
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0335AL257_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_2-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    A       5      A       8           #
LGA    K       6      R       9           -
LGA    I       7      I      10           -
LGA    A       8      N      11           -
LGA    R       9      E      12           #
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    I      10      A      15          5.133
LGA    N      11      K      16          3.960
LGA    -       -      A      17           -
LGA    E      12      K      18          5.318
LGA    L      13      A      19          3.716
LGA    A      14      G      20          3.040
LGA    A      15      V      21          2.466
LGA    K      16      I      22          2.421
LGA    A      17      T      23          1.110
LGA    K      18      E      24          2.103
LGA    A      19      -       -           -
LGA    G      20      E      25          0.472
LGA    V      21      E      26          1.147
LGA    T      23      K      27          2.124
LGA    E      24      A      28          1.897
LGA    E      25      E      29          0.887
LGA    E      26      Q      30          1.487
LGA    K      27      Q      31          1.459
LGA    A      28      K      32          0.356
LGA    E      29      L      33          1.485
LGA    Q      30      R      34          2.760
LGA    Q      31      Q      35          2.677
LGA    K      32      E      36          1.419
LGA    L      33      Y      37          1.261
LGA    R      34      L      38          2.354
LGA    Q      35      K      39          2.413
LGA    E      36      G      40          1.444
LGA    Y      37      -       -           -
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   36    5.0     25    2.53     8.00     57.323     0.951

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.247515 * X  +  -0.585363 * Y  +   0.772067 * Z  +   7.435822
  Y_new =  -0.116923 * X  +  -0.772992 * Y  +  -0.623548 * Z  +   8.540631
  Z_new =   0.961803 * X  +  -0.244610 * Y  +   0.122885 * Z  + -22.078842 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.105253    2.036340  [ DEG:   -63.3263    116.6737 ]
  Theta =  -1.293515   -1.848078  [ DEG:   -74.1129   -105.8871 ]
  Phi   =  -2.700279    0.441314  [ DEG:  -154.7146     25.2854 ]
 
# 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: T0335AL257_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_2-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   36   5.0   25   2.53    8.00  57.323
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_2-D1
REMARK Aligment from pdb entry: 2cru_A
ATOM     17  N   ALA     5      -8.348 -11.769 -10.292  1.00  0.00              
ATOM     18  CA  ALA     5      -9.343 -11.181 -11.181  1.00  0.00              
ATOM     19  C   ALA     5     -10.724 -11.187 -10.532  1.00  0.00              
ATOM     20  O   ALA     5     -11.581 -11.999 -10.884  1.00  0.00              
ATOM     21  N   LYS     6     -10.932 -10.279  -9.584  1.00  0.00              
ATOM     22  CA  LYS     6     -12.208 -10.182  -8.886  1.00  0.00              
ATOM     23  C   LYS     6     -12.319  -8.857  -8.139  1.00  0.00              
ATOM     24  O   LYS     6     -11.414  -8.472  -7.398  1.00  0.00              
ATOM     25  N   ILE     7     -13.434  -8.163  -8.339  1.00  0.00              
ATOM     26  CA  ILE     7     -13.664  -6.879  -7.684  1.00  0.00              
ATOM     27  C   ILE     7     -14.512  -7.052  -6.428  1.00  0.00              
ATOM     28  O   ILE     7     -15.362  -7.940  -6.359  1.00  0.00              
ATOM     29  N   ALA     8     -14.275  -6.198  -5.438  1.00  0.00              
ATOM     30  CA  ALA     8     -15.019  -6.254  -4.186  1.00  0.00              
ATOM     31  C   ALA     8     -14.987  -4.910  -3.467  1.00  0.00              
ATOM     32  O   ALA     8     -14.004  -4.174  -3.555  1.00  0.00              
ATOM     33  N   ARG     9     -16.065  -4.597  -2.757  1.00  0.00              
ATOM     34  CA  ARG     9     -16.159  -3.340  -2.024  1.00  0.00              
ATOM     35  C   ARG     9     -14.900  -3.100  -1.194  1.00  0.00              
ATOM     36  O   ARG     9     -14.197  -4.041  -0.826  1.00  0.00              
ATOM     37  N   ILE    10     -14.624  -1.833  -0.903  1.00  0.00              
ATOM     38  CA  ILE    10     -13.450  -1.468  -0.117  1.00  0.00              
ATOM     39  C   ILE    10     -13.625  -1.873   1.343  1.00  0.00              
ATOM     40  O   ILE    10     -14.719  -2.245   1.767  1.00  0.00              
ATOM     41  N   ASN    11     -12.541  -1.797   2.108  1.00  0.00              
ATOM     42  CA  ASN    11     -12.575  -2.154   3.520  1.00  0.00              
ATOM     43  C   ASN    11     -12.290  -0.939   4.397  1.00  0.00              
ATOM     44  O   ASN    11     -11.134  -0.583   4.623  1.00  0.00              
ATOM     45  N   GLU    12     -13.350  -0.307   4.888  1.00  0.00              
ATOM     46  CA  GLU    12     -13.213   0.867   5.741  1.00  0.00              
ATOM     47  C   GLU    12     -12.748   0.478   7.140  1.00  0.00              
ATOM     48  O   GLU    12     -13.529  -0.020   7.950  1.00  0.00              
ATOM     49  N   LEU    13     -11.468   0.709   7.417  1.00  0.00              
ATOM     50  CA  LEU    13     -10.896   0.382   8.718  1.00  0.00              
ATOM     51  C   LEU    13     -11.055   1.548   9.689  1.00  0.00              
ATOM     52  O   LEU    13     -10.680   2.680   9.383  1.00  0.00              
ATOM     53  N   ALA    14     -11.612   1.264  10.862  1.00  0.00              
ATOM     54  CA  ALA    14     -11.818   2.288  11.880  1.00  0.00              
ATOM     55  C   ALA    14     -10.511   3.008  12.198  1.00  0.00              
ATOM     56  O   ALA    14      -9.436   2.411  12.157  1.00  0.00              
ATOM     57  N   ALA    15     -10.611   4.295  12.516  1.00  0.00              
ATOM     58  CA  ALA    15      -9.429   5.074  12.837  1.00  0.00              
ATOM     59  C   ALA    15      -8.447   5.138  11.685  1.00  0.00              
ATOM     60  O   ALA    15      -8.846   5.260  10.526  1.00  0.00              
ATOM     61  N   LYS    16      -7.160   5.057  12.002  1.00  0.00              
ATOM     62  CA  LYS    16      -6.116   5.107  10.984  1.00  0.00              
ATOM     63  C   LYS    16      -4.742   4.871  11.602  1.00  0.00              
ATOM     64  O   LYS    16      -4.432   5.355  12.691  1.00  0.00              
ATOM     65  N   ALA    17      -3.898   4.107  10.894  1.00  0.00              
ATOM     66  CA  ALA    17      -2.543   3.788  11.355  1.00  0.00              
ATOM     67  C   ALA    17      -1.621   5.002  11.329  1.00  0.00              
ATOM     68  O   ALA    17      -0.933   5.293  12.306  1.00  0.00              
ATOM     69  N   LYS    18      -1.613   5.709  10.202  1.00  0.00              
ATOM     70  CA  LYS    18      -0.772   6.885  10.071  1.00  0.00              
ATOM     71  C   LYS    18       0.564   6.574   9.425  1.00  0.00              
ATOM     72  O   LYS    18       0.618   5.946   8.367  1.00  0.00              
ATOM     73  N   ALA    19       1.643   7.013  10.061  1.00  0.00              
ATOM     74  CA  ALA    19       2.986   6.777   9.542  1.00  0.00              
ATOM     75  C   ALA    19       3.300   5.285   9.505  1.00  0.00              
ATOM     76  O   ALA    19       3.821   4.776   8.514  1.00  0.00              
ATOM     77  N   GLY    20       2.980   4.590  10.592  1.00  0.00              
ATOM     78  CA  GLY    20       3.227   3.156  10.682  1.00  0.00              
ATOM     79  C   GLY    20       2.966   2.469   9.347  1.00  0.00              
ATOM     80  O   GLY    20       3.843   1.802   8.799  1.00  0.00              
ATOM     81  N   VAL    21       1.753   2.635   8.828  1.00  0.00              
ATOM     82  CA  VAL    21       1.378   2.031   7.556  1.00  0.00              
ATOM     83  C   VAL    21       1.999   2.787   6.385  1.00  0.00              
ATOM     84  O   VAL    21       2.551   2.180   5.468  1.00  0.00              
ATOM     85  N   THR    23       1.904   4.112   6.424  1.00  0.00              
ATOM     86  CA  THR    23       2.455   4.948   5.364  1.00  0.00              
ATOM     87  C   THR    23       3.797   4.405   4.886  1.00  0.00              
ATOM     88  O   THR    23       3.972   4.113   3.703  1.00  0.00              
ATOM     89  N   GLU    24       4.741   4.273   5.812  1.00  0.00              
ATOM     90  CA  GLU    24       6.068   3.767   5.482  1.00  0.00              
ATOM     91  C   GLU    24       5.987   2.676   4.419  1.00  0.00              
ATOM     92  O   GLU    24       6.808   2.625   3.505  1.00  0.00              
ATOM     93  N   GLU    25       4.989   1.806   4.546  1.00  0.00              
ATOM     94  CA  GLU    25       4.801   0.716   3.596  1.00  0.00              
ATOM     95  C   GLU    25       4.265   1.239   2.267  1.00  0.00              
ATOM     96  O   GLU    25       4.837   0.978   1.209  1.00  0.00              
ATOM     97  N   GLU    26       3.163   1.980   2.330  1.00  0.00              
ATOM     98  CA  GLU    26       2.550   2.542   1.133  1.00  0.00              
ATOM     99  C   GLU    26       3.568   3.322   0.310  1.00  0.00              
ATOM    100  O   GLU    26       3.715   3.097  -0.892  1.00  0.00              
ATOM    101  N   LYS    27       4.270   4.243   0.963  1.00  0.00              
ATOM    102  CA  LYS    27       5.276   5.058   0.293  1.00  0.00              
ATOM    103  C   LYS    27       6.346   4.182  -0.350  1.00  0.00              
ATOM    104  O   LYS    27       6.986   4.581  -1.324  1.00  0.00              
ATOM    105  N   ALA    28       6.534   2.986   0.199  1.00  0.00              
ATOM    106  CA  ALA    28       7.525   2.053  -0.323  1.00  0.00              
ATOM    107  C   ALA    28       7.110   1.530  -1.695  1.00  0.00              
ATOM    108  O   ALA    28       7.909   1.512  -2.632  1.00  0.00              
ATOM    109  N   GLU    29       5.856   1.103  -1.805  1.00  0.00              
ATOM    110  CA  GLU    29       5.336   0.577  -3.061  1.00  0.00              
ATOM    111  C   GLU    29       5.379   1.639  -4.155  1.00  0.00              
ATOM    112  O   GLU    29       5.690   1.344  -5.309  1.00  0.00              
ATOM    113  N   GLN    30       5.067   2.878  -3.785  1.00  0.00              
ATOM    114  CA  GLN    30       5.070   3.984  -4.735  1.00  0.00              
ATOM    115  C   GLN    30       6.446   4.149  -5.372  1.00  0.00              
ATOM    116  O   GLN    30       6.584   4.770  -6.426  1.00  0.00              
ATOM    117  N   GLN    31       7.463   3.590  -4.724  1.00  0.00              
ATOM    118  CA  GLN    31       8.828   3.675  -5.227  1.00  0.00              
ATOM    119  C   GLN    31       9.173   2.463  -6.088  1.00  0.00              
ATOM    120  O   GLN    31      10.078   2.518  -6.919  1.00  0.00              
ATOM    121  N   LYS    32       8.444   1.370  -5.881  1.00  0.00              
ATOM    122  CA  LYS    32       8.674   0.145  -6.637  1.00  0.00              
ATOM    123  C   LYS    32       8.006   0.217  -8.006  1.00  0.00              
ATOM    124  O   LYS    32       8.595  -0.166  -9.017  1.00  0.00              
ATOM    125  N   LEU    33       6.772   0.711  -8.031  1.00  0.00              
ATOM    126  CA  LEU    33       6.023   0.834  -9.276  1.00  0.00              
ATOM    127  C   LEU    33       6.692   1.833 -10.216  1.00  0.00              
ATOM    128  O   LEU    33       6.880   1.555 -11.400  1.00  0.00              
ATOM    129  N   ARG    34       7.048   2.996  -9.681  1.00  0.00              
ATOM    130  CA  ARG    34       7.693   4.036 -10.471  1.00  0.00              
ATOM    131  C   ARG    34       8.951   3.501 -11.150  1.00  0.00              
ATOM    132  O   ARG    34       9.176   3.736 -12.337  1.00  0.00              
ATOM    133  N   GLN    35       9.768   2.782 -10.387  1.00  0.00              
ATOM    134  CA  GLN    35      11.004   2.214 -10.914  1.00  0.00              
ATOM    135  C   GLN    35      10.739   1.429 -12.195  1.00  0.00              
ATOM    136  O   GLN    35      11.311   1.724 -13.245  1.00  0.00              
ATOM    137  N   GLU    36       9.869   0.430 -12.101  1.00  0.00              
ATOM    138  CA  GLU    36       9.530  -0.400 -13.252  1.00  0.00              
ATOM    139  C   GLU    36       9.008   0.454 -14.403  1.00  0.00              
ATOM    140  O   GLU    36       9.112   0.073 -15.569  1.00  0.00              
ATOM    141  N   TYR    37       8.448   1.611 -14.066  1.00  0.00              
ATOM    142  CA  TYR    37       7.911   2.520 -15.072  1.00  0.00              
ATOM    143  C   TYR    37       9.025   3.314 -15.746  1.00  0.00              
ATOM    144  O   TYR    37       8.960   3.603 -16.941  1.00  0.00              
ATOM    145  N   LEU    38      10.046   3.663 -14.972  1.00  0.00              
ATOM    146  CA  LEU    38      11.177   4.422 -15.494  1.00  0.00              
ATOM    147  C   LEU    38      12.160   3.507 -16.217  1.00  0.00              
ATOM    148  O   LEU    38      12.807   3.914 -17.181  1.00  0.00              
ATOM    149  N   LYS    39      12.263   2.269 -15.746  1.00  0.00              
ATOM    150  CA  LYS    39      13.164   1.294 -16.350  1.00  0.00              
ATOM    151  C   LYS    39      12.597   0.764 -17.663  1.00  0.00              
ATOM    152  O   LYS    39      13.339   0.279 -18.518  1.00  0.00              
ATOM    153  N   GLY    40      11.281   0.859 -17.815  1.00  0.00              
ATOM    154  CA  GLY    40      10.616   0.387 -19.024  1.00  0.00              
ATOM    155  C   GLY    40      10.566   1.484 -20.082  1.00  0.00              
ATOM    156  O   GLY    40      10.645   1.210 -21.280  1.00  0.00              
END
