 
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 
ATOM    581  N   SER    63      23.675  -2.156 -19.966  1.00  0.00 
ATOM    582  HN  SER    63      23.793  -3.029 -20.440  1.00  0.00 
ATOM    583  CA  SER    63      23.496  -0.895 -20.652  1.00  0.00 
ATOM    584  C   SER    63      22.039  -0.500 -20.730  1.00  0.00 
ATOM    585  O   SER    63      21.641   0.661 -20.633  1.00  0.00 
ATOM    586  CB  SER    63      24.032  -0.984 -22.077  1.00  0.00 
ATOM    587  OG  SER    63      23.949   0.200 -22.807  1.00  0.00 
ATOM    588  HG  SER    63      23.009   0.541 -22.784  1.00  0.00 
ATOM    589  N   SER    64      21.124  -1.551 -20.964  1.00  0.00 
ATOM    590  HN  SER    64      21.377  -2.518 -20.951  1.00  0.00 
ATOM    591  CA  SER    64      19.631  -1.023 -21.253  1.00  0.00 
ATOM    592  C   SER    64      19.043  -0.300 -19.986  1.00  0.00 
ATOM    593  O   SER    64      17.949   0.542 -20.270  1.00  0.00 
ATOM    594  CB  SER    64      18.740  -2.454 -21.256  1.00  0.00 
ATOM    595  OG  SER    64      17.361  -2.260 -21.272  1.00  0.00 
ATOM    596  HG  SER    64      16.974  -2.680 -22.093  1.00  0.00 
ATOM    597  N   SER    65      19.445  -0.659 -18.989  1.00  0.00 
ATOM    598  HN  SER    65      20.038  -1.463 -18.942  1.00  0.00 
ATOM    599  CA  SER    65      19.135  -0.033 -17.942  1.00  0.00 
ATOM    600  C   SER    65      19.151   1.388 -17.942  1.00  0.00 
ATOM    601  O   SER    65      19.917   2.056 -18.208  1.00  0.00 
ATOM    602  CB  SER    65      20.123  -0.304 -16.671  1.00  0.00 
ATOM    603  OG  SER    65      19.779  -1.548 -16.145  1.00  0.00 
ATOM    604  HG  SER    65      19.621  -1.462 -15.161  1.00  0.00 
ATOM    605  N   VAL    66      18.228   2.031 -17.445  1.00  0.00 
ATOM    606  HN  VAL    66      17.494   1.565 -16.950  1.00  0.00 
ATOM    607  CA  VAL    66      18.218   3.642 -17.603  1.00  0.00 
ATOM    608  C   VAL    66      18.885   3.989 -16.368  1.00  0.00 
ATOM    609  O   VAL    66      19.417   5.243 -15.956  1.00  0.00 
ATOM    610  CB  VAL    66      16.653   4.007 -17.504  1.00  0.00 
ATOM    611  CG1 VAL    66      15.779   3.082 -18.333  1.00  0.00 
ATOM    612  CG2 VAL    66      16.122   4.136 -16.093  1.00  0.00 
ATOM    613  N   VAL    67      19.237   2.832 -15.452  1.00  0.00 
ATOM    614  HN  VAL    67      19.151   1.874 -15.725  1.00  0.00 
ATOM    615  CA  VAL    67      19.705   3.239 -14.155  1.00  0.00 
ATOM    616  C   VAL    67      20.128   2.089 -13.270  1.00  0.00 
ATOM    617  O   VAL    67      19.450   1.013 -13.513  1.00  0.00 
ATOM    618  CB  VAL    67      18.318   4.031 -13.494  1.00  0.00 
ATOM    619  CG1 VAL    67      18.041   5.424 -14.033  1.00  0.00 
ATOM    620  CG2 VAL    67      17.133   3.117 -13.708  1.00  0.00 
ATOM    621  N   PRO    68      21.046   2.301 -12.618  1.00  0.00 
ATOM    622  CA  PRO    68      21.911   1.200 -11.706  1.00  0.00 
ATOM    623  CD  PRO    68      22.234   3.370 -12.659  1.00  0.00 
ATOM    624  C   PRO    68      21.629   1.249 -10.381  1.00  0.00 
ATOM    625  O   PRO    68      21.158   2.331 -10.129  1.00  0.00 
ATOM    626  CB  PRO    68      23.126   1.041 -12.346  1.00  0.00 
ATOM    627  CG  PRO    68      23.505   2.529 -12.426  1.00  0.00 
ATOM    628  N   ALA    69      21.884   0.364  -9.739  1.00  0.00 
ATOM    629  HN  ALA    69      22.335  -0.391 -10.216  1.00  0.00 
ATOM    630  CA  ALA    69      21.667   0.157  -8.373  1.00  0.00 
ATOM    631  C   ALA    69      22.857   0.346  -7.490  1.00  0.00 
ATOM    632  O   ALA    69      24.015  -0.049  -7.898  1.00  0.00 
ATOM    633  CB  ALA    69      21.187  -1.260  -8.074  1.00  0.00 
ATOM    634  N   PHE    70      22.695   0.826  -6.217  1.00  0.00 
ATOM    635  HN  PHE    70      21.791   1.032  -5.841  1.00  0.00 
ATOM    636  CA  PHE    70      23.737   0.992  -5.554  1.00  0.00 
ATOM    637  C   PHE    70      23.458   0.385  -4.005  1.00  0.00 
ATOM    638  O   PHE    70      22.867   0.863  -3.184  1.00  0.00 
ATOM    639  CB  PHE    70      24.033   2.552  -5.051  1.00  0.00 
ATOM    640  CG  PHE    70      25.295   2.844  -4.354  1.00  0.00 
ATOM    641  CD1 PHE    70      26.488   2.240  -4.676  1.00  0.00 
ATOM    642  CE1 PHE    70      27.656   2.518  -4.021  1.00  0.00 
ATOM    643  CZ  PHE    70      27.642   3.450  -2.991  1.00  0.00 
ATOM    644  CE2 PHE    70      26.470   4.083  -2.634  1.00  0.00 
ATOM    645  CD2 PHE    70      25.325   3.762  -3.326  1.00  0.00 
ATOM    646  N   ASN    71      23.994  -0.559  -3.664  1.00  0.00 
ATOM    647  HN  ASN    71      24.717  -0.910  -4.259  1.00  0.00 
ATOM    648  CA  ASN    71      23.728  -1.295  -2.456  1.00  0.00 
ATOM    649  C   ASN    71      23.960  -0.558  -1.099  1.00  0.00 
ATOM    650  O   ASN    71      23.124  -0.546   0.041  1.00  0.00 
ATOM    651  CB  ASN    71      24.710  -2.688  -2.524  1.00  0.00 
ATOM    652  CG  ASN    71      26.131  -2.358  -2.953  1.00  0.00 
ATOM    653  OD1 ASN    71      26.906  -1.779  -2.192  1.00  0.00 
ATOM    654  ND2 ASN    71      26.453  -2.733  -4.177  1.00  0.00 
ATOM    655  HD21ASN    71      25.780  -3.201  -4.750  1.00  0.00 
ATOM    656  HD22ASN    71      27.370  -2.549  -4.531  1.00  0.00 
ATOM    657  N   THR    72      25.012   0.331  -0.794  1.00  0.00 
ATOM    658  HN  THR    72      25.605   0.538  -1.572  1.00  0.00 
ATOM    659  CA  THR    72      25.438   1.073   0.564  1.00  0.00 
ATOM    660  C   THR    72      25.674   2.423   0.125  1.00  0.00 
ATOM    661  O   THR    72      26.485   2.463  -0.585  1.00  0.00 
ATOM    662  CB  THR    72      26.885   0.580   0.745  1.00  0.00 
ATOM    663  OG1 THR    72      26.739  -0.841   0.636  1.00  0.00 
ATOM    664  HG1 THR    72      26.930  -1.125  -0.304  1.00  0.00 
ATOM    665  CG2 THR    72      27.289   0.973   2.151  1.00  0.00 
ATOM    666  N   GLY    73      24.900   3.217   0.533  1.00  0.00 
ATOM    667  HN  GLY    73      24.145   2.829   1.062  1.00  0.00 
ATOM    668  CA  GLY    73      24.860   4.742   0.386  1.00  0.00 
ATOM    669  C   GLY    73      24.232   5.496   1.388  1.00  0.00 
ATOM    670  O   GLY    73      23.741   4.975   2.224  1.00  0.00 
ATOM    671  N   THR    74      24.075   6.638   1.382  1.00  0.00 
ATOM    672  HN  THR    74      24.335   7.110   0.539  1.00  0.00 
ATOM    673  CA  THR    74      23.542   7.489   2.454  1.00  0.00 
ATOM    674  C   THR    74      22.103   6.904   2.878  1.00  0.00 
ATOM    675  O   THR    74      21.443   7.010   4.101  1.00  0.00 
ATOM    676  CB  THR    74      23.210   8.863   1.869  1.00  0.00 
ATOM    677  OG1 THR    74      24.511   9.372   1.560  1.00  0.00 
ATOM    678  HG1 THR    74      24.749  10.095   2.208  1.00  0.00 
ATOM    679  CG2 THR    74      22.519   9.733   2.897  1.00  0.00 
ATOM    680  N   ILE    75      21.193   6.284   1.923  1.00  0.00 
ATOM    681  HN  ILE    75      21.468   6.357   0.964  1.00  0.00 
ATOM    682  CA  ILE    75      19.957   5.582   2.153  1.00  0.00 
ATOM    683  C   ILE    75      20.111   4.079   2.249  1.00  0.00 
ATOM    684  O   ILE    75      20.438   3.361   1.286  1.00  0.00 
ATOM    685  CB  ILE    75      18.864   6.088   1.341  1.00  0.00 
ATOM    686  CG2 ILE    75      17.613   5.262   1.597  1.00  0.00 
ATOM    687  CG1 ILE    75      18.527   7.560   1.521  1.00  0.00 
ATOM    688  CD1 ILE    75      18.278   7.995   2.966  1.00  0.00 
ATOM    689  N   THR    76      19.940   3.270   3.533  1.00  0.00 
ATOM    690  HN  THR    76      19.812   3.794   4.375  1.00  0.00 
ATOM    691  CA  THR    76      19.943   1.735   3.673  1.00  0.00 
ATOM    692  C   THR    76      19.138   1.119   2.574  1.00  0.00 
ATOM    693  O   THR    76      17.837   1.479   2.647  1.00  0.00 
ATOM    694  CB  THR    76      19.433   1.397   5.004  1.00  0.00 
ATOM    695  OG1 THR    76      20.395   1.861   5.959  1.00  0.00 
ATOM    696  HG1 THR    76      20.850   1.077   6.382  1.00  0.00 
ATOM    697  CG2 THR    76      19.274  -0.105   5.089  1.00  0.00 
ATOM    698  N   GLN    77      19.677   0.487   1.625  1.00  0.00 
ATOM    699  HN  GLN    77      20.670   0.466   1.512  1.00  0.00 
ATOM    700  CA  GLN    77      18.731  -0.263   0.632  1.00  0.00 
ATOM    701  C   GLN    77      18.217   0.601  -0.319  1.00  0.00 
ATOM    702  O   GLN    77      16.940   0.494  -0.915  1.00  0.00 
ATOM    703  CB  GLN    77      17.960  -1.240   1.315  1.00  0.00 
ATOM    704  CG  GLN    77      16.888  -2.020   0.550  1.00  0.00 
ATOM    705  CD  GLN    77      17.458  -3.317  -0.024  1.00  0.00 
ATOM    706  OE1 GLN    77      16.744  -4.255  -0.338  1.00  0.00 
ATOM    707  NE2 GLN    77      18.785  -3.318  -0.145  1.00  0.00 
ATOM    708  HE21GLN    77      19.313  -2.515   0.131  1.00  0.00 
ATOM    709  HE22GLN    77      19.253  -4.122  -0.512  1.00  0.00 
ATOM    710  N   VAL    78      19.019   1.630  -0.789  1.00  0.00 
ATOM    711  HN  VAL    78      19.982   1.688  -0.527  1.00  0.00 
ATOM    712  CA  VAL    78      18.400   2.669  -1.713  1.00  0.00 
ATOM    713  C   VAL    78      18.721   2.280  -3.140  1.00  0.00 
ATOM    714  O   VAL    78      19.844   2.223  -3.771  1.00  0.00 
ATOM    715  CB  VAL    78      18.865   4.127  -1.457  1.00  0.00 
ATOM    716  CG1 VAL    78      20.364   4.213  -1.674  1.00  0.00 
ATOM    717  CG2 VAL    78      18.129   5.117  -2.330  1.00  0.00 
ATOM    718  N   ILE    79      17.782   1.987  -3.797  1.00  0.00 
ATOM    719  HN  ILE    79      16.853   1.969  -3.427  1.00  0.00 
ATOM    720  CA  ILE    79      18.078   1.654  -5.186  1.00  0.00 
ATOM    721  C   ILE    79      17.778   2.888  -6.024  1.00  0.00 
ATOM    722  O   ILE    79      16.614   3.309  -6.112  1.00  0.00 
ATOM    723  CB  ILE    79      17.239   0.484  -5.702  1.00  0.00 
ATOM    724  CG2 ILE    79      17.609   0.173  -7.141  1.00  0.00 
ATOM    725  CG1 ILE    79      17.490  -0.749  -4.849  1.00  0.00 
ATOM    726  CD1 ILE    79      16.568  -1.936  -5.140  1.00  0.00 
ATOM    727  N   LYS    80      18.794   3.334  -6.329  1.00  0.00 
ATOM    728  HN  LYS    80      19.595   2.831  -6.005  1.00  0.00 
ATOM    729  CA  LYS    80      19.096   4.574  -7.151  1.00  0.00 
ATOM    730  C   LYS    80      19.271   4.156  -8.408  1.00  0.00 
ATOM    731  O   LYS    80      19.749   2.826  -8.452  1.00  0.00 
ATOM    732  CB  LYS    80      20.055   5.490  -6.658  1.00  0.00 
ATOM    733  CG  LYS    80      21.532   5.087  -6.694  1.00  0.00 
ATOM    734  CD  LYS    80      22.411   6.275  -7.098  1.00  0.00 
ATOM    735  CE  LYS    80      23.882   5.991  -6.796  1.00  0.00 
ATOM    736  NZ  LYS    80      24.755   6.527  -7.865  1.00  0.00 
ATOM    737  HZ1 LYS    80      24.547   6.066  -8.728  1.00  0.00 
ATOM    738  HZ2 LYS    80      24.595   7.509  -7.965  1.00  0.00 
ATOM    739  HZ3 LYS    80      25.712   6.368  -7.624  1.00  0.00 
ATOM    740  N   VAL    81      19.098   5.002  -9.167  1.00  0.00 
ATOM    741  HN  VAL    81      18.987   5.941  -8.842  1.00  0.00 
ATOM    742  CA  VAL    81      19.045   4.756 -10.428  1.00  0.00 
ATOM    743  C   VAL    81      19.535   6.140 -11.219  1.00  0.00 
ATOM    744  O   VAL    81      18.961   7.173 -10.740  1.00  0.00 
ATOM    745  CB  VAL    81      17.604   4.441 -11.057  1.00  0.00 
ATOM    746  CG1 VAL    81      17.200   3.106 -10.453  1.00  0.00 
ATOM    747  CG2 VAL    81      16.605   5.522 -10.707  1.00  0.00 
ATOM    748  N   LEU    82      20.601   6.144 -12.246  1.00  0.00 
ATOM    749  HN  LEU    82      21.070   5.275 -12.405  1.00  0.00 
ATOM    750  CA  LEU    82      20.998   7.167 -12.973  1.00  0.00 
ATOM    751  C   LEU    82      19.963   8.254 -13.451  1.00  0.00 
ATOM    752  O   LEU    82      19.872   9.515 -12.962  1.00  0.00 
ATOM    753  CB  LEU    82      21.552   6.740 -14.493  1.00  0.00 
ATOM    754  CG  LEU    82      23.041   6.390 -14.503  1.00  0.00 
ATOM    755  CD1 LEU    82      23.590   5.963 -15.853  1.00  0.00 
ATOM    756  CD2 LEU    82      23.795   7.601 -13.924  1.00  0.00 
ATOM    757  N   ASN    83      19.325   7.760 -14.503  1.00  0.00 
ATOM    758  HN  ASN    83      19.481   6.792 -14.699  1.00  0.00 
ATOM    759  CA  ASN    83      18.311   8.549 -15.520  1.00  0.00 
ATOM    760  C   ASN    83      17.220   7.603 -16.171  1.00  0.00 
ATOM    761  O   ASN    83      17.340   6.535 -16.723  1.00  0.00 
ATOM    762  CB  ASN    83      19.063   9.425 -16.358  1.00  0.00 
ATOM    763  CG  ASN    83      20.186   8.628 -17.002  1.00  0.00 
ATOM    764  OD1 ASN    83      21.348   8.740 -16.611  1.00  0.00 
ATOM    765  ND2 ASN    83      19.823   7.830 -17.987  1.00  0.00 
ATOM    766  HD21ASN    83      18.863   7.780 -18.262  1.00  0.00 
ATOM    767  HD22ASN    83      20.508   7.275 -18.459  1.00  0.00 
ATOM    768  N   PRO    84      16.166   8.110 -16.234  1.00  0.00 
ATOM    769  CA  PRO    84      14.779   7.257 -16.684  1.00  0.00 
ATOM    770  CD  PRO    84      15.977   9.387 -16.519  1.00  0.00 
ATOM    771  C   PRO    84      14.949   6.664 -18.254  1.00  0.00 
ATOM    772  O   PRO    84      16.045   7.187 -18.909  1.00  0.00 
ATOM    773  CB  PRO    84      13.779   8.211 -16.521  1.00  0.00 
ATOM    774  CG  PRO    84      14.499   9.521 -16.879  1.00  0.00 
TER 
END 
