
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   44 (  176),  selected   44 , name T0358AL243_5
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL243_5.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    S       4      -       -           -
LGA    V       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      G      10           #
LGA    T      23      P      11          4.179
LGA    S      25      F      12          3.671
LGA    N      26      T      13          3.083
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    I      27      A      17          0.808
LGA    T      28      Q      18          1.919
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    L      29      T      28          5.322
LGA    E      30      L      29          5.420
LGA    D      31      E      30          4.583
LGA    -       -      D      31           -
LGA    D      32      D      32          1.630
LGA    -       -      Q      33           -
LGA    Q      33      G      34          2.450
LGA    G      34      S      35          3.455
LGA    S      35      H      36          2.306
LGA    H      36      F      37          4.670
LGA    F      37      R      38          3.674
LGA    R      38      -       -           -
LGA    L      39      L      39          3.511
LGA    V      40      V      40          2.493
LGA    V      41      V      41          0.998
LGA    R      42      R      42          1.864
LGA    D      43      D      43          3.024
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    E      45      R      47          2.515
LGA    G      46      M      48          0.922
LGA    R      47      V      49          1.187
LGA    M      48      W      50          1.922
LGA    V      49      R      51          4.272
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   66    5.0     24    3.21    25.00     22.335     0.725

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.275504 * X  +  -0.296558 * Y  +  -0.914413 * Z  +  47.840336
  Y_new =   0.890860 * X  +   0.278652 * Y  +  -0.358779 * Z  +  33.463821
  Z_new =   0.361202 * X  +  -0.913459 * Y  +   0.187422 * Z  +  21.409592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.368427    1.773166  [ DEG:   -78.4051    101.5949 ]
  Theta =  -0.369556   -2.772037  [ DEG:   -21.1740   -158.8260 ]
  Phi   =   1.870724   -1.270869  [ DEG:   107.1846    -72.8154 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0358AL243_5                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL243_5.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   66   5.0   24   3.21   25.00  22.335
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL243_5
REMARK Aligment from pdb entry: 1k8wA
ATOM      1  N   SER     4     -17.356   5.977  20.529  1.00  0.00              
ATOM      2  CA  SER     4     -18.232   6.215  19.375  1.00  0.00              
ATOM      3  C   SER     4     -18.285   7.686  18.937  1.00  0.00              
ATOM      4  O   SER     4     -18.697   7.994  17.821  1.00  0.00              
ATOM      5  N   VAL     5     -17.859   8.592  19.812  1.00  0.00              
ATOM      6  CA  VAL     5     -17.885  10.017  19.491  1.00  0.00              
ATOM      7  C   VAL     5     -16.780  10.437  18.529  1.00  0.00              
ATOM      8  O   VAL     5     -16.857  11.502  17.916  1.00  0.00              
ATOM      9  N   LEU     6     -15.757   9.599  18.396  1.00  0.00              
ATOM     10  CA  LEU     6     -14.608   9.915  17.550  1.00  0.00              
ATOM     11  C   LEU     6     -14.774   9.710  16.048  1.00  0.00              
ATOM     12  O   LEU     6     -15.442   8.775  15.605  1.00  0.00              
ATOM     13  N   LEU     7     -14.157  10.601  15.274  1.00  0.00              
ATOM     14  CA  LEU     7     -14.166  10.502  13.818  1.00  0.00              
ATOM     15  C   LEU     7     -12.943   9.627  13.539  1.00  0.00              
ATOM     16  O   LEU     7     -12.024   9.571  14.358  1.00  0.00              
ATOM     17  N   PRO     8     -12.908   8.935  12.390  1.00  0.00              
ATOM     18  CA  PRO     8     -11.765   8.074  12.061  1.00  0.00              
ATOM     19  C   PRO     8     -10.416   8.798  12.136  1.00  0.00              
ATOM     20  O   PRO     8     -10.338  10.006  11.904  1.00  0.00              
ATOM     21  N   PRO     9      -8.091   8.772  10.120  1.00  0.00              
ATOM     22  CA  PRO     9      -7.661   9.294   8.830  1.00  0.00              
ATOM     23  C   PRO     9      -8.547  10.438   8.338  1.00  0.00              
ATOM     24  O   PRO     9      -8.275  11.026   7.298  1.00  0.00              
ATOM     25  N   GLY    10      -8.665  13.473   9.038  1.00  0.00              
ATOM     26  CA  GLY    10      -7.975  14.726   8.712  1.00  0.00              
ATOM     27  C   GLY    10      -7.480  14.761   7.259  1.00  0.00              
ATOM     28  O   GLY    10      -7.289  15.836   6.680  1.00  0.00              
ATOM     29  N   PRO    11      -5.769   1.709  -2.389  1.00  0.00              
ATOM     30  CA  PRO    11      -5.754   0.442  -1.677  1.00  0.00              
ATOM     31  C   PRO    11      -4.687  -0.485  -2.235  1.00  0.00              
ATOM     32  O   PRO    11      -4.517  -0.596  -3.450  1.00  0.00              
ATOM     33  N   PHE    12      -3.966  -1.144  -1.337  1.00  0.00              
ATOM     34  CA  PHE    12      -2.903  -2.065  -1.722  1.00  0.00              
ATOM     35  C   PHE    12      -3.185  -3.464  -1.207  1.00  0.00              
ATOM     36  O   PHE    12      -3.621  -3.636  -0.069  1.00  0.00              
ATOM     37  N   THR    13      -2.946  -4.487  -2.042  1.00  0.00              
ATOM     38  CA  THR    13      -3.189  -5.850  -1.570  1.00  0.00              
ATOM     39  C   THR    13      -2.122  -6.101  -0.506  1.00  0.00              
ATOM     40  O   THR    13      -1.035  -5.526  -0.577  1.00  0.00              
ATOM     41  N   ARG    14      -2.424  -6.939   0.479  1.00  0.00              
ATOM     42  CA  ARG    14      -1.467  -7.212   1.546  1.00  0.00              
ATOM     43  C   ARG    14      -0.086  -7.625   1.035  1.00  0.00              
ATOM     44  O   ARG    14       0.922  -7.412   1.713  1.00  0.00              
ATOM     45  N   ARG    15      -0.041  -8.206  -0.162  1.00  0.00              
ATOM     46  CA  ARG    15       1.222  -8.638  -0.752  1.00  0.00              
ATOM     47  C   ARG    15       2.089  -7.449  -1.156  1.00  0.00              
ATOM     48  O   ARG    15       3.293  -7.592  -1.364  1.00  0.00              
ATOM     49  N   GLN    16       1.471  -6.276  -1.267  1.00  0.00              
ATOM     50  CA  GLN    16       2.196  -5.063  -1.633  1.00  0.00              
ATOM     51  C   GLN    16       2.452  -4.192  -0.405  1.00  0.00              
ATOM     52  O   GLN    16       3.498  -3.553  -0.297  1.00  0.00              
ATOM     53  N   ALA    17       1.496  -4.172   0.519  1.00  0.00              
ATOM     54  CA  ALA    17       1.620  -3.359   1.722  1.00  0.00              
ATOM     55  C   ALA    17       2.772  -3.783   2.629  1.00  0.00              
ATOM     56  O   ALA    17       3.308  -2.967   3.376  1.00  0.00              
ATOM     57  N   GLN    18       3.152  -5.055   2.578  1.00  0.00              
ATOM     58  CA  GLN    18       4.249  -5.517   3.420  1.00  0.00              
ATOM     59  C   GLN    18       5.541  -4.777   3.058  1.00  0.00              
ATOM     60  O   GLN    18       6.323  -4.398   3.935  1.00  0.00              
ATOM     61  N   ALA    19       5.753  -4.547   1.767  1.00  0.00              
ATOM     62  CA  ALA    19       6.937  -3.826   1.320  1.00  0.00              
ATOM     63  C   ALA    19       6.771  -2.342   1.637  1.00  0.00              
ATOM     64  O   ALA    19       7.712  -1.675   2.070  1.00  0.00              
ATOM     65  N   VAL    20       5.557  -1.841   1.425  1.00  0.00              
ATOM     66  CA  VAL    20       5.225  -0.443   1.684  1.00  0.00              
ATOM     67  C   VAL    20       5.541  -0.076   3.131  1.00  0.00              
ATOM     68  O   VAL    20       6.152   0.959   3.403  1.00  0.00              
ATOM     69  N   THR    21       5.120  -0.931   4.059  1.00  0.00              
ATOM     70  CA  THR    21       5.353  -0.684   5.475  1.00  0.00              
ATOM     71  C   THR    21       6.814  -0.840   5.880  1.00  0.00              
ATOM     72  O   THR    21       7.181  -0.539   7.014  1.00  0.00              
ATOM     73  N   THR    22       7.640  -1.318   4.955  1.00  0.00              
ATOM     74  CA  THR    22       9.069  -1.467   5.213  1.00  0.00              
ATOM     75  C   THR    22       9.807  -0.274   4.609  1.00  0.00              
ATOM     76  O   THR    22      11.036  -0.259   4.537  1.00  0.00              
ATOM     77  N   THR    23       9.040   0.719   4.162  1.00  0.00              
ATOM     78  CA  THR    23       9.628   1.921   3.592  1.00  0.00              
ATOM     79  C   THR    23       9.868   1.894   2.096  1.00  0.00              
ATOM     80  O   THR    23      10.503   2.801   1.551  1.00  0.00              
ATOM     81  N   SER    25       9.355   0.869   1.425  1.00  0.00              
ATOM     82  CA  SER    25       9.540   0.737  -0.016  1.00  0.00              
ATOM     83  C   SER    25       8.369   1.269  -0.831  1.00  0.00              
ATOM     84  O   SER    25       7.212   0.999  -0.519  1.00  0.00              
ATOM     85  N   ASN    26       8.656   2.048  -1.883  1.00  0.00              
ATOM     86  CA  ASN    26       7.585   2.583  -2.727  1.00  0.00              
ATOM     87  C   ASN    26       7.024   1.385  -3.494  1.00  0.00              
ATOM     88  O   ASN    26       7.771   0.461  -3.821  1.00  0.00              
ATOM     89  N   ILE    27       5.726   1.384  -3.773  1.00  0.00              
ATOM     90  CA  ILE    27       5.123   0.266  -4.490  1.00  0.00              
ATOM     91  C   ILE    27       4.199   0.710  -5.618  1.00  0.00              
ATOM     92  O   ILE    27       3.651   1.812  -5.590  1.00  0.00              
ATOM     93  N   THR    28       4.035  -0.156  -6.615  1.00  0.00              
ATOM     94  CA  THR    28       3.159   0.143  -7.740  1.00  0.00              
ATOM     95  C   THR    28       1.785  -0.464  -7.510  1.00  0.00              
ATOM     96  O   THR    28       1.664  -1.566  -6.973  1.00  0.00              
ATOM     97  N   LEU    29       0.751   0.265  -7.915  1.00  0.00              
ATOM     98  CA  LEU    29      -0.620  -0.201  -7.755  1.00  0.00              
ATOM     99  C   LEU    29      -1.485   0.295  -8.906  1.00  0.00              
ATOM    100  O   LEU    29      -1.180   1.312  -9.528  1.00  0.00              
ATOM    101  N   GLU    30      -2.560  -0.434  -9.184  1.00  0.00              
ATOM    102  CA  GLU    30      -3.475  -0.083 -10.265  1.00  0.00              
ATOM    103  C   GLU    30      -4.020   1.335 -10.125  1.00  0.00              
ATOM    104  O   GLU    30      -3.555   2.258 -10.793  1.00  0.00              
ATOM    105  N   ASP    31      -5.011   1.500  -9.254  1.00  0.00              
ATOM    106  CA  ASP    31      -5.605   2.809  -9.050  1.00  0.00              
ATOM    107  C   ASP    31      -4.722   3.733  -8.237  1.00  0.00              
ATOM    108  O   ASP    31      -4.677   3.639  -7.010  1.00  0.00              
ATOM    109  N   ASP    32      -3.209   8.014  -8.446  1.00  0.00              
ATOM    110  CA  ASP    32      -3.096   9.302  -9.135  1.00  0.00              
ATOM    111  C   ASP    32      -1.695   9.548  -9.681  1.00  0.00              
ATOM    112  O   ASP    32      -0.743   8.866  -9.305  1.00  0.00              
ATOM    113  N   GLN    33      -1.576  10.528 -10.569  1.00  0.00              
ATOM    114  CA  GLN    33      -0.291  10.855 -11.171  1.00  0.00              
ATOM    115  C   GLN    33       0.638  11.571 -10.199  1.00  0.00              
ATOM    116  O   GLN    33       1.848  11.623 -10.416  1.00  0.00              
ATOM    117  N   GLY    34       0.074  12.128  -9.130  1.00  0.00              
ATOM    118  CA  GLY    34       0.885  12.834  -8.145  1.00  0.00              
ATOM    119  C   GLY    34       0.102  13.219  -6.894  1.00  0.00              
ATOM    120  O   GLY    34      -1.081  12.900  -6.756  1.00  0.00              
ATOM    121  N   SER    35       0.783  13.909  -5.984  1.00  0.00              
ATOM    122  CA  SER    35       0.158  14.348  -4.751  1.00  0.00              
ATOM    123  C   SER    35       0.131  13.302  -3.654  1.00  0.00              
ATOM    124  O   SER    35       0.568  12.165  -3.843  1.00  0.00              
ATOM    125  N   HIS    36      -0.383  13.702  -2.495  1.00  0.00              
ATOM    126  CA  HIS    36      -0.494  12.815  -1.346  1.00  0.00              
ATOM    127  C   HIS    36      -1.707  11.913  -1.526  1.00  0.00              
ATOM    128  O   HIS    36      -2.645  12.263  -2.241  1.00  0.00              
ATOM    129  N   PHE    37      -1.683  10.755  -0.875  1.00  0.00              
ATOM    130  CA  PHE    37      -2.794   9.812  -0.946  1.00  0.00              
ATOM    131  C   PHE    37      -2.906   9.003   0.337  1.00  0.00              
ATOM    132  O   PHE    37      -1.904   8.723   0.997  1.00  0.00              
ATOM    133  N   ARG    38      -4.132   8.645   0.698  1.00  0.00              
ATOM    134  CA  ARG    38      -4.359   7.823   1.874  1.00  0.00              
ATOM    135  C   ARG    38      -4.184   6.394   1.381  1.00  0.00              
ATOM    136  O   ARG    38      -4.658   6.048   0.299  1.00  0.00              
ATOM    137  N   LEU    39      -3.497   5.568   2.161  1.00  0.00              
ATOM    138  CA  LEU    39      -3.256   4.187   1.763  1.00  0.00              
ATOM    139  C   LEU    39      -3.923   3.185   2.694  1.00  0.00              
ATOM    140  O   LEU    39      -3.812   3.288   3.916  1.00  0.00              
ATOM    141  N   VAL    40      -4.619   2.214   2.104  1.00  0.00              
ATOM    142  CA  VAL    40      -5.295   1.176   2.874  1.00  0.00              
ATOM    143  C   VAL    40      -4.795  -0.211   2.471  1.00  0.00              
ATOM    144  O   VAL    40      -4.192  -0.376   1.411  1.00  0.00              
ATOM    145  N   VAL    41      -5.050  -1.199   3.327  1.00  0.00              
ATOM    146  CA  VAL    41      -4.645  -2.583   3.075  1.00  0.00              
ATOM    147  C   VAL    41      -5.822  -3.489   2.746  1.00  0.00              
ATOM    148  O   VAL    41      -6.976  -3.142   2.985  1.00  0.00              
ATOM    149  N   ARG    42      -5.490  -4.669   2.226  1.00  0.00              
ATOM    150  CA  ARG    42      -6.464  -5.691   1.875  1.00  0.00              
ATOM    151  C   ARG    42      -7.900  -5.321   1.556  1.00  0.00              
ATOM    152  O   ARG    42      -8.196  -4.223   1.083  1.00  0.00              
ATOM    153  N   ASP    43      -8.794  -6.272   1.817  1.00  0.00              
ATOM    154  CA  ASP    43     -10.222  -6.112   1.563  1.00  0.00              
ATOM    155  C   ASP    43     -10.899  -5.239   2.612  1.00  0.00              
ATOM    156  O   ASP    43     -11.742  -4.402   2.281  1.00  0.00              
ATOM    157  N   GLU    45     -10.533  -5.438   3.875  1.00  0.00              
ATOM    158  CA  GLU    45     -11.105  -4.665   4.973  1.00  0.00              
ATOM    159  C   GLU    45     -10.844  -3.169   4.799  1.00  0.00              
ATOM    160  O   GLU    45     -11.405  -2.347   5.524  1.00  0.00              
ATOM    161  N   GLY    46      -9.990  -2.828   3.835  1.00  0.00              
ATOM    162  CA  GLY    46      -9.670  -1.434   3.572  1.00  0.00              
ATOM    163  C   GLY    46      -9.105  -0.692   4.771  1.00  0.00              
ATOM    164  O   GLY    46      -9.448   0.466   5.010  1.00  0.00              
ATOM    165  N   ARG    47      -8.232  -1.355   5.522  1.00  0.00              
ATOM    166  CA  ARG    47      -7.623  -0.752   6.702  1.00  0.00              
ATOM    167  C   ARG    47      -6.643   0.353   6.320  1.00  0.00              
ATOM    168  O   ARG    47      -5.798   0.170   5.446  1.00  0.00              
ATOM    169  N   MET    48      -6.771   1.502   6.978  1.00  0.00              
ATOM    170  CA  MET    48      -5.893   2.643   6.732  1.00  0.00              
ATOM    171  C   MET    48      -4.540   2.364   7.378  1.00  0.00              
ATOM    172  O   MET    48      -4.477   2.015   8.554  1.00  0.00              
ATOM    173  N   VAL    49      -3.458   2.518   6.619  1.00  0.00              
ATOM    174  CA  VAL    49      -2.134   2.277   7.177  1.00  0.00              
ATOM    175  C   VAL    49      -1.244   3.517   7.162  1.00  0.00              
ATOM    176  O   VAL    49      -0.121   3.484   7.663  1.00  0.00              
END
