 
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    466  N   VAL    51      26.666  -8.417   6.984  1.00  0.00 
ATOM    467  HN  VAL    51      27.174  -7.948   6.262  1.00  0.00 
ATOM    468  CA  VAL    51      26.101  -7.580   8.042  1.00  0.00 
ATOM    469  C   VAL    51      24.940  -6.816   7.549  1.00  0.00 
ATOM    470  O   VAL    51      24.954  -6.103   6.767  1.00  0.00 
ATOM    471  CB  VAL    51      27.169  -6.592   8.580  1.00  0.00 
ATOM    472  CG1 VAL    51      26.774  -6.151   9.978  1.00  0.00 
ATOM    473  CG2 VAL    51      28.555  -7.196   8.568  1.00  0.00 
ATOM    474  N   PRO    52      23.744  -6.877   8.082  1.00  0.00 
ATOM    475  CA  PRO    52      22.346  -6.071   7.597  1.00  0.00 
ATOM    476  CD  PRO    52      23.542  -7.161   9.524  1.00  0.00 
ATOM    477  C   PRO    52      22.549  -4.802   7.163  1.00  0.00 
ATOM    478  O   PRO    52      21.954  -4.340   6.364  1.00  0.00 
ATOM    479  CB  PRO    52      21.428  -6.407   8.683  1.00  0.00 
ATOM    480  CG  PRO    52      22.336  -6.235   9.913  1.00  0.00 
ATOM    481  N   LYS    53      23.632  -4.032   7.919  1.00  0.00 
ATOM    482  HN  LYS    53      24.133  -4.510   8.641  1.00  0.00 
ATOM    483  CA  LYS    53      23.974  -2.651   7.650  1.00  0.00 
ATOM    484  C   LYS    53      24.531  -2.518   6.239  1.00  0.00 
ATOM    485  O   LYS    53      24.116  -1.641   5.485  1.00  0.00 
ATOM    486  CB  LYS    53      25.030  -2.145   8.635  1.00  0.00 
ATOM    487  CG  LYS    53      25.341  -0.677   8.342  1.00  0.00 
ATOM    488  CD  LYS    53      26.595  -0.222   9.092  1.00  0.00 
ATOM    489  CE  LYS    53      26.506  -0.584  10.577  1.00  0.00 
ATOM    490  NZ  LYS    53      27.686  -0.082  11.317  1.00  0.00 
ATOM    491  HZ1 LYS    53      28.390   0.205  10.667  1.00  0.00 
ATOM    492  HZ2 LYS    53      27.417   0.697  11.883  1.00  0.00 
ATOM    493  HZ3 LYS    53      28.048  -0.809  11.900  1.00  0.00 
ATOM    494  N   THR    54      25.501  -3.202   5.980  1.00  0.00 
ATOM    495  HN  THR    54      25.910  -3.723   6.729  1.00  0.00 
ATOM    496  CA  THR    54      26.094  -3.320   4.713  1.00  0.00 
ATOM    497  C   THR    54      25.387  -4.372   3.761  1.00  0.00 
ATOM    498  O   THR    54      24.652  -5.083   4.316  1.00  0.00 
ATOM    499  CB  THR    54      27.586  -3.726   4.649  1.00  0.00 
ATOM    500  OG1 THR    54      27.682  -4.961   5.365  1.00  0.00 
ATOM    501  HG1 THR    54      27.372  -5.711   4.780  1.00  0.00 
ATOM    502  CG2 THR    54      28.361  -2.633   5.354  1.00  0.00 
ATOM    503  N   PHE    55      25.677  -4.107   2.449  1.00  0.00 
ATOM    504  HN  PHE    55      26.304  -3.339   2.319  1.00  0.00 
ATOM    505  CA  PHE    55      25.259  -4.713   1.248  1.00  0.00 
ATOM    506  C   PHE    55      26.151  -4.865   0.285  1.00  0.00 
ATOM    507  O   PHE    55      27.300  -4.006   0.447  1.00  0.00 
ATOM    508  CB  PHE    55      23.963  -4.292   0.786  1.00  0.00 
ATOM    509  CG  PHE    55      22.842  -4.602   1.688  1.00  0.00 
ATOM    510  CD1 PHE    55      22.301  -5.862   1.808  1.00  0.00 
ATOM    511  CE1 PHE    55      21.259  -6.138   2.651  1.00  0.00 
ATOM    512  CZ  PHE    55      20.726  -5.111   3.418  1.00  0.00 
ATOM    513  CE2 PHE    55      21.235  -3.832   3.331  1.00  0.00 
ATOM    514  CD2 PHE    55      22.283  -3.611   2.466  1.00  0.00 
ATOM    515  N   GLN    56      25.973  -5.653  -0.614  1.00  0.00 
ATOM    516  HN  GLN    56      25.182  -6.253  -0.493  1.00  0.00 
ATOM    517  CA  GLN    56      26.701  -5.866  -1.811  1.00  0.00 
ATOM    518  C   GLN    56      25.945  -6.240  -3.029  1.00  0.00 
ATOM    519  O   GLN    56      24.712  -6.799  -2.692  1.00  0.00 
ATOM    520  CB  GLN    56      27.636  -7.240  -1.464  1.00  0.00 
ATOM    521  CG  GLN    56      28.758  -6.858  -0.496  1.00  0.00 
ATOM    522  CD  GLN    56      29.588  -8.085  -0.107  1.00  0.00 
ATOM    523  OE1 GLN    56      29.072  -9.104   0.314  1.00  0.00 
ATOM    524  NE2 GLN    56      30.898  -7.924  -0.273  1.00  0.00 
ATOM    525  HE21GLN    56      31.255  -7.058  -0.624  1.00  0.00 
ATOM    526  HE22GLN    56      31.526  -8.669  -0.047  1.00  0.00 
ATOM    527  N   LEU    57      26.479  -6.135  -4.363  1.00  0.00 
ATOM    528  HN  LEU    57      27.411  -5.821  -4.545  1.00  0.00 
ATOM    529  CA  LEU    57      25.660  -6.479  -5.315  1.00  0.00 
ATOM    530  C   LEU    57      26.236  -7.712  -6.035  1.00  0.00 
ATOM    531  O   LEU    57      27.514  -7.561  -6.509  1.00  0.00 
ATOM    532  CB  LEU    57      25.588  -5.362  -6.344  1.00  0.00 
ATOM    533  CG  LEU    57      24.467  -4.345  -6.118  1.00  0.00 
ATOM    534  CD1 LEU    57      24.473  -3.161  -7.067  1.00  0.00 
ATOM    535  CD2 LEU    57      23.139  -5.124  -6.166  1.00  0.00 
ATOM    536  N   GLN    58      25.639  -8.691  -6.064  1.00  0.00 
ATOM    537  HN  GLN    58      24.746  -8.710  -5.614  1.00  0.00 
ATOM    538  CA  GLN    58      26.122  -9.964  -6.746  1.00  0.00 
ATOM    539  C   GLN    58      26.134  -9.655  -8.304  1.00  0.00 
ATOM    540  O   GLN    58      26.999 -10.022  -8.850  1.00  0.00 
ATOM    541  CB  GLN    58      25.355 -11.144  -6.486  1.00  0.00 
ATOM    542  CG  GLN    58      25.235 -11.400  -4.982  1.00  0.00 
ATOM    543  CD  GLN    58      25.102 -12.894  -4.689  1.00  0.00 
ATOM    544  OE1 GLN    58      24.275 -13.593  -5.251  1.00  0.00 
ATOM    545  NE2 GLN    58      25.962 -13.347  -3.779  1.00  0.00 
ATOM    546  HE21GLN    58      26.616 -12.721  -3.354  1.00  0.00 
ATOM    547  HE22GLN    58      25.954 -14.313  -3.520  1.00  0.00 
ATOM    548  N   LEU    59      25.112  -8.996  -8.948  1.00  0.00 
ATOM    549  HN  LEU    59      24.343  -8.608  -8.440  1.00  0.00 
ATOM    550  CA  LEU    59      25.192  -8.888 -10.366  1.00  0.00 
ATOM    551  C   LEU    59      25.263  -7.246 -10.689  1.00  0.00 
ATOM    552  O   LEU    59      24.967  -6.329  -9.735  1.00  0.00 
ATOM    553  CB  LEU    59      23.670  -9.102 -10.931  1.00  0.00 
ATOM    554  CG  LEU    59      23.591 -10.059 -12.121  1.00  0.00 
ATOM    555  CD1 LEU    59      24.250 -11.412 -11.902  1.00  0.00 
ATOM    556  CD2 LEU    59      22.104 -10.190 -12.498  1.00  0.00 
ATOM    557  N   LEU    60      25.627  -7.015 -11.744  1.00  0.00 
ATOM    558  HN  LEU    60      25.834  -7.764 -12.374  1.00  0.00 
ATOM    559  CA  LEU    60      25.790  -5.651 -12.175  1.00  0.00 
ATOM    560  C   LEU    60      24.702  -5.231 -13.181  1.00  0.00 
ATOM    561  O   LEU    60      24.131  -6.211 -13.992  1.00  0.00 
ATOM    562  CB  LEU    60      27.130  -5.426 -12.856  1.00  0.00 
ATOM    563  CG  LEU    60      28.342  -5.442 -11.922  1.00  0.00 
ATOM    564  CD1 LEU    60      29.690  -5.496 -12.621  1.00  0.00 
ATOM    565  CD2 LEU    60      28.212  -4.219 -10.994  1.00  0.00 
ATOM    566  N   SER    61      24.186  -4.071 -13.173  1.00  0.00 
ATOM    567  HN  SER    61      24.385  -3.454 -12.412  1.00  0.00 
ATOM    568  CA  SER    61      23.351  -3.638 -14.197  1.00  0.00 
ATOM    569  C   SER    61      24.025  -3.589 -15.513  1.00  0.00 
ATOM    570  O   SER    61      25.075  -3.824 -15.545  1.00  0.00 
ATOM    571  CB  SER    61      23.165  -2.065 -13.793  1.00  0.00 
ATOM    572  OG  SER    61      24.335  -1.308 -13.833  1.00  0.00 
ATOM    573  HG  SER    61      24.407  -0.851 -14.719  1.00  0.00 
ATOM    574  N   PRO    62      23.414  -3.342 -16.550  1.00  0.00 
ATOM    575  CA  PRO    62      23.961  -3.325 -18.024  1.00  0.00 
ATOM    576  CD  PRO    62      21.897  -3.412 -16.709  1.00  0.00 
ATOM    577  C   PRO    62      23.668  -2.047 -18.754  1.00  0.00 
ATOM    578  O   PRO    62      23.540  -0.947 -18.204  1.00  0.00 
ATOM    579  CB  PRO    62      23.023  -4.392 -18.890  1.00  0.00 
ATOM    580  CG  PRO    62      21.690  -4.311 -18.125  1.00  0.00 
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 
TER 
END 
