
#######################################################
#                                                     #
#                        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   36 (  178),  selected   36 , name T0335TS121_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS121_5-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5           -
LGA    K       6      K       6           -
LGA    I       7      I       7           -
LGA    A       8      A       8           -
LGA    R       9      R       9           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      -       -           -
LGA    A      15      -       -           -
LGA    K      16      -       -           -
LGA    A      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      I      10          3.868
LGA    G      20      N      11          3.643
LGA    V      21      E      12          2.807
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    I      22      K      16          1.707
LGA    T      23      A      17          0.802
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    E      24      V      21          4.949
LGA    E      25      I      22          1.561
LGA    E      26      T      23          0.667
LGA    K      27      E      24          1.429
LGA    A      28      E      25          1.260
LGA    E      29      E      26          0.785
LGA    Q      30      K      27          0.880
LGA    Q      31      A      28          0.902
LGA    K      32      E      29          0.700
LGA    L      33      Q      30          0.702
LGA    R      34      Q      31          0.728
LGA    Q      35      K      32          0.387
LGA    E      36      L      33          0.475
LGA    Y      37      R      34          1.466
LGA    L      38      Q      35          2.136
LGA    K      39      E      36          1.837
LGA    G      40      Y      37          1.477
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     22    1.99     4.55     55.970     1.053

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.486405 * X  +   0.826319 * Y  +   0.283915 * Z  +   1.249157
  Y_new =   0.281074 * X  +  -0.455653 * Y  +   0.844617 * Z  +   3.314964
  Z_new =   0.827290 * X  +  -0.331025 * Y  +  -0.453888 * Z  +  -5.966836 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.511466    0.630127  [ DEG:  -143.8964     36.1036 ]
  Theta =  -0.974266   -2.167327  [ DEG:   -55.8213   -124.1787 ]
  Phi   =   0.523981   -2.617612  [ DEG:    30.0219   -149.9781 ]
 
# 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: T0335TS121_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS121_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   22   1.99    4.55  55.970
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS121_5-D1
PFRMAT    TS
TARGET    T0335
MODEL     5
PARENT    N/A
ATOM      5  N   ALA     5      11.807  11.973  -4.415  1.00  0.00          
ATOM      5  CA  ALA     5      10.850  12.970  -3.908  1.00  0.00          
ATOM      5  C   ALA     5       9.586  12.890  -4.764  1.00  0.00          
ATOM      5  O   ALA     5       8.450  12.939  -4.266  1.00  0.00          
ATOM      5  CB  ALA     5      11.467  14.375  -4.076  1.00  0.00          
ATOM      6  N   LYS     6       9.823  12.767  -6.056  1.00  0.00          
ATOM      6  CA  LYS     6       8.754  12.673  -7.058  1.00  0.00          
ATOM      6  C   LYS     6       7.931  11.426  -6.726  1.00  0.00          
ATOM      6  O   LYS     6       6.698  11.404  -6.842  1.00  0.00          
ATOM      6  CB  LYS     6       9.384  12.480  -8.453  1.00  0.00          
ATOM      7  N   ILE     7       8.651  10.400  -6.314  1.00  0.00          
ATOM      7  CA  ILE     7       8.062   9.104  -5.943  1.00  0.00          
ATOM      7  C   ILE     7       6.928   9.313  -4.938  1.00  0.00          
ATOM      7  O   ILE     7       5.888   8.639  -4.973  1.00  0.00          
ATOM      7  CB  ILE     7       9.164   8.287  -5.234  1.00  0.00          
ATOM      8  N   ALA     8       7.165  10.260  -4.049  1.00  0.00          
ATOM      8  CA  ALA     8       6.210  10.625  -2.994  1.00  0.00          
ATOM      8  C   ALA     8       4.871  11.051  -3.602  1.00  0.00          
ATOM      8  O   ALA     8       3.787  10.675  -3.134  1.00  0.00          
ATOM      8  CB  ALA     8       6.794  11.837  -2.242  1.00  0.00          
ATOM      9  N   ARG     9       4.986  11.842  -4.653  1.00  0.00          
ATOM      9  CA  ARG     9       3.826  12.369  -5.390  1.00  0.00          
ATOM      9  C   ARG     9       3.000  11.221  -5.972  1.00  0.00          
ATOM      9  O   ARG     9       1.764  11.183  -5.872  1.00  0.00          
ATOM      9  CB  ARG     9       4.345  13.212  -6.575  1.00  0.00          
ATOM     10  N   ILE    10       3.721  10.295  -6.579  1.00  0.00          
ATOM     10  CA  ILE    10       3.129   9.106  -7.207  1.00  0.00          
ATOM     10  C   ILE    10       2.398   8.340  -6.103  1.00  0.00          
ATOM     10  O   ILE    10       1.308   7.784  -6.301  1.00  0.00          
ATOM     10  CB  ILE    10       4.235   8.216  -7.812  1.00  0.00          
ATOM     11  N   ASN    11       3.032   8.329  -4.946  1.00  0.00          
ATOM     11  CA  ASN    11       2.509   7.651  -3.752  1.00  0.00          
ATOM     11  C   ASN    11       1.109   8.120  -3.343  1.00  0.00          
ATOM     11  O   ASN    11       0.220   7.323  -3.017  1.00  0.00          
ATOM     11  CB  ASN    11       3.436   8.059  -2.591  1.00  0.00          
ATOM     12  N   GLU    12       0.948   9.429  -3.372  1.00  0.00          
ATOM     12  CA  GLU    12      -0.317  10.093  -3.017  1.00  0.00          
ATOM     12  C   GLU    12      -1.427   9.596  -3.943  1.00  0.00          
ATOM     12  O   GLU    12      -2.551   9.292  -3.519  1.00  0.00          
ATOM     12  CB  GLU    12      -0.150  11.608  -3.254  1.00  0.00          
ATOM     13  N   LEU    13      -1.073   9.526  -5.214  1.00  0.00          
ATOM     13  CA  LEU    13      -1.985   9.075  -6.274  1.00  0.00          
ATOM     13  C   LEU    13      -2.412   7.633  -5.991  1.00  0.00          
ATOM     13  O   LEU    13      -3.583   7.253  -6.140  1.00  0.00          
ATOM     13  CB  LEU    13      -1.203   9.128  -7.602  1.00  0.00          
ATOM     14  N   ALA    14      -1.430   6.852  -5.580  1.00  0.00          
ATOM     14  CA  ALA    14      -1.620   5.431  -5.251  1.00  0.00          
ATOM     14  C   ALA    14      -2.648   5.228  -4.136  1.00  0.00          
ATOM     14  O   ALA    14      -3.502   4.330  -4.186  1.00  0.00          
ATOM     14  CB  ALA    14      -0.277   4.920  -4.697  1.00  0.00          
ATOM     15  N   ALA    15      -2.536   6.086  -3.139  1.00  0.00          
ATOM     15  CA  ALA    15      -3.421   6.069  -1.965  1.00  0.00          
ATOM     15  C   ALA    15      -4.874   6.196  -2.431  1.00  0.00          
ATOM     15  O   ALA    15      -5.794   5.561  -1.895  1.00  0.00          
ATOM     15  CB  ALA    15      -3.050   7.259  -1.061  1.00  0.00          
ATOM     16  N   LYS    16      -5.045   7.033  -3.438  1.00  0.00          
ATOM     16  CA  LYS    16      -6.359   7.304  -4.040  1.00  0.00          
ATOM     16  C   LYS    16      -6.950   5.980  -4.528  1.00  0.00          
ATOM     16  O   LYS    16      -8.154   5.712  -4.399  1.00  0.00          
ATOM     16  CB  LYS    16      -6.157   8.210  -5.273  1.00  0.00          
ATOM     17  N   ALA    17      -6.070   5.172  -5.088  1.00  0.00          
ATOM     17  CA  ALA    17      -6.425   3.851  -5.626  1.00  0.00          
ATOM     17  C   ALA    17      -7.013   3.028  -4.480  1.00  0.00          
ATOM     17  O   ALA    17      -7.975   2.262  -4.646  1.00  0.00          
ATOM     17  CB  ALA    17      -5.150   3.138  -6.126  1.00  0.00          
ATOM     18  N   LYS    18      -6.408   3.215  -3.322  1.00  0.00          
ATOM     18  CA  LYS    18      -6.811   2.525  -2.090  1.00  0.00          
ATOM     18  C   LYS    18      -6.250   1.105  -2.197  1.00  0.00          
ATOM     18  O   LYS    18      -6.972   0.104  -2.080  1.00  0.00          
ATOM     18  CB  LYS    18      -8.349   2.465  -2.043  1.00  0.00          
ATOM     19  N   ALA    19      -4.952   1.055  -2.421  1.00  0.00          
ATOM     19  CA  ALA    19      -4.209  -0.207  -2.558  1.00  0.00          
ATOM     19  C   ALA    19      -4.385  -1.113  -1.336  1.00  0.00          
ATOM     19  O   ALA    19      -3.925  -2.262  -1.300  1.00  0.00          
ATOM     19  CB  ALA    19      -2.717   0.148  -2.666  1.00  0.00          
ATOM     20  N   GLY    20      -5.063  -0.560  -0.347  1.00  0.00          
ATOM     20  CA  GLY    20      -5.347  -1.254   0.919  1.00  0.00          
ATOM     20  C   GLY    20      -6.845  -1.446   1.165  1.00  0.00          
ATOM     20  O   GLY    20      -7.618  -0.488   1.287  1.00  0.00          
ATOM     21  N   VAL    21      -7.222  -2.710   1.233  1.00  0.00          
ATOM     21  CA  VAL    21      -8.616  -3.121   1.463  1.00  0.00          
ATOM     21  C   VAL    21      -8.907  -3.034   2.963  1.00  0.00          
ATOM     21  O   VAL    21     -10.035  -2.768   3.398  1.00  0.00          
ATOM     21  CB  VAL    21      -8.745  -4.597   1.044  1.00  0.00          
ATOM     22  N   ILE    22      -7.857  -3.265   3.730  1.00  0.00          
ATOM     22  CA  ILE    22      -7.913  -3.232   5.198  1.00  0.00          
ATOM     22  C   ILE    22      -7.153  -1.975   5.631  1.00  0.00          
ATOM     22  O   ILE    22      -5.925  -1.876   5.510  1.00  0.00          
ATOM     22  CB  ILE    22      -7.182  -4.481   5.721  1.00  0.00          
ATOM     23  N   THR    23      -7.922  -1.026   6.135  1.00  0.00          
ATOM     23  CA  THR    23      -7.398   0.263   6.612  1.00  0.00          
ATOM     23  C   THR    23      -7.354   0.292   8.143  1.00  0.00          
ATOM     23  O   THR    23      -8.347   0.575   8.822  1.00  0.00          
ATOM     23  CB  THR    23      -8.379   1.360   6.163  1.00  0.00          
ATOM     24  N   GLU    24      -6.175  -0.008   8.656  1.00  0.00          
ATOM     24  CA  GLU    24      -5.911  -0.039  10.104  1.00  0.00          
ATOM     24  C   GLU    24      -6.227   1.346  10.672  1.00  0.00          
ATOM     24  O   GLU    24      -6.758   1.495  11.783  1.00  0.00          
ATOM     24  CB  GLU    24      -4.420  -0.351  10.336  1.00  0.00          
ATOM     25  N   GLU    25      -5.884   2.342   9.877  1.00  0.00          
ATOM     25  CA  GLU    25      -6.098   3.754  10.226  1.00  0.00          
ATOM     25  C   GLU    25      -4.933   4.258  11.081  1.00  0.00          
ATOM     25  O   GLU    25      -5.114   4.882  12.137  1.00  0.00          
ATOM     25  CB  GLU    25      -7.371   3.852  11.087  1.00  0.00          
ATOM     26  N   GLU    26      -3.741   3.966  10.593  1.00  0.00          
ATOM     26  CA  GLU    26      -2.486   4.355  11.255  1.00  0.00          
ATOM     26  C   GLU    26      -1.603   4.925  10.142  1.00  0.00          
ATOM     26  O   GLU    26      -1.537   4.399   9.023  1.00  0.00          
ATOM     26  CB  GLU    26      -1.804   3.106  11.843  1.00  0.00          
ATOM     27  N   LYS    27      -0.934   6.010  10.487  1.00  0.00          
ATOM     27  CA  LYS    27      -0.028   6.720   9.572  1.00  0.00          
ATOM     27  C   LYS    27       1.036   5.759   9.035  1.00  0.00          
ATOM     27  O   LYS    27       1.427   5.803   7.860  1.00  0.00          
ATOM     27  CB  LYS    27       0.695   7.818  10.370  1.00  0.00          
ATOM     28  N   ALA    28       1.484   4.897   9.929  1.00  0.00          
ATOM     28  CA  ALA    28       2.507   3.885   9.625  1.00  0.00          
ATOM     28  C   ALA    28       2.073   3.008   8.448  1.00  0.00          
ATOM     28  O   ALA    28       2.862   2.676   7.551  1.00  0.00          
ATOM     28  CB  ALA    28       2.647   2.977  10.862  1.00  0.00          
ATOM     29  N   GLU    29       0.804   2.649   8.482  1.00  0.00          
ATOM     29  CA  GLU    29       0.179   1.808   7.451  1.00  0.00          
ATOM     29  C   GLU    29       0.267   2.497   6.088  1.00  0.00          
ATOM     29  O   GLU    29       0.608   1.886   5.063  1.00  0.00          
ATOM     29  CB  GLU    29      -1.321   1.656   7.779  1.00  0.00          
ATOM     30  N   GLN    30      -0.049   3.778   6.112  1.00  0.00          
ATOM     30  CA  GLN    30      -0.031   4.630   4.916  1.00  0.00          
ATOM     30  C   GLN    30       1.388   4.645   4.341  1.00  0.00          
ATOM     30  O   GLN    30       1.604   4.586   3.122  1.00  0.00          
ATOM     30  CB  GLN    30      -0.408   6.059   5.356  1.00  0.00          
ATOM     31  N   GLN    31       2.337   4.725   5.255  1.00  0.00          
ATOM     31  CA  GLN    31       3.769   4.754   4.923  1.00  0.00          
ATOM     31  C   GLN    31       4.164   3.500   4.139  1.00  0.00          
ATOM     31  O   GLN    31       4.931   3.548   3.167  1.00  0.00          
ATOM     31  CB  GLN    31       4.557   4.744   6.246  1.00  0.00          
ATOM     32  N   LYS    32       3.617   2.387   4.592  1.00  0.00          
ATOM     32  CA  LYS    32       3.861   1.069   3.986  1.00  0.00          
ATOM     32  C   LYS    32       3.445   1.026   2.513  1.00  0.00          
ATOM     32  O   LYS    32       4.167   0.520   1.643  1.00  0.00          
ATOM     32  CB  LYS    32       2.990   0.049   4.743  1.00  0.00          
ATOM     33  N   LEU    33       2.268   1.569   2.269  1.00  0.00          
ATOM     33  CA  LEU    33       1.677   1.634   0.924  1.00  0.00          
ATOM     33  C   LEU    33       2.609   2.429   0.007  1.00  0.00          
ATOM     33  O   LEU    33       2.844   2.074  -1.158  1.00  0.00          
ATOM     33  CB  LEU    33       0.348   2.412   0.992  1.00  0.00          
ATOM     34  N   ARG    34       3.125   3.505   0.569  1.00  0.00          
ATOM     34  CA  ARG    34       4.046   4.411  -0.133  1.00  0.00          
ATOM     34  C   ARG    34       5.324   3.732  -0.633  1.00  0.00          
ATOM     34  O   ARG    34       5.751   3.903  -1.783  1.00  0.00          
ATOM     34  CB  ARG    34       4.480   5.496   0.871  1.00  0.00          
ATOM     35  N   GLN    35       5.913   2.964   0.265  1.00  0.00          
ATOM     35  CA  GLN    35       7.152   2.218  -0.005  1.00  0.00          
ATOM     35  C   GLN    35       6.970   1.240  -1.167  1.00  0.00          
ATOM     35  O   GLN    35       7.822   1.112  -2.058  1.00  0.00          
ATOM     35  CB  GLN    35       7.495   1.398   1.252  1.00  0.00          
ATOM     36  N   GLU    36       5.838   0.561  -1.125  1.00  0.00          
ATOM     36  CA  GLU    36       5.462  -0.432  -2.142  1.00  0.00          
ATOM     36  C   GLU    36       5.378   0.184  -3.542  1.00  0.00          
ATOM     36  O   GLU    36       5.856  -0.380  -4.536  1.00  0.00          
ATOM     36  CB  GLU    36       4.074  -0.967  -1.749  1.00  0.00          
ATOM     37  N   TYR    37       4.760   1.349  -3.583  1.00  0.00          
ATOM     37  CA  TYR    37       4.569   2.114  -4.826  1.00  0.00          
ATOM     37  C   TYR    37       5.899   2.468  -5.496  1.00  0.00          
ATOM     37  O   TYR    37       6.079   2.324  -6.714  1.00  0.00          
ATOM     37  CB  TYR    37       3.918   3.455  -4.442  1.00  0.00          
ATOM     38  N   LEU    38       6.814   2.931  -4.666  1.00  0.00          
ATOM     38  CA  LEU    38       8.162   3.332  -5.099  1.00  0.00          
ATOM     38  C   LEU    38       8.918   2.171  -5.749  1.00  0.00          
ATOM     38  O   LEU    38       9.563   2.313  -6.798  1.00  0.00          
ATOM     38  CB  LEU    38       8.934   3.711  -3.822  1.00  0.00          
ATOM     39  N   LYS    39       8.816   1.030  -5.093  1.00  0.00          
ATOM     39  CA  LYS    39       9.465  -0.212  -5.541  1.00  0.00          
ATOM     39  C   LYS    39       9.001  -0.621  -6.940  1.00  0.00          
ATOM     39  O   LYS    39       9.788  -1.065  -7.790  1.00  0.00          
ATOM     39  CB  LYS    39       9.067  -1.334  -4.566  1.00  0.00          
ATOM     40  N   GLY    40       7.707  -0.457  -7.145  1.00  0.00          
ATOM     40  CA  GLY    40       7.051  -0.787  -8.418  1.00  0.00          
ATOM     40  C   GLY    40       7.428   0.234  -9.494  1.00  0.00          
ATOM     40  O   GLY    40       7.706  -0.105 -10.652  1.00  0.00          
TER
END
