    220  OG1 THR    23      16.224  -9.703   7.566  1.00  0.00 
ATOM    221  HG1 THR    23      16.674  -9.290   8.357  1.00  0.00 
ATOM    222  CG2 THR    23      18.134 -11.118   8.050  1.00  0.00 
ATOM    223  N   ASN    24      17.488 -12.344   5.047  1.00  0.00 
ATOM    224  HN  ASN    24      16.619 -12.353   5.542  1.00  0.00 
ATOM    225  CA  ASN    24      17.924 -13.587   4.397  1.00  0.00 
ATOM    226  C   ASN    24      18.590 -13.005   2.903  1.00  0.00 
ATOM    227  O   ASN    24      18.064 -11.763   2.577  1.00  0.00 
ATOM    228  CB  ASN    24      16.483 -14.145   3.626  1.00  0.00 
ATOM    229  CG  ASN    24      15.702 -14.862   4.712  1.00  0.00 
ATOM    230  OD1 ASN    24      16.223 -15.146   5.789  1.00  0.00 
ATOM    231  ND2 ASN    24      14.449 -15.151   4.411  1.00  0.00 
ATOM    232  HD21ASN    24      14.078 -14.896   3.518  1.00  0.00 
ATOM    233  HD22ASN    24      13.872 -15.625   5.076  1.00  0.00 
ATOM    234  N   PRO    25      19.576 -13.729   2.086  1.00  0.00 
ATOM    235  CA  PRO    25      20.176 -13.093   0.619  1.00  0.00 
ATOM    236  CD  PRO    25      20.102 -15.126   2.140  1.00  0.00 
ATOM    237  C   PRO    25      19.433 -13.505  -0.874  1.00  0.00 
ATOM    238  O   PRO    25      19.806 -13.293  -1.850  1.00  0.00 
ATOM    239  CB  PRO    25      21.549 -14.092   0.498  1.00  0.00 
ATOM    240  CG  PRO    25      21.076 -15.460   1.019  1.00  0.00 
ATOM    241  N   SER    26      18.106 -14.098  -1.134  1.00  0.00 
ATOM    242  HN  SER    26      17.511 -14.456  -0.415  1.00  0.00 
ATOM    243  CA  SER    26      17.761 -14.107  -2.520  1.00  0.00 
ATOM    244  C   SER    26      16.639 -13.045  -3.076  1.00  0.00 
ATOM    245  O   SER    26      15.505 -13.127  -3.266  1.00  0.00 
ATOM    246  CB  SER    26      17.280 -15.456  -3.003  1.00  0.00 
ATOM    247  OG  SER    26      18.226 -16.465  -2.848  1.00  0.00 
ATOM    248  HG  SER    26      19.077 -16.074  -2.497  1.00  0.00 
ATOM    249  N   VAL    27      16.939 -12.021  -3.514  1.00  0.00 
ATOM    250  HN  VAL    27      17.895 -11.769  -3.661  1.00  0.00 
ATOM    251  CA  VAL    27      15.896 -11.158  -3.825  1.00  0.00 
ATOM    252  C   VAL    27      15.654 -11.022  -5.292  1.00  0.00 
ATOM    253  O   VAL    27      16.509 -11.049  -6.335  1.00  0.00 
ATOM    254  CB  VAL    27      16.264  -9.651  -3.287  1.00  0.00 
ATOM    255  CG1 VAL    27      17.018  -8.928  -4.390  1.00  0.00 
ATOM    256  CG2 VAL    27      15.059  -8.857  -2.839  1.00  0.00 
ATOM    257  N   THR    28      14.263 -10.990  -5.754  1.00  0.00 
ATOM    258  HN  THR    28      13.485 -11.107  -5.136  1.00  0.00 
ATOM    259  CA  THR    28      14.115 -10.787  -7.098  1.00  0.00 
ATOM    260  C   THR    28      13.776  -9.421  -7.457  1.00  0.00 
ATOM    261  O   THR    28      12.744  -8.771  -6.772  1.00  0.00 
ATOM    262  CB  THR    28      12.681 -11.647  -7.488  1.00  0.00 
ATOM    263  OG1 THR    28      12.889 -12.925  -6.875  1.00  0.00 
ATOM    264  HG1 THR    28      12.757 -13.647  -7.555  1.00  0.00 
ATOM    265  CG2 THR    28      12.431 -11.797  -8.973  1.00  0.00 
ATOM    266  N   VAL    29      14.415  -8.772  -8.629  1.00  0.00 
ATOM    267  HN  VAL    29      15.160  -9.259  -9.085  1.00  0.00 
ATOM    268  CA  VAL    29      14.077  -7.637  -9.091  1.00  0.00 
ATOM    269  C   VAL    29      13.767  -7.883 -10.478  1.00  0.00 
ATOM    270  O   VAL    29      14.715  -8.348 -11.240  1.00  0.00 
ATOM    271  CB  VAL    29      15.206  -6.530  -9.088  1.00  0.00 
ATOM    272  CG1 VAL    29      14.808  -5.259  -9.821  1.00  0.00 
ATOM    273  CG2 VAL    29      15.558  -6.239  -7.647  1.00  0.00 
ATOM    274  N   ILE    30      12.363  -7.805 -11.009  1.00  0.00 
ATOM    275  HN  ILE    30      11.598  -7.680 -10.377  1.00  0.00 
ATOM    276  CA  ILE    30      12.079  -7.925 -12.631  1.00  0.00 
ATOM    277  C   ILE    30      12.314  -6.384 -13.355  1.00  0.00 
ATOM    278  O   ILE    30      12.868  -5.663 -12.660  1.00  0.00 
ATOM    279  CB  ILE    30      10.433  -8.052 -12.850  1.00  0.00 
ATOM    280  CG2 ILE    30      10.135  -8.665 -14.208  1.00  0.00 
ATOM    281  CG1 ILE    30      10.013  -9.031 -11.764  1.00  0.00 
ATOM    282  CD1 ILE    30      10.453 -10.478 -11.994  1.00  0.00 
ATOM    283  N   THR    31      11.892  -6.122 -14.689  1.00  0.00 
ATOM    284  HN  THR    31      11.426  -6.898 -15.114  1.00  0.00 
ATOM    285  CA  THR    31      12.004  -4.858 -15.647  1.00  0.00 
ATOM    286  C   THR    31      10.847  -4.647 -16.807  1.00  0.00 
ATOM    287  O   THR    31      10.781  -5.272 -17.643  1.00  0.00 
ATOM    288  CB  THR    31      13.243  -4.607 -16.279  1.00  0.00 
ATOM    289  OG1 THR    31      14.210  -4.399 -15.243  1.00  0.00 
ATOM    290  HG1 THR    31      13.912  -4.865 -14.410  1.00  0.00 
ATOM    291  CG2 THR    31      13.228  -3.443 -17.244  1.00  0.00 
ATOM    292  N   ILE    32      10.039  -3.415 -16.675  1.00  0.00 
ATOM    293  HN  ILE    32      10.205  -2.855 -15.863  1.00  0.00 
ATOM    294  CA  ILE    32       8.908  -2.876 -17.714  1.00  0.00 
ATOM    295  C   ILE    32       9.568  -2.474 -18.818  1.00  0.00 
ATOM    296  O   ILE    32       9.951  -1.437 -19.085  1.00  0.00 
ATOM    297  CB  ILE    32       7.905  -1.709 -17.136  1.00  0.00 
ATOM    298  CG2 ILE    32       8.256  -0.382 -17.789  1.00  0.00 
ATOM    299  CG1 ILE    32       6.513  -2.126 -17.580  1.00  0.00 
ATOM    300  CD1 ILE    32       5.785  -1.107 -18.460  1.00  0.00 
ATOM    301  N   GLN    33       9.840  -3.419 -19.427  1.00  0.00 
ATOM    302  HN  GLN    33       9.727  -4.342 -19.060  1.00  0.00 
ATOM    303  CA  GLN    33      10.297  -3.201 -20.606  1.00  0.00 
ATOM    304  C   GLN    33       9.296  -2.097 -21.311  1.00  0.00 
ATOM    305  O   GLN    33       7.913  -2.103 -21.188  1.00  0.00 
ATOM    306  CB  GLN    33      10.070  -4.425 -21.655  1.00  0.00 
ATOM    307  CG  GLN    33      10.691  -5.740 -21.176  1.00  0.00 
ATOM    308  CD  GLN    33      10.476  -6.853 -22.204  1.00  0.00 
ATOM    309  OE1 GLN    33      10.931  -7.974 -22.049  1.00  0.00 
ATOM    310  NE2 GLN    33       9.760  -6.480 -23.261  1.00  0.00 
ATOM    311  HE21GLN    33       9.416  -5.543 -23.326  1.00  0.00 
ATOM    312  HE22GLN    33       9.566  -7.136 -23.990  1.00  0.00 
ATOM    313  N   ALA    34       9.724  -1.185 -22.192  1.00  0.00 
ATOM    314  HN  ALA    34      10.677  -1.306 -22.472  1.00  0.00 
ATOM    315  CA  ALA    34       9.037  -0.006 -22.844  1.00  0.00 
ATOM    316  C   ALA    34       8.649  -0.328 -24.211  1.00  0.00 
ATOM    317  O   ALA    34       9.604  -0.854 -25.102  1.00  0.00 
ATOM    318  CB  ALA    34      10.227   1.142 -23.207  1.00  0.00 
ATOM    319  N   SER    35       7.408   0.125 -24.510  1.00  0.00 
ATOM    320  HN  SER    35       6.860   0.569 -23.801  1.00  0.00 
ATOM    321  CA  SER    35       6.833  -0.035 -25.922  1.00  0.00 
ATOM    322  C   SER    35       7.614   0.318 -27.089  1.00  0.00 
ATOM    323  O   SER    35       7.552  -0.297 -28.270  1.00  0.00 
ATOM    324  CB  SER    35       5.476   0.456 -25.967  1.00  0.00 
ATOM    325  OG  SER    35       4.679  -0.302 -25.111  1.00  0.00 
ATOM    326  HG  SER    35       4.101  -0.915 -25.649  1.00  0.00 
TER 
END 
