 
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 
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 
ATOM    327  N   ASN    36       8.642   1.327 -26.741  1.00  0.00 
ATOM    328  HN  ASN    36       8.670   1.725 -25.824  1.00  0.00 
ATOM    329  CA  ASN    36       9.637   1.744 -27.777  1.00  0.00 
ATOM    330  C   ASN    36      11.055   1.794 -26.969  1.00  0.00 
ATOM    331  O   ASN    36      11.871   1.567 -27.557  1.00  0.00 
ATOM    332  CB  ASN    36       9.388   3.009 -28.355  1.00  0.00 
ATOM    333  CG  ASN    36       8.432   2.837 -29.523  1.00  0.00 
ATOM    334  OD1 ASN    36       7.235   2.617 -29.339  1.00  0.00 
ATOM    335  ND2 ASN    36       8.978   2.941 -30.721  1.00  0.00 
ATOM    336  HD21ASN    36       9.958   3.121 -30.810  1.00  0.00 
ATOM    337  HD22ASN    36       8.412   2.840 -31.539  1.00  0.00 
ATOM    338  N   SER    37      11.286   2.291 -25.586  1.00  0.00 
ATOM    339  HN  SER    37      10.596   2.784 -25.056  1.00  0.00 
ATOM    340  CA  SER    37      12.743   1.959 -25.033  1.00  0.00 
ATOM    341  C   SER    37      12.787   0.735 -24.344  1.00  0.00 
ATOM    342  O   SER    37      13.537   0.304 -23.371  1.00  0.00 
ATOM    343  CB  SER    37      13.343   3.086 -24.445  1.00  0.00 
ATOM    344  OG  SER    37      14.664   2.873 -24.054  1.00  0.00 
ATOM    345  HG  SER    37      14.874   1.897 -24.105  1.00  0.00 
ATOM    346  N   THR    38      12.139  -0.389 -24.655  1.00  0.00 
ATOM    347  HN  THR    38      11.501  -0.430 -25.424  1.00  0.00 
ATOM    348  CA  THR    38      12.403  -1.545 -23.826  1.00  0.00 
ATOM    349  C   THR    38      13.489  -2.691 -24.541  1.00  0.00 
ATOM    350  O   THR    38      13.312  -3.495 -25.643  1.00  0.00 
ATOM    351  CB  THR    38      11.358  -2.198 -23.221  1.00  0.00 
ATOM    352  OG1 THR    38      11.865  -2.984 -22.140  1.00  0.00 
ATOM    353  HG1 THR    38      12.522  -3.651 -22.492  1.00  0.00 
ATOM    354  CG2 THR    38      10.753  -3.078 -24.293  1.00  0.00 
ATOM    355  N   GLU    39      14.551  -3.022 -24.070  1.00  0.00 
ATOM    356  HN  GLU    39      14.956  -2.578 -23.271  1.00  0.00 
ATOM    357  CA  GLU    39      15.127  -4.024 -24.707  1.00  0.00 
ATOM    358  C   GLU    39      14.647  -5.402 -23.953  1.00  0.00 
ATOM    359  O   GLU    39      14.735  -5.387 -22.806  1.00  0.00 
ATOM    360  CB  GLU    39      16.730  -4.188 -24.127  1.00  0.00 
ATOM    361  CG  GLU    39      17.714  -4.748 -25.158  1.00  0.00 
ATOM    362  CD  GLU    39      19.079  -5.014 -24.522  1.00  0.00 
ATOM    363  OE1 GLU    39      19.765  -4.055 -24.076  1.00  0.00 
ATOM    364  OE2 GLU    39      19.522  -6.192 -24.448  1.00  0.00 
ATOM    365  N   LEU    40      14.036  -6.340 -24.759  1.00  0.00 
ATOM    366  HN  LEU    40      13.848  -6.105 -25.713  1.00  0.00 
ATOM    367  CA  LEU    40      13.661  -7.635 -24.283  1.00  0.00 
ATOM    368  C   LEU    40      14.669  -8.166 -22.999  1.00  0.00 
ATOM    369  O   LEU    40      14.003  -8.505 -21.966  1.00  0.00 
ATOM    370  CB  LEU    40      13.894  -8.629 -25.458  1.00  0.00 
ATOM    371  CG  LEU    40      13.510 -10.078 -25.159  1.00  0.00 
ATOM    372  CD1 LEU    40      12.069 -10.284 -24.722  1.00  0.00 
ATOM    373  CD2 LEU    40      13.867 -10.907 -26.408  1.00  0.00 
ATOM    374  N   ASP    41      16.102  -7.979 -23.213  1.00  0.00 
ATOM    375  HN  ASP    41      16.504  -7.600 -24.046  1.00  0.00 
ATOM    376  CA  ASP    41      16.884  -8.425 -22.032  1.00  0.00 
ATOM    377  C   ASP    41      16.826  -7.386 -21.009  1.00  0.00 
ATOM    378  O   ASP    41      17.816  -6.438 -21.202  1.00  0.00 
ATOM    379  CB  ASP    41      18.319  -8.583 -22.592  1.00  0.00 
ATOM    380  CG  ASP    41      18.410  -9.702 -23.630  1.00  0.00 
ATOM    381  OD1 ASP    41      17.612 -10.673 -23.581  1.00  0.00 
ATOM    382  OD2 ASP    41      19.283  -9.651 -24.538  1.00  0.00 
ATOM    383  N   MET    42      15.867  -7.459 -20.298  1.00  0.00 
ATOM    384  HN  MET    42      15.154  -8.138 -20.476  1.00  0.00 
ATOM    385  CA  MET    42      15.765  -6.651 -19.300  1.00  0.00 
ATOM    386  C   MET    42      16.903  -6.631 -18.374  1.00  0.00 
ATOM    387  O   MET    42      18.231  -6.822 -18.599  1.00  0.00 
ATOM    388  CB  MET    42      14.550  -7.012 -18.281  1.00  0.00 
ATOM    389  CG  MET    42      13.271  -7.456 -19.079  1.00  0.00 
ATOM    390  SD  MET    42      12.148  -8.283 -18.040  1.00  0.00 
ATOM    391  CE  MET    42      12.410  -9.872 -18.487  1.00  0.00 
ATOM    392  N   THR    43      16.830  -6.473 -17.124  1.00  0.00 
ATOM    393  HN  THR    43      15.905  -6.404 -16.750  1.00  0.00 
ATOM    394  CA  THR    43      17.948  -6.374 -16.120  1.00  0.00 
ATOM    395  C   THR    43      17.563  -6.587 -14.793  1.00  0.00 
ATOM    396  O   THR    43      16.627  -5.896 -14.451  1.00  0.00 
ATOM    397  CB  THR    43      18.674  -5.002 -16.289  1.00  0.00 
ATOM    398  OG1 THR    43      19.641  -5.071 -15.233  1.00  0.00 
ATOM    399  HG1 THR    43      19.500  -5.908 -14.705  1.00  0.00 
ATOM    400  CG2 THR    43      17.742  -3.830 -16.090  1.00  0.00 
ATOM    401  N   ASP    44      18.071  -7.523 -14.201  1.00  0.00 
ATOM    402  HN  ASP    44      18.710  -8.075 -14.737  1.00  0.00 
ATOM    403  CA  ASP    44      17.859  -7.997 -12.677  1.00  0.00 
ATOM    404  C   ASP    44      19.175  -7.565 -11.699  1.00  0.00 
ATOM    405  O   ASP    44      20.577  -7.567 -11.989  1.00  0.00 
ATOM    406  CB  ASP    44      17.584  -9.499 -12.574  1.00  0.00 
ATOM    407  CG  ASP    44      18.611 -10.300 -13.380  1.00  0.00 
ATOM    408  OD1 ASP    44      18.758 -10.078 -14.610  1.00  0.00 
ATOM    409  OD2 ASP    44      19.305 -11.184 -12.809  1.00  0.00 
ATOM    410  N   PHE    45      18.883  -7.149 -10.432  1.00  0.00 
ATOM    411  HN  PHE    45      17.925  -7.047 -10.163  1.00  0.00 
ATOM    412  CA  PHE    45      19.913  -6.854  -9.475  1.00  0.00 
ATOM    413  C   PHE    45      19.865  -7.864  -8.354  1.00  0.00 
ATOM    414  O   PHE    45      18.673  -8.031  -7.966  1.00  0.00 
ATOM    415  CB  PHE    45      19.738  -5.435  -8.864  1.00  0.00 
ATOM    416  CG  PHE    45      19.686  -4.362  -9.869  1.00  0.00 
ATOM    417  CD1 PHE    45      20.805  -3.707 -10.329  1.00  0.00 
ATOM    418  CE1 PHE    45      20.746  -2.710 -11.264  1.00  0.00 
ATOM    419  CZ  PHE    45      19.507  -2.342 -11.772  1.00  0.00 
ATOM    420  CE2 PHE    45      18.356  -2.970 -11.341  1.00  0.00 
ATOM    421  CD2 PHE    45      18.478  -3.966 -10.400  1.00  0.00 
ATOM    422  N   VAL    46      21.023  -8.334  -7.969  1.00  0.00 
ATOM    423  HN  VAL    46      21.877  -8.017  -8.381  1.00  0.00 
ATOM    424  CA  VAL    46      21.015  -9.299  -6.956  1.00  0.00 
ATOM    425  C   VAL    46      21.805  -8.592  -5.669  1.00  0.00 
ATOM    426  O   VAL    46      22.804  -8.255  -5.627  1.00  0.00 
ATOM    427  CB  VAL    46      22.138 -10.553  -7.242  1.00  0.00 
ATOM    428  CG1 VAL    46      21.965 -11.655  -6.211  1.00  0.00 
ATOM    429  CG2 VAL    46      21.836 -11.055  -8.637  1.00  0.00 
ATOM    430  N   PHE    47      21.215  -8.280  -4.658  1.00  0.00 
ATOM    431  HN  PHE    47      20.224  -8.415  -4.650  1.00  0.00 
ATOM    432  CA  PHE    47      21.844  -7.701  -3.399  1.00  0.00 
ATOM    433  C   PHE    47      22.040  -8.824  -2.459  1.00  0.00 
ATOM    434  O   PHE    47      21.309  -9.734  -2.360  1.00  0.00 
ATOM    435  CB  PHE    47      21.339  -6.498  -2.929  1.00  0.00 
ATOM    436  CG  PHE    47      20.150  -6.701  -2.089  1.00  0.00 
ATOM    437  CD1 PHE    47      20.215  -6.945  -0.737  1.00  0.00 
ATOM    438  CE1 PHE    47      19.101  -7.133   0.035  1.00  0.00 
ATOM    439  CZ  PHE    47      17.852  -7.075  -0.567  1.00  0.00 
ATOM    440  CE2 PHE    47      17.734  -6.833  -1.921  1.00  0.00 
ATOM    441  CD2 PHE    47      18.889  -6.652  -2.648  1.00  0.00 
TER 
END 
