
#######################################################
#                                                     #
#                        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   24 (  192),  selected   24 , name T0335TS349_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS349_5-D1.T0335_D1.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    A      17      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    K      18      L      13           #
LGA    -       -      A      14           -
LGA    A      19      A      15          4.465
LGA    G      20      K      16          2.708
LGA    V      21      A      17          2.818
LGA    I      22      K      18          3.843
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    T      23      I      22          2.958
LGA    E      24      T      23          0.559
LGA    -       -      E      24           -
LGA    E      25      E      25          2.150
LGA    E      26      E      26          0.905
LGA    K      27      K      27          0.484
LGA    A      28      A      28          0.848
LGA    E      29      E      29          1.385
LGA    Q      30      Q      30          0.784
LGA    Q      31      Q      31          0.569
LGA    K      32      K      32          1.056
LGA    L      33      L      33          0.979
LGA    R      34      R      34          0.736
LGA    Q      35      Q      35          0.861
LGA    E      36      E      36          0.441
LGA    Y      37      Y      37          0.344
LGA    L      38      L      38          0.570
LGA    K      39      K      39          0.728
LGA    G      40      G      40          0.856

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   36    5.0     22    1.83    77.27     55.883     1.141

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.204372 * X  +   0.502293 * Y  +   0.840199 * Z  + -22.875547
  Y_new =   0.976475 * X  +   0.164901 * Y  +   0.138938 * Z  + -49.755249
  Z_new =  -0.068762 * X  +   0.848828 * Y  +  -0.524178 * Z  + -24.885040 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.124006   -1.017586  [ DEG:   121.6966    -58.3034 ]
  Theta =   0.068816    3.072777  [ DEG:     3.9429    176.0571 ]
  Phi   =   1.777114   -1.364479  [ DEG:   101.8211    -78.1789 ]
 
# 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: T0335TS349_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS349_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   36   5.0   22   1.83   77.27  55.883
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS349_5-D1
PFRMAT TS
TARGET T0335
MODEL  5  REFINED
PARENT 1WDT_A
ATOM      1  N   ALA    17     -16.281  -7.353  -0.706  1.00  0.00
ATOM      2  CA  ALA    17     -15.663  -7.066   0.579  1.00  0.00
ATOM      3  C   ALA    17     -15.620  -5.541   0.828  1.00  0.00
ATOM      4  O   ALA    17     -15.073  -4.809   0.005  1.00  0.00
ATOM      5  CB  ALA    17     -14.253  -7.691   0.598  1.00  0.00
ATOM      6  N   LYS    18     -15.914  -5.151   2.074  1.00  0.00
ATOM      7  CA  LYS    18     -15.879  -3.731   2.531  1.00  0.00
ATOM      8  C   LYS    18     -14.458  -3.163   2.474  1.00  0.00
ATOM      9  O   LYS    18     -13.521  -3.741   3.071  1.00  0.00
ATOM     10  CB  LYS    18     -16.331  -3.599   3.963  1.00  0.00
ATOM     11  CG  LYS    18     -17.639  -2.913   4.105  1.00  0.00
ATOM     12  CD  LYS    18     -18.846  -3.701   3.754  1.00  0.00
ATOM     13  CE  LYS    18     -19.957  -2.696   3.884  1.00  0.00
ATOM     14  NZ  LYS    18     -21.084  -3.041   3.048  1.00  0.00
ATOM     15  N   ALA    19     -14.386  -1.892   2.075  1.00  0.00
ATOM     16  CA  ALA    19     -13.106  -1.197   1.982  1.00  0.00
ATOM     17  C   ALA    19     -12.715  -0.547   3.334  1.00  0.00
ATOM     18  O   ALA    19     -13.274   0.501   3.702  1.00  0.00
ATOM     19  CB  ALA    19     -13.195  -0.148   0.879  1.00  0.00
ATOM     20  N   GLY    20     -11.774  -1.185   4.052  1.00  0.00
ATOM     21  CA  GLY    20     -11.276  -0.683   5.317  1.00  0.00
ATOM     22  C   GLY    20     -10.302   0.497   5.109  1.00  0.00
ATOM     23  O   GLY    20     -10.185   1.045   4.006  1.00  0.00
ATOM     24  N   VAL    21      -9.819   1.072   6.197  1.00  0.00
ATOM     25  CA  VAL    21      -8.894   2.199   6.144  1.00  0.00
ATOM     26  C   VAL    21      -7.434   1.707   6.307  1.00  0.00
ATOM     27  O   VAL    21      -7.193   0.831   7.164  1.00  0.00
ATOM     28  CB  VAL    21      -9.254   3.210   7.242  1.00  0.00
ATOM     29  CG1 VAL    21      -8.278   4.378   7.322  1.00  0.00
ATOM     30  CG2 VAL    21     -10.633   3.833   6.982  1.00  0.00
ATOM     31  N   ILE    22      -6.497   2.186   5.466  1.00  0.00
ATOM     32  CA  ILE    22      -5.090   1.794   5.625  1.00  0.00
ATOM     33  C   ILE    22      -4.678   2.196   7.028  1.00  0.00
ATOM     34  O   ILE    22      -4.565   3.406   7.282  1.00  0.00
ATOM     35  CB  ILE    22      -4.228   2.413   4.533  1.00  0.00
ATOM     36  CG1 ILE    22      -4.711   2.070   3.097  1.00  0.00
ATOM     37  CG2 ILE    22      -2.706   2.072   4.722  1.00  0.00
ATOM     38  CD1 ILE    22      -4.573   0.551   2.779  1.00  0.00
ATOM     39  N   THR    23      -4.191   1.236   7.788  1.00  0.00
ATOM     40  CA  THR    23      -3.820   1.545   9.132  1.00  0.00
ATOM     41  C   THR    23      -2.680   2.625   9.286  1.00  0.00
ATOM     42  O   THR    23      -1.856   2.778   8.376  1.00  0.00
ATOM     43  CB  THR    23      -3.538   0.123   9.796  1.00  0.00
ATOM     44  OG1 THR    23      -2.402  -0.534   9.152  1.00  0.00
ATOM     45  CG2 THR    23      -4.777  -0.846   9.815  1.00  0.00
ATOM     46  N   GLU    24      -2.994   3.596  10.083  1.00  0.00
ATOM     47  CA  GLU    24      -2.075   4.710  10.301  1.00  0.00
ATOM     48  C   GLU    24      -0.583   4.231  10.371  1.00  0.00
ATOM     49  O   GLU    24       0.264   4.878   9.749  1.00  0.00
ATOM     50  CB  GLU    24      -2.470   5.400  11.567  1.00  0.00
ATOM     51  CG  GLU    24      -1.840   6.526  12.308  1.00  0.00
ATOM     52  CD  GLU    24      -1.434   6.148  13.753  1.00  0.00
ATOM     53  OE1 GLU    24      -2.303   5.996  14.624  1.00  0.00
ATOM     54  OE2 GLU    24      -0.234   5.989  14.030  1.00  0.00
ATOM     55  N   GLU    25      -0.308   3.093  11.022  1.00  0.00
ATOM     56  CA  GLU    25       1.028   2.527  11.209  1.00  0.00
ATOM     57  C   GLU    25       1.706   1.998   9.898  1.00  0.00
ATOM     58  O   GLU    25       2.933   1.871   9.892  1.00  0.00
ATOM     59  CB  GLU    25       0.835   1.399  12.249  1.00  0.00
ATOM     60  CG  GLU    25       0.540   1.908  13.673  1.00  0.00
ATOM     61  CD  GLU    25      -0.907   2.091  13.958  1.00  0.00
ATOM     62  OE1 GLU    25      -1.569   2.059  12.846  1.00  0.00
ATOM     63  OE2 GLU    25      -1.415   2.246  15.079  1.00  0.00
ATOM     64  N   GLU    26       0.943   1.684   8.867  1.00  0.00
ATOM     65  CA  GLU    26       1.419   1.128   7.636  1.00  0.00
ATOM     66  C   GLU    26       1.511   2.150   6.469  1.00  0.00
ATOM     67  O   GLU    26       2.004   1.728   5.438  1.00  0.00
ATOM     68  CB  GLU    26       0.442   0.019   7.225  1.00  0.00
ATOM     69  CG  GLU    26       0.461  -1.232   8.035  1.00  0.00
ATOM     70  CD  GLU    26       1.677  -1.879   8.512  1.00  0.00
ATOM     71  OE1 GLU    26       2.384  -1.653   9.513  1.00  0.00
ATOM     72  OE2 GLU    26       2.156  -2.826   7.661  1.00  0.00
ATOM     73  N   LYS    27       0.838   3.328   6.514  1.00  0.00
ATOM     74  CA  LYS    27       0.911   4.324   5.475  1.00  0.00
ATOM     75  C   LYS    27       2.366   4.521   4.941  1.00  0.00
ATOM     76  O   LYS    27       2.469   4.681   3.736  1.00  0.00
ATOM     77  CB  LYS    27       0.336   5.637   6.030  1.00  0.00
ATOM     78  CG  LYS    27      -1.110   5.485   6.460  1.00  0.00
ATOM     79  CD  LYS    27      -1.831   6.813   6.565  1.00  0.00
ATOM     80  CE  LYS    27      -2.151   7.426   5.197  1.00  0.00
ATOM     81  NZ  LYS    27      -3.174   6.698   4.481  1.00  0.00
ATOM     82  N   ALA    28       3.362   4.808   5.781  1.00  0.00
ATOM     83  CA  ALA    28       4.751   4.974   5.342  1.00  0.00
ATOM     84  C   ALA    28       5.213   3.745   4.498  1.00  0.00
ATOM     85  O   ALA    28       5.819   3.989   3.455  1.00  0.00
ATOM     86  CB  ALA    28       5.621   5.215   6.583  1.00  0.00
ATOM     87  N   GLU    29       5.210   2.505   5.024  1.00  0.00
ATOM     88  CA  GLU    29       5.586   1.294   4.303  1.00  0.00
ATOM     89  C   GLU    29       4.792   1.172   2.965  1.00  0.00
ATOM     90  O   GLU    29       5.416   0.720   2.012  1.00  0.00
ATOM     91  CB  GLU    29       5.387   0.089   5.229  1.00  0.00
ATOM     92  CG  GLU    29       6.210  -0.063   6.481  1.00  0.00
ATOM     93  CD  GLU    29       7.744   0.068   6.360  1.00  0.00
ATOM     94  OE1 GLU    29       8.367  -0.649   5.562  1.00  0.00
ATOM     95  OE2 GLU    29       8.325   0.888   7.090  1.00  0.00
ATOM     96  N   GLN    30       3.452   1.266   2.993  1.00  0.00
ATOM     97  CA  GLN    30       2.602   1.271   1.828  1.00  0.00
ATOM     98  C   GLN    30       3.056   2.374   0.830  1.00  0.00
ATOM     99  O   GLN    30       3.020   2.079  -0.365  1.00  0.00
ATOM    100  CB  GLN    30       1.105   1.255   2.156  1.00  0.00
ATOM    101  CG  GLN    30       0.701  -0.077   2.805  1.00  0.00
ATOM    102  CD  GLN    30      -0.792  -0.140   2.894  1.00  0.00
ATOM    103  OE1 GLN    30      -1.559   0.521   2.206  1.00  0.00
ATOM    104  NE2 GLN    30      -1.324  -1.067   3.688  1.00  0.00
ATOM    105  N   GLN    31       3.284   3.615   1.267  1.00  0.00
ATOM    106  CA  GLN    31       3.797   4.654   0.405  1.00  0.00
ATOM    107  C   GLN    31       5.079   4.194  -0.312  1.00  0.00
ATOM    108  O   GLN    31       5.193   4.461  -1.497  1.00  0.00
ATOM    109  CB  GLN    31       4.025   5.934   1.274  1.00  0.00
ATOM    110  CG  GLN    31       4.470   7.114   0.406  1.00  0.00
ATOM    111  CD  GLN    31       4.655   8.366   1.238  1.00  0.00
ATOM    112  OE1 GLN    31       5.452   8.389   2.181  1.00  0.00
ATOM    113  NE2 GLN    31       3.922   9.419   0.895  1.00  0.00
ATOM    114  N   LYS    32       6.122   3.747   0.425  1.00  0.00
ATOM    115  CA  LYS    32       7.375   3.203  -0.146  1.00  0.00
ATOM    116  C   LYS    32       7.001   2.130  -1.242  1.00  0.00
ATOM    117  O   LYS    32       7.649   2.182  -2.286  1.00  0.00
ATOM    118  CB  LYS    32       8.435   2.809   0.942  1.00  0.00
ATOM    119  CG  LYS    32       9.681   3.725   0.800  1.00  0.00
ATOM    120  CD  LYS    32       9.377   5.144   1.252  1.00  0.00
ATOM    121  CE  LYS    32      10.441   5.725   2.093  1.00  0.00
ATOM    122  NZ  LYS    32      10.353   7.255   2.066  1.00  0.00
ATOM    123  N   LEU    33       6.235   1.081  -0.907  1.00  0.00
ATOM    124  CA  LEU    33       5.812   0.087  -1.901  1.00  0.00
ATOM    125  C   LEU    33       5.259   0.788  -3.185  1.00  0.00
ATOM    126  O   LEU    33       5.553   0.272  -4.281  1.00  0.00
ATOM    127  CB  LEU    33       4.797  -0.869  -1.213  1.00  0.00
ATOM    128  CG  LEU    33       5.375  -2.118  -0.551  1.00  0.00
ATOM    129  CD1 LEU    33       6.848  -2.063  -0.155  1.00  0.00
ATOM    130  CD2 LEU    33       4.517  -2.394   0.697  1.00  0.00
ATOM    131  N   ARG    34       4.323   1.741  -3.067  1.00  0.00
ATOM    132  CA  ARG    34       3.724   2.484  -4.175  1.00  0.00
ATOM    133  C   ARG    34       4.826   3.133  -5.042  1.00  0.00
ATOM    134  O   ARG    34       4.643   3.077  -6.278  1.00  0.00
ATOM    135  CB  ARG    34       2.672   3.474  -3.624  1.00  0.00
ATOM    136  CG  ARG    34       2.000   4.245  -4.775  1.00  0.00
ATOM    137  CD  ARG    34       1.015   5.280  -4.263  1.00  0.00
ATOM    138  NE  ARG    34       0.406   6.007  -5.376  1.00  0.00
ATOM    139  CZ  ARG    34      -0.390   7.064  -5.245  1.00  0.00
ATOM    140  NH1 ARG    34      -0.685   7.534  -4.038  1.00  0.00
ATOM    141  NH2 ARG    34      -0.891   7.656  -6.321  1.00  0.00
ATOM    142  N   GLN    35       5.708   3.982  -4.502  1.00  0.00
ATOM    143  CA  GLN    35       6.821   4.590  -5.231  1.00  0.00
ATOM    144  C   GLN    35       7.570   3.475  -6.032  1.00  0.00
ATOM    145  O   GLN    35       7.890   3.719  -7.204  1.00  0.00
ATOM    146  CB  GLN    35       7.769   5.308  -4.249  1.00  0.00
ATOM    147  CG  GLN    35       7.138   6.553  -3.656  1.00  0.00
ATOM    148  CD  GLN    35       8.095   7.346  -2.777  1.00  0.00
ATOM    149  OE1 GLN    35       8.610   6.838  -1.782  1.00  0.00
ATOM    150  NE2 GLN    35       8.327   8.603  -3.141  1.00  0.00
ATOM    151  N   GLU    36       7.980   2.370  -5.416  1.00  0.00
ATOM    152  CA  GLU    36       8.638   1.220  -6.058  1.00  0.00
ATOM    153  C   GLU    36       7.770   0.747  -7.282  1.00  0.00
ATOM    154  O   GLU    36       8.386   0.392  -8.291  1.00  0.00
ATOM    155  CB  GLU    36       8.903   0.150  -5.002  1.00  0.00
ATOM    156  CG  GLU    36       9.590  -1.108  -5.589  1.00  0.00
ATOM    157  CD  GLU    36       9.733  -2.259  -4.626  1.00  0.00
ATOM    158  OE1 GLU    36       9.898  -3.407  -5.027  1.00  0.00
ATOM    159  OE2 GLU    36       9.668  -1.917  -3.359  1.00  0.00
ATOM    160  N   TYR    37       6.475   0.466  -7.097  1.00  0.00
ATOM    161  CA  TYR    37       5.528   0.073  -8.165  1.00  0.00
ATOM    162  C   TYR    37       5.654   1.043  -9.372  1.00  0.00
ATOM    163  O   TYR    37       5.811   0.525 -10.484  1.00  0.00
ATOM    164  CB  TYR    37       4.103   0.013  -7.661  1.00  0.00
ATOM    165  CG  TYR    37       3.800  -1.264  -6.970  1.00  0.00
ATOM    166  CD1 TYR    37       3.833  -1.388  -5.568  1.00  0.00
ATOM    167  CD2 TYR    37       3.476  -2.360  -7.746  1.00  0.00
ATOM    168  CE1 TYR    37       3.512  -2.593  -4.992  1.00  0.00
ATOM    169  CE2 TYR    37       3.203  -3.606  -7.170  1.00  0.00
ATOM    170  CZ  TYR    37       3.193  -3.704  -5.756  1.00  0.00
ATOM    171  OH  TYR    37       2.903  -4.965  -5.257  1.00  0.00
ATOM    172  N   LEU    38       5.511   2.361  -9.190  1.00  0.00
ATOM    173  CA  LEU    38       5.649   3.344 -10.241  1.00  0.00
ATOM    174  C   LEU    38       7.024   3.298 -10.901  1.00  0.00
ATOM    175  O   LEU    38       7.037   3.345 -12.138  1.00  0.00
ATOM    176  CB  LEU    38       5.325   4.715  -9.646  1.00  0.00
ATOM    177  CG  LEU    38       3.928   5.023  -9.210  1.00  0.00
ATOM    178  CD1 LEU    38       3.848   6.432  -8.642  1.00  0.00
ATOM    179  CD2 LEU    38       2.969   4.868 -10.383  1.00  0.00
ATOM    180  N   LYS    39       8.088   3.508 -10.135  1.00  0.00
ATOM    181  CA  LYS    39       9.444   3.437 -10.688  1.00  0.00
ATOM    182  C   LYS    39       9.633   2.188 -11.566  1.00  0.00
ATOM    183  O   LYS    39      10.363   2.333 -12.570  1.00  0.00
ATOM    184  CB  LYS    39      10.510   3.444  -9.611  1.00  0.00
ATOM    185  CG  LYS    39      10.857   4.548  -8.690  1.00  0.00
ATOM    186  CD  LYS    39      12.004   4.096  -7.759  1.00  0.00
ATOM    187  CE  LYS    39      11.991   4.746  -6.406  1.00  0.00
ATOM    188  NZ  LYS    39      11.321   3.883  -5.389  1.00  0.00
ATOM    189  N   GLY    40       9.301   1.001 -11.060  1.00  0.00
ATOM    190  CA  GLY    40       9.413  -0.245 -11.830  1.00  0.00
ATOM    191  C   GLY    40       8.681  -0.146 -13.202  1.00  0.00
ATOM    192  O   GLY    40       9.313  -0.387 -14.221  1.00  0.00
TER
END
