
#######################################################
#                                                     #
#                        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 T0335TS757_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS757_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      A       5          4.239
LGA    K       6      K       6          3.256
LGA    -       -      I       7           -
LGA    I       7      A       8          3.005
LGA    A       8      R       9          3.061
LGA    R       9      I      10          2.522
LGA    I      10      N      11          2.213
LGA    N      11      E      12          1.260
LGA    E      12      L      13          1.016
LGA    L      13      A      14          2.449
LGA    A      14      A      15          2.513
LGA    A      15      K      16          5.427
LGA    K      16      A      17           #
LGA    A      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      K      18          2.976
LGA    G      20      A      19           #
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    V      21      T      23          0.717
LGA    I      22      E      24           #
LGA    T      23      E      25          3.748
LGA    E      24      E      26          3.791
LGA    E      25      K      27          2.580
LGA    E      26      A      28          1.423
LGA    K      27      E      29          1.287
LGA    A      28      Q      30          0.991
LGA    E      29      Q      31          1.856
LGA    Q      30      K      32          2.241
LGA    Q      31      L      33          1.745
LGA    K      32      R      34          0.993
LGA    L      33      Q      35          1.743
LGA    R      34      E      36          2.405
LGA    Q      35      Y      37          1.822
LGA    E      36      L      38          1.138
LGA    Y      37      K      39          1.476
LGA    L      38      G      40          2.286
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     29    2.53    13.79     60.395     1.104

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.060076 * X  +   0.864837 * Y  +  -0.498446 * Z  +  -6.358146
  Y_new =   0.302485 * X  +   0.491641 * Y  +   0.816573 * Z  + -16.008188
  Z_new =   0.951259 * X  +  -0.101717 * Y  +  -0.291136 * Z  + -12.348327 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.805472    0.336121  [ DEG:  -160.7417     19.2583 ]
  Theta =  -1.257293   -1.884300  [ DEG:   -72.0376   -107.9624 ]
  Phi   =   1.766852   -1.374741  [ DEG:   101.2331    -78.7669 ]
 
# 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: T0335TS757_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS757_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   29   2.53   13.79  60.395
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS757_1-D1
PFRMAT TS
TARGET T0335
MODEL  1
PARENT N/A
ATOM     31  N   ALA     5      -1.514 -12.625  -1.879  1.00 10.00    
ATOM     32  CA  ALA     5      -0.866 -11.494  -1.236  1.00 10.00    
ATOM     33  C   ALA     5      -1.234 -10.210  -1.982  1.00 10.00    
ATOM     34  O   ALA     5      -1.490  -9.180  -1.362  1.00 10.00    
ATOM     35  CB  ALA     5       0.646 -11.729  -1.192  1.00 10.00    
ATOM     36  N   LYS     6      -1.248 -10.314  -3.303  1.00 10.00    
ATOM     37  CA  LYS     6      -1.580  -9.173  -4.140  1.00 10.00    
ATOM     38  C   LYS     6      -3.037  -8.775  -3.897  1.00 10.00    
ATOM     39  O   LYS     6      -3.393  -7.604  -4.023  1.00 10.00    
ATOM     40  CB  LYS     6      -1.262  -9.474  -5.606  1.00 10.00    
ATOM     45  N   ILE     7      -3.840  -9.771  -3.552  1.00 10.00    
ATOM     46  CA  ILE     7      -5.250  -9.539  -3.290  1.00 10.00    
ATOM     47  C   ILE     7      -5.403  -8.822  -1.947  1.00 10.00    
ATOM     48  O   ILE     7      -6.298  -7.993  -1.780  1.00 10.00    
ATOM     49  CB  ILE     7      -6.256 -11.486  -1.925  1.00 10.00    
ATOM     53  N   ALA     8      -4.518  -9.167  -1.023  1.00 10.00    
ATOM     54  CA  ALA     8      -4.544  -8.567   0.299  1.00 10.00    
ATOM     55  C   ALA     8      -4.145  -7.093   0.194  1.00 10.00    
ATOM     56  O   ALA     8      -4.681  -6.249   0.910  1.00 10.00    
ATOM     57  CB  ALA     8      -3.625  -9.353   1.236  1.00 10.00    
ATOM     58  N   ARG     9      -3.207  -6.830  -0.705  1.00 10.00    
ATOM     59  CA  ARG     9      -2.731  -5.474  -0.913  1.00 10.00    
ATOM     60  C   ARG     9      -3.840  -4.608  -1.514  1.00 10.00    
ATOM     61  O   ARG     9      -3.812  -3.385  -1.392  1.00 10.00    
ATOM     62  CB  ARG     9      -1.516  -5.454  -1.844  1.00 10.00    
ATOM     69  N   ILE    10      -4.789  -5.277  -2.151  1.00 10.00    
ATOM     70  CA  ILE    10      -5.905  -4.584  -2.772  1.00 10.00    
ATOM     71  C   ILE    10      -6.741  -3.900  -1.689  1.00 10.00    
ATOM     72  O   ILE    10      -7.143  -2.747  -1.845  1.00 10.00    
ATOM     73  CB  ILE    10      -8.079  -4.867  -4.137  1.00 10.00    
ATOM     77  N   ASN    11      -6.980  -4.638  -0.615  1.00 10.00    
ATOM     78  CA  ASN    11      -7.760  -4.117   0.494  1.00 10.00    
ATOM     79  C   ASN    11      -6.874  -3.219   1.358  1.00 10.00    
ATOM     80  O   ASN    11      -7.362  -2.283   1.991  1.00 10.00    
ATOM     81  CB  ASN    11      -8.289  -5.250   1.375  1.00 10.00    
ATOM     85  N   GLU    12      -5.588  -3.536   1.359  1.00 10.00    
ATOM     86  CA  GLU    12      -4.628  -2.769   2.136  1.00 10.00    
ATOM     87  C   GLU    12      -4.297  -1.456   1.424  1.00 10.00    
ATOM     88  O   GLU    12      -3.711  -0.553   2.020  1.00 10.00    
ATOM     89  CB  GLU    12      -3.362  -3.584   2.403  1.00 10.00    
ATOM     94  N   LEU    13      -4.685  -1.392   0.159  1.00 10.00    
ATOM     95  CA  LEU    13      -4.437  -0.204  -0.641  1.00 10.00    
ATOM     96  C   LEU    13      -5.132   0.995   0.005  1.00 10.00    
ATOM     97  O   LEU    13      -4.591   2.100   0.016  1.00 10.00    
ATOM     98  CB  LEU    13      -4.846  -0.442  -2.095  1.00 10.00    
ATOM    102  N   ALA    14      -6.323   0.738   0.527  1.00 10.00    
ATOM    103  CA  ALA    14      -7.099   1.783   1.173  1.00 10.00    
ATOM    104  C   ALA    14      -6.319   2.323   2.374  1.00 10.00    
ATOM    105  O   ALA    14      -6.322   3.525   2.629  1.00 10.00    
ATOM    106  CB  ALA    14      -8.469   1.229   1.569  1.00 10.00    
ATOM    107  N   ALA    15      -5.669   1.408   3.077  1.00 10.00    
ATOM    108  CA  ALA    15      -4.887   1.776   4.244  1.00 10.00    
ATOM    109  C   ALA    15      -3.622   2.511   3.794  1.00 10.00    
ATOM    110  O   ALA    15      -3.258   3.537   4.368  1.00 10.00    
ATOM    111  CB  ALA    15      -4.572   0.525   5.066  1.00 10.00    
ATOM    112  N   LYS    16      -2.989   1.957   2.771  1.00 10.00    
ATOM    113  CA  LYS    16      -1.772   2.547   2.236  1.00 10.00    
ATOM    114  C   LYS    16      -2.083   3.946   1.698  1.00 10.00    
ATOM    115  O   LYS    16      -1.206   4.808   1.657  1.00 10.00    
ATOM    116  CB  LYS    16      -1.137   1.617   1.201  1.00 10.00    
ATOM    121  N   ALA    17      -3.333   4.128   1.299  1.00 10.00    
ATOM    122  CA  ALA    17      -3.769   5.406   0.765  1.00 10.00    
ATOM    123  C   ALA    17      -3.619   6.481   1.842  1.00 10.00    
ATOM    124  O   ALA    17      -3.374   7.646   1.531  1.00 10.00    
ATOM    125  CB  ALA    17      -5.208   5.284   0.260  1.00 10.00    
ATOM    126  N   LYS    18      -3.773   6.053   3.086  1.00 10.00    
ATOM    127  CA  LYS    18      -3.658   6.965   4.212  1.00 10.00    
ATOM    128  C   LYS    18      -4.660   6.561   5.295  1.00 10.00    
ATOM    129  O   LYS    18      -4.410   6.759   6.483  1.00 10.00    
ATOM    130  CB  LYS    18      -3.810   8.414   3.745  1.00 10.00    
ATOM    135  N   ALA    19      -5.774   6.001   4.846  1.00 10.00    
ATOM    136  CA  ALA    19      -6.815   5.567   5.763  1.00 10.00    
ATOM    137  C   ALA    19      -6.255   4.485   6.688  1.00 10.00    
ATOM    138  O   ALA    19      -5.819   3.433   6.225  1.00 10.00    
ATOM    139  CB  ALA    19      -8.028   5.083   4.966  1.00 10.00    
ATOM    140  N   GLY    20      -6.287   4.782   7.979  1.00 10.00    
ATOM    141  CA  GLY    20      -5.789   3.847   8.973  1.00 10.00    
ATOM    142  C   GLY    20      -4.276   3.990   9.150  1.00 10.00    
ATOM    143  O   GLY    20      -3.544   4.140   8.174  1.00 10.00    
ATOM    144  N   VAL    21      -3.851   3.938  10.405  1.00 10.00    
ATOM    145  CA  VAL    21      -2.439   4.060  10.722  1.00 10.00    
ATOM    146  C   VAL    21      -1.845   2.665  10.931  1.00 10.00    
ATOM    147  O   VAL    21      -1.891   2.125  12.035  1.00 10.00    
ATOM    148  CB  VAL    21      -2.681   4.234  13.287  1.00 10.00    
ATOM    151  N   ILE    22      -1.300   2.121   9.853  1.00 10.00    
ATOM    152  CA  ILE    22      -0.698   0.800   9.904  1.00 10.00    
ATOM    153  C   ILE    22       0.611   0.810   9.113  1.00 10.00    
ATOM    154  O   ILE    22       0.875   1.741   8.354  1.00 10.00    
ATOM    155  CB  ILE    22      -2.989  -0.297  10.374  1.00 10.00    
ATOM    159  N   THR    23       1.397  -0.237   9.319  1.00 10.00    
ATOM    160  CA  THR    23       2.674  -0.360   8.635  1.00 10.00    
ATOM    161  C   THR    23       2.456  -0.652   7.148  1.00 10.00    
ATOM    162  O   THR    23       3.302  -0.326   6.317  1.00 10.00    
ATOM    163  CB  THR    23       3.069  -2.920   8.920  1.00 10.00    
ATOM    166  N   GLU    24       1.317  -1.264   6.859  1.00 10.00    
ATOM    167  CA  GLU    24       0.977  -1.603   5.487  1.00 10.00    
ATOM    168  C   GLU    24       0.626  -0.340   4.699  1.00 10.00    
ATOM    169  O   GLU    24       0.762  -0.309   3.477  1.00 10.00    
ATOM    170  CB  GLU    24      -0.169  -2.616   5.442  1.00 10.00    
ATOM    175  N   GLU    25       0.182   0.671   5.431  1.00 10.00    
ATOM    176  CA  GLU    25      -0.189   1.934   4.816  1.00 10.00    
ATOM    177  C   GLU    25       1.059   2.684   4.347  1.00 10.00    
ATOM    178  O   GLU    25       1.128   3.126   3.201  1.00 10.00    
ATOM    179  CB  GLU    25      -1.017   2.790   5.777  1.00 10.00    
ATOM    184  N   GLU    26       2.015   2.804   5.258  1.00 10.00    
ATOM    185  CA  GLU    26       3.257   3.492   4.952  1.00 10.00    
ATOM    186  C   GLU    26       4.059   2.704   3.914  1.00 10.00    
ATOM    187  O   GLU    26       4.684   3.290   3.031  1.00 10.00    
ATOM    188  CB  GLU    26       4.080   3.727   6.220  1.00 10.00    
ATOM    193  N   LYS    27       4.016   1.387   4.056  1.00 10.00    
ATOM    194  CA  LYS    27       4.732   0.513   3.142  1.00 10.00    
ATOM    195  C   LYS    27       4.032   0.521   1.782  1.00 10.00    
ATOM    196  O   LYS    27       4.680   0.386   0.745  1.00 10.00    
ATOM    197  CB  LYS    27       4.884  -0.885   3.746  1.00 10.00    
ATOM    202  N   ALA    28       2.717   0.681   1.830  1.00 10.00    
ATOM    203  CA  ALA    28       1.922   0.708   0.614  1.00 10.00    
ATOM    204  C   ALA    28       2.127   2.049  -0.094  1.00 10.00    
ATOM    205  O   ALA    28       2.269   2.095  -1.315  1.00 10.00    
ATOM    206  CB  ALA    28       0.454   0.449   0.957  1.00 10.00    
ATOM    207  N   GLU    29       2.135   3.107   0.703  1.00 10.00    
ATOM    208  CA  GLU    29       2.320   4.446   0.167  1.00 10.00    
ATOM    209  C   GLU    29       3.735   4.603  -0.394  1.00 10.00    
ATOM    210  O   GLU    29       3.926   5.215  -1.443  1.00 10.00    
ATOM    211  CB  GLU    29       2.031   5.506   1.232  1.00 10.00    
ATOM    216  N   GLN    30       4.690   4.037   0.330  1.00 10.00    
ATOM    217  CA  GLN    30       6.082   4.106  -0.082  1.00 10.00    
ATOM    218  C   GLN    30       6.325   3.192  -1.285  1.00 10.00    
ATOM    219  O   GLN    30       7.097   3.530  -2.180  1.00 10.00    
ATOM    220  CB  GLN    30       7.015   3.750   1.076  1.00 10.00    
ATOM    225  N   GLN    31       5.650   2.051  -1.267  1.00 10.00    
ATOM    226  CA  GLN    31       5.783   1.086  -2.344  1.00 10.00    
ATOM    227  C   GLN    31       5.136   1.624  -3.622  1.00 10.00    
ATOM    228  O   GLN    31       5.608   1.351  -4.724  1.00 10.00    
ATOM    229  CB  GLN    31       5.180  -0.263  -1.949  1.00 10.00    
ATOM    234  N   LYS    32       4.063   2.378  -3.431  1.00 10.00    
ATOM    235  CA  LYS    32       3.346   2.958  -4.554  1.00 10.00    
ATOM    236  C   LYS    32       4.214   4.032  -5.210  1.00 10.00    
ATOM    237  O   LYS    32       4.267   4.131  -6.435  1.00 10.00    
ATOM    238  CB  LYS    32       1.973   3.465  -4.109  1.00 10.00    
ATOM    243  N   LEU    33       4.875   4.811  -4.366  1.00 10.00    
ATOM    244  CA  LEU    33       5.740   5.875  -4.847  1.00 10.00    
ATOM    245  C   LEU    33       7.016   5.264  -5.430  1.00 10.00    
ATOM    246  O   LEU    33       7.545   5.757  -6.425  1.00 10.00    
ATOM    247  CB  LEU    33       5.998   6.897  -3.740  1.00 10.00    
ATOM    251  N   ARG    34       7.473   4.201  -4.786  1.00 10.00    
ATOM    252  CA  ARG    34       8.677   3.518  -5.227  1.00 10.00    
ATOM    253  C   ARG    34       8.394   2.706  -6.493  1.00 10.00    
ATOM    254  O   ARG    34       9.267   2.554  -7.346  1.00 10.00    
ATOM    255  CB  ARG    34       9.210   2.582  -4.140  1.00 10.00    
ATOM    262  N   GLN    35       7.168   2.208  -6.576  1.00 10.00    
ATOM    263  CA  GLN    35       6.758   1.415  -7.722  1.00 10.00    
ATOM    264  C   GLN    35       6.605   2.307  -8.956  1.00 10.00    
ATOM    265  O   GLN    35       6.791   1.851 -10.083  1.00 10.00    
ATOM    266  CB  GLN    35       5.463   0.656  -7.430  1.00 10.00    
ATOM    271  N   GLU    36       6.268   3.563  -8.701  1.00 10.00    
ATOM    272  CA  GLU    36       6.089   4.524  -9.777  1.00 10.00    
ATOM    273  C   GLU    36       7.434   4.847 -10.430  1.00 10.00    
ATOM    274  O   GLU    36       7.493   5.142 -11.622  1.00 10.00    
ATOM    275  CB  GLU    36       5.405   5.794  -9.267  1.00 10.00    
ATOM    280  N   TYR    37       8.480   4.782  -9.620  1.00 10.00    
ATOM    281  CA  TYR    37       9.820   5.063 -10.104  1.00 10.00    
ATOM    282  C   TYR    37      10.394   3.779 -10.706  1.00 10.00    
ATOM    283  O   TYR    37      11.053   3.816 -11.743  1.00 10.00    
ATOM    284  CB  TYR    37      10.633   5.479  -8.877  1.00 10.00    
ATOM    292  N   LEU    38      10.122   2.673 -10.028  1.00 10.00    
ATOM    293  CA  LEU    38      10.603   1.379 -10.483  1.00 10.00    
ATOM    294  C   LEU    38       9.982   1.059 -11.845  1.00 10.00    
ATOM    295  O   LEU    38      10.628   0.454 -12.699  1.00 10.00    
ATOM    296  CB  LEU    38      10.343   0.308  -9.423  1.00 10.00    
ATOM    300  N   LYS    39       8.735   1.480 -12.005  1.00 10.00    
ATOM    301  CA  LYS    39       8.021   1.245 -13.247  1.00 10.00    
ATOM    302  C   LYS    39       8.736   1.972 -14.388  1.00 10.00    
ATOM    303  O   LYS    39       8.700   1.524 -15.532  1.00 10.00    
ATOM    304  CB  LYS    39       6.548   1.634 -13.099  1.00 10.00    
ATOM    309  N   GLY    40       9.371   3.080 -14.035  1.00 10.00    
ATOM    310  CA  GLY    40      10.095   3.872 -15.014  1.00 10.00    
ATOM    311  C   GLY    40      11.268   3.084 -15.598  1.00 10.00    
ATOM    312  O   GLY    40      11.444   3.035 -16.815  1.00 10.00    
TER
END
