
#######################################################
#                                                     #
#                        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 (  144),  selected   36 , name T0335AL509_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL509_1-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    A       5      K       6          1.647
LGA    K       6      I       7          0.547
LGA    I       7      A       8          1.110
LGA    A       8      R       9          1.401
LGA    R       9      I      10          1.024
LGA    I      10      N      11          0.296
LGA    N      11      E      12          0.460
LGA    E      12      L      13          0.654
LGA    L      13      A      14          0.608
LGA    A      14      A      15          0.556
LGA    A      15      K      16          0.505
LGA    K      16      A      17          0.366
LGA    A      17      K      18          0.704
LGA    K      18      A      19          0.999
LGA    A      19      G      20          0.972
LGA    -       -      V      21           -
LGA    G      20      I      22          2.782
LGA    V      21      T      23          3.250
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    I      22      K      27          1.643
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    T      23      Q      30          2.627
LGA    E      24      Q      31          1.362
LGA    E      25      K      32          3.028
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    E      26      E      36          2.083
LGA    K      27      Y      37          2.535
LGA    -       -      L      38           -
LGA    A      28      K      39          1.726
LGA    E      29      G      40           -
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    Q      35      -       -           -
LGA    E      36      -       -           -
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)   36   36    5.0     24    1.64     8.33     62.147     1.383

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.533142 * X  +  -0.682973 * Y  +  -0.499307 * Z  +  10.809763
  Y_new =   0.690989 * X  +   0.692051 * Y  +  -0.208802 * Z  + -34.350517
  Z_new =   0.488153 * X  +  -0.233695 * Y  +   0.840889 * Z  + -42.616547 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.271073    2.870519  [ DEG:   -15.5314    164.4686 ]
  Theta =  -0.509972   -2.631621  [ DEG:   -29.2192   -150.7808 ]
  Phi   =   0.913637   -2.227956  [ DEG:    52.3475   -127.6525 ]
 
# 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: T0335AL509_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL509_1-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   24   1.64    8.33  62.147
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL509_1-D1
REMARK Aligment from pdb entry: 1u6tA_
ATOM      9  N   ALA     5      -0.679  -9.230  -6.770  1.00  0.00              
ATOM     10  CA  ALA     5      -0.018  -8.339  -5.823  1.00  0.00              
ATOM     11  C   ALA     5      -0.807  -7.032  -5.718  1.00  0.00              
ATOM     12  O   ALA     5      -1.084  -6.540  -4.621  1.00  0.00              
ATOM     13  N   LYS     6      -1.172  -6.476  -6.869  1.00  0.00              
ATOM     14  CA  LYS     6      -1.930  -5.235  -6.914  1.00  0.00              
ATOM     15  C   LYS     6      -3.196  -5.364  -6.065  1.00  0.00              
ATOM     16  O   LYS     6      -3.516  -4.481  -5.263  1.00  0.00              
ATOM     17  N   ILE     7      -3.903  -6.477  -6.229  1.00  0.00              
ATOM     18  CA  ILE     7      -5.128  -6.706  -5.477  1.00  0.00              
ATOM     19  C   ILE     7      -4.849  -6.883  -3.984  1.00  0.00              
ATOM     20  O   ILE     7      -5.605  -6.391  -3.149  1.00  0.00              
ATOM     21  N   ALA     8      -3.766  -7.575  -3.640  1.00  0.00              
ATOM     22  CA  ALA     8      -3.433  -7.772  -2.232  1.00  0.00              
ATOM     23  C   ALA     8      -3.126  -6.430  -1.563  1.00  0.00              
ATOM     24  O   ALA     8      -3.517  -6.194  -0.418  1.00  0.00              
ATOM     25  N   ARG     9      -2.439  -5.548  -2.286  1.00  0.00              
ATOM     26  CA  ARG     9      -2.097  -4.232  -1.752  1.00  0.00              
ATOM     27  C   ARG     9      -3.363  -3.408  -1.520  1.00  0.00              
ATOM     28  O   ARG     9      -3.532  -2.795  -0.466  1.00  0.00              
ATOM     29  N   ILE    10      -4.254  -3.401  -2.503  1.00  0.00              
ATOM     30  CA  ILE    10      -5.495  -2.647  -2.368  1.00  0.00              
ATOM     31  C   ILE    10      -6.332  -3.187  -1.215  1.00  0.00              
ATOM     32  O   ILE    10      -7.023  -2.431  -0.529  1.00  0.00              
ATOM     33  N   ASN    11      -6.256  -4.496  -0.996  1.00  0.00              
ATOM     34  CA  ASN    11      -6.995  -5.131   0.087  1.00  0.00              
ATOM     35  C   ASN    11      -6.546  -4.531   1.423  1.00  0.00              
ATOM     36  O   ASN    11      -7.370  -4.091   2.225  1.00  0.00              
ATOM     37  N   GLU    12      -5.237  -4.504   1.654  1.00  0.00              
ATOM     38  CA  GLU    12      -4.698  -3.957   2.896  1.00  0.00              
ATOM     39  C   GLU    12      -5.009  -2.467   3.048  1.00  0.00              
ATOM     40  O   GLU    12      -5.528  -2.038   4.078  1.00  0.00              
ATOM     41  N   LEU    13      -4.699  -1.683   2.020  1.00  0.00              
ATOM     42  CA  LEU    13      -4.943  -0.244   2.069  1.00  0.00              
ATOM     43  C   LEU    13      -6.417   0.063   2.332  1.00  0.00              
ATOM     44  O   LEU    13      -6.743   0.949   3.125  1.00  0.00              
ATOM     45  N   ALA    14      -7.300  -0.677   1.669  1.00  0.00              
ATOM     46  CA  ALA    14      -8.725  -0.467   1.847  1.00  0.00              
ATOM     47  C   ALA    14      -9.186  -0.771   3.259  1.00  0.00              
ATOM     48  O   ALA    14     -10.024  -0.059   3.812  1.00  0.00              
ATOM     49  N   ALA    15      -8.643  -1.833   3.846  1.00  0.00              
ATOM     50  CA  ALA    15      -9.008  -2.223   5.203  1.00  0.00              
ATOM     51  C   ALA    15      -8.643  -1.143   6.217  1.00  0.00              
ATOM     52  O   ALA    15      -9.439  -0.805   7.097  1.00  0.00              
ATOM     53  N   LYS    16      -7.431  -0.618   6.100  1.00  0.00              
ATOM     54  CA  LYS    16      -6.956   0.417   7.008  1.00  0.00              
ATOM     55  C   LYS    16      -7.844   1.647   6.915  1.00  0.00              
ATOM     56  O   LYS    16      -8.235   2.225   7.930  1.00  0.00              
ATOM     57  N   ALA    17      -8.166   2.035   5.688  1.00  0.00              
ATOM     58  CA  ALA    17      -9.022   3.189   5.445  1.00  0.00              
ATOM     59  C   ALA    17     -10.389   2.967   6.083  1.00  0.00              
ATOM     60  O   ALA    17     -10.889   3.821   6.816  1.00  0.00              
ATOM     61  N   LYS    18     -10.979   1.808   5.808  1.00  0.00              
ATOM     62  CA  LYS    18     -12.292   1.465   6.338  1.00  0.00              
ATOM     63  C   LYS    18     -12.360   1.506   7.859  1.00  0.00              
ATOM     64  O   LYS    18     -13.347   1.977   8.429  1.00  0.00              
ATOM     65  N   ALA    19     -11.314   1.015   8.516  1.00  0.00              
ATOM     66  CA  ALA    19     -11.286   0.982   9.972  1.00  0.00              
ATOM     67  C   ALA    19     -10.678   2.227  10.597  1.00  0.00              
ATOM     68  O   ALA    19     -10.430   2.267  11.802  1.00  0.00              
ATOM     69  N   GLY    20      -4.754   4.946  11.142  1.00  0.00              
ATOM     70  CA  GLY    20      -3.803   5.855  10.523  1.00  0.00              
ATOM     71  C   GLY    20      -2.756   5.083   9.741  1.00  0.00              
ATOM     72  O   GLY    20      -2.079   4.218  10.298  1.00  0.00              
ATOM     73  N   VAL    21      -2.610   5.393   8.456  1.00  0.00              
ATOM     74  CA  VAL    21      -1.643   4.689   7.628  1.00  0.00              
ATOM     75  C   VAL    21      -1.109   5.539   6.485  1.00  0.00              
ATOM     76  O   VAL    21      -1.642   6.605   6.169  1.00  0.00              
ATOM     77  N   ILE    22      -0.052   5.042   5.860  1.00  0.00              
ATOM     78  CA  ILE    22       0.552   5.702   4.716  1.00  0.00              
ATOM     79  C   ILE    22       1.183   4.636   3.842  1.00  0.00              
ATOM     80  O   ILE    22       1.742   3.657   4.341  1.00  0.00              
ATOM     81  N   THR    23       1.071   4.806   2.535  1.00  0.00              
ATOM     82  CA  THR    23       1.665   3.846   1.631  1.00  0.00              
ATOM     83  C   THR    23       3.068   4.314   1.303  1.00  0.00              
ATOM     84  O   THR    23       3.337   5.512   1.259  1.00  0.00              
ATOM     85  N   GLU    24       3.965   3.358   1.103  1.00  0.00              
ATOM     86  CA  GLU    24       5.346   3.650   0.743  1.00  0.00              
ATOM     87  C   GLU    24       5.549   2.816  -0.514  1.00  0.00              
ATOM     88  O   GLU    24       5.650   1.590  -0.441  1.00  0.00              
ATOM     89  N   GLU    25       5.572   3.483  -1.664  1.00  0.00              
ATOM     90  CA  GLU    25       5.718   2.808  -2.953  1.00  0.00              
ATOM     91  C   GLU    25       7.190   2.521  -3.233  1.00  0.00              
ATOM     92  O   GLU    25       8.024   3.423  -3.195  1.00  0.00              
ATOM     93  N   GLU    26       7.498   1.257  -3.510  1.00  0.00              
ATOM     94  CA  GLU    26       8.867   0.837  -3.787  1.00  0.00              
ATOM     95  C   GLU    26       9.103   0.697  -5.284  1.00  0.00              
ATOM     96  O   GLU    26      10.236   0.513  -5.726  1.00  0.00              
ATOM     97  N   LYS    27       8.027   0.783  -6.059  1.00  0.00              
ATOM     98  CA  LYS    27       8.109   0.623  -7.507  1.00  0.00              
ATOM     99  C   LYS    27       9.067   1.591  -8.194  1.00  0.00              
ATOM    100  O   LYS    27       9.837   1.190  -9.068  1.00  0.00              
ATOM    101  N   ALA    28       9.021   2.859  -7.795  1.00  0.00              
ATOM    102  CA  ALA    28       9.872   3.879  -8.394  1.00  0.00              
ATOM    103  C   ALA    28      10.594   4.748  -7.368  1.00  0.00              
ATOM    104  O   ALA    28      10.824   5.939  -7.599  1.00  0.00              
ATOM    105  N   GLU    29      10.951   4.149  -6.237  1.00  0.00              
ATOM    106  CA  GLU    29      11.663   4.859  -5.181  1.00  0.00              
ATOM    107  C   GLU    29      12.676   3.893  -4.575  1.00  0.00              
ATOM    108  O   GLU    29      12.308   2.950  -3.875  1.00  0.00              
ATOM    109  N   GLN    30      13.954   4.133  -4.849  1.00  0.00              
ATOM    110  CA  GLN    30      15.001   3.258  -4.345  1.00  0.00              
ATOM    111  C   GLN    30      15.079   3.199  -2.824  1.00  0.00              
ATOM    112  O   GLN    30      15.297   2.126  -2.259  1.00  0.00              
ATOM    113  N   GLN    31      14.905   4.337  -2.156  1.00  0.00              
ATOM    114  CA  GLN    31      14.957   4.348  -0.698  1.00  0.00              
ATOM    115  C   GLN    31      13.865   3.442  -0.130  1.00  0.00              
ATOM    116  O   GLN    31      14.136   2.576   0.703  1.00  0.00              
ATOM    117  N   LYS    32      12.630   3.643  -0.580  1.00  0.00              
ATOM    118  CA  LYS    32      11.513   2.821  -0.114  1.00  0.00              
ATOM    119  C   LYS    32      11.769   1.344  -0.403  1.00  0.00              
ATOM    120  O   LYS    32      11.555   0.492   0.457  1.00  0.00              
ATOM    121  N   LEU    33      12.228   1.047  -1.617  1.00  0.00              
ATOM    122  CA  LEU    33      12.487  -0.335  -2.012  1.00  0.00              
ATOM    123  C   LEU    33      13.576  -0.993  -1.165  1.00  0.00              
ATOM    124  O   LEU    33      13.371  -2.087  -0.634  1.00  0.00              
ATOM    125  N   ARG    34      14.723  -0.328  -1.032  1.00  0.00              
ATOM    126  CA  ARG    34      15.818  -0.871  -0.232  1.00  0.00              
ATOM    127  C   ARG    34      15.397  -1.005   1.231  1.00  0.00              
ATOM    128  O   ARG    34      15.635  -2.036   1.864  1.00  0.00              
ATOM    129  N   GLN    35      14.768   0.039   1.770  1.00  0.00              
ATOM    130  CA  GLN    35      14.338   0.010   3.165  1.00  0.00              
ATOM    131  C   GLN    35      13.450  -1.195   3.448  1.00  0.00              
ATOM    132  O   GLN    35      13.671  -1.926   4.417  1.00  0.00              
ATOM    133  N   GLU    36      12.442  -1.405   2.606  1.00  0.00              
ATOM    134  CA  GLU    36      11.539  -2.531   2.804  1.00  0.00              
ATOM    135  C   GLU    36      12.296  -3.854   2.809  1.00  0.00              
ATOM    136  O   GLU    36      12.186  -4.647   3.747  1.00  0.00              
ATOM    137  N   TYR    37      13.071  -4.087   1.757  1.00  0.00              
ATOM    138  CA  TYR    37      13.827  -5.328   1.628  1.00  0.00              
ATOM    139  C   TYR    37      14.760  -5.623   2.802  1.00  0.00              
ATOM    140  O   TYR    37      14.913  -6.779   3.194  1.00  0.00              
ATOM    141  N   LEU    38      15.367  -4.588   3.370  1.00  0.00              
ATOM    142  CA  LEU    38      16.271  -4.780   4.501  1.00  0.00              
ATOM    143  C   LEU    38      15.531  -4.923   5.823  1.00  0.00              
ATOM    144  O   LEU    38      15.948  -5.683   6.700  1.00  0.00              
ATOM    145  N   LYS    39      14.425  -4.202   5.971  1.00  0.00              
ATOM    146  CA  LYS    39      13.683  -4.249   7.220  1.00  0.00              
ATOM    147  C   LYS    39      12.682  -5.380   7.378  1.00  0.00              
ATOM    148  O   LYS    39      12.057  -5.522   8.427  1.00  0.00              
ATOM    149  N   GLY    40      12.518  -6.183   6.335  1.00  0.00              
ATOM    150  CA  GLY    40      11.658  -7.348   6.455  1.00  0.00              
ATOM    151  C   GLY    40      12.621  -8.353   7.084  1.00  0.00              
ATOM    152  O   GLY    40      13.687  -8.625   6.532  1.00  0.00              
END
