
#######################################################
#                                                     #
#                        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 T0335TS437_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS437_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    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      A       5          1.854
LGA    R       9      K       6          1.556
LGA    I      10      I       7          1.386
LGA    N      11      A       8          1.083
LGA    E      12      R       9          1.167
LGA    L      13      I      10          1.270
LGA    A      14      N      11          1.313
LGA    A      15      E      12          0.942
LGA    K      16      L      13          0.831
LGA    A      17      A      14          0.884
LGA    K      18      A      15          1.043
LGA    A      19      K      16          0.871
LGA    G      20      A      17          0.747
LGA    V      21      K      18           -
LGA    I      22      A      19           -
LGA    -       -      G      20           -
LGA    T      23      V      21          3.431
LGA    E      24      I      22          4.357
LGA    E      25      T      23           #
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      E      24          2.644
LGA    L      33      E      25          0.677
LGA    R      34      E      26          2.959
LGA    Q      35      K      27          2.602
LGA    E      36      A      28          0.519
LGA    Y      37      E      29          2.182
LGA    L      38      Q      30          2.639
LGA    K      39      Q      31          0.529
LGA    G      40      K      32          2.746
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    1.96    12.50     52.577     1.166

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.369433 * X  +  -0.636090 * Y  +  -0.677428 * Z  + -86.512360
  Y_new =  -0.277564 * X  +  -0.771254 * Y  +   0.572822 * Z  +   3.888440
  Z_new =  -0.886836 * X  +  -0.023589 * Y  +  -0.461483 * Z  + 124.471870 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.090521    0.051072  [ DEG:  -177.0738      2.9262 ]
  Theta =   1.090451    2.051141  [ DEG:    62.4783    117.5217 ]
  Phi   =  -0.644349    2.497243  [ DEG:   -36.9185    143.0815 ]
 
# 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: T0335TS437_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS437_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   1.96   12.50  52.577
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS437_1-D1
PFRMAT TS
TARGET T0335
MODEL     1 REFINED
PARENT N/A
ATOM     31  N   ALA     5       2.485 -14.199 -10.155  1.00   .00
ATOM     32  CA  ALA     5       3.465 -13.581  -9.123  1.00   .00
ATOM     33  C   ALA     5       3.091 -11.974  -9.122  1.00   .00
ATOM     34  O   ALA     5       2.636 -11.437  -8.108  1.00   .00
ATOM     35  CB  ALA     5       4.953 -13.949  -9.479  1.00   .00
ATOM     36  N   LYS     6       3.234 -11.276 -10.348  1.00   .00
ATOM     37  CA  LYS     6       2.791  -9.801 -10.516  1.00   .00
ATOM     38  C   LYS     6       1.170  -9.635 -10.280  1.00   .00
ATOM     39  O   LYS     6       0.760  -8.730  -9.563  1.00   .00
ATOM     40  CB  LYS     6       3.266  -9.330 -11.929  1.00   .00
ATOM     45  N   ILE     7       0.275 -10.562 -10.866  1.00   .00
ATOM     46  CA  ILE     7      -1.282 -10.504 -10.581  1.00   .00
ATOM     47  C   ILE     7      -1.619 -10.698  -8.973  1.00   .00
ATOM     48  O   ILE     7      -2.382  -9.913  -8.382  1.00   .00
ATOM     49  CB  ILE     7      -1.980 -11.587 -11.500  1.00   .00
ATOM     53  N   ALA     8      -0.959 -11.731  -8.288  1.00   .00
ATOM     54  CA  ALA     8      -1.132 -11.947  -6.743  1.00   .00
ATOM     55  C   ALA     8      -0.562 -10.667  -5.870  1.00   .00
ATOM     56  O   ALA     8      -1.269 -10.165  -4.985  1.00   .00
ATOM     57  CB  ALA     8      -0.433 -13.303  -6.419  1.00   .00
ATOM     58  N   ARG     9       0.692 -10.142  -6.207  1.00   .00
ATOM     59  CA  ARG     9       1.261  -8.874  -5.496  1.00   .00
ATOM     60  C   ARG     9       0.313  -7.551  -5.766  1.00   .00
ATOM     61  O   ARG     9      -0.010  -6.828  -4.802  1.00   .00
ATOM     62  CB  ARG     9       2.729  -8.714  -5.994  1.00   .00
ATOM     69  N   ILE    10      -0.153  -7.312  -7.068  1.00   .00
ATOM     70  CA  ILE    10      -1.138  -6.142  -7.382  1.00   .00
ATOM     71  C   ILE    10      -2.560  -6.300  -6.531  1.00   .00
ATOM     72  O   ILE    10      -3.012  -5.333  -5.903  1.00   .00
ATOM     73  CB  ILE    10      -1.330  -6.104  -8.942  1.00   .00
ATOM     77  N   ASN    11      -3.179  -7.567  -6.511  1.00   .00
ATOM     78  CA  ASN    11      -4.456  -7.821  -5.667  1.00   .00
ATOM     79  C   ASN    11      -4.160  -7.624  -4.040  1.00   .00
ATOM     80  O   ASN    11      -4.914  -6.925  -3.355  1.00   .00
ATOM     81  CB  ASN    11      -4.944  -9.261  -6.018  1.00   .00
ATOM     85  N   GLU    12      -3.006  -8.212  -3.491  1.00   .00
ATOM     86  CA  GLU    12      -2.603  -7.989  -1.988  1.00   .00
ATOM     87  C   GLU    12      -2.331  -6.390  -1.654  1.00   .00
ATOM     88  O   GLU    12      -2.853  -5.864  -0.663  1.00   .00
ATOM     89  CB  GLU    12      -1.357  -8.885  -1.742  1.00   .00
ATOM     94  N   LEU    13      -1.551  -5.650  -2.555  1.00   .00
ATOM     95  CA  LEU    13      -1.328  -4.123  -2.379  1.00   .00
ATOM     96  C   LEU    13      -2.732  -3.260  -2.490  1.00   .00
ATOM     97  O   LEU    13      -2.976  -2.385  -1.652  1.00   .00
ATOM     98  CB  LEU    13      -0.282  -3.721  -3.452  1.00   .00
ATOM    102  N   ALA    14      -3.637  -3.568  -3.516  1.00   .00
ATOM    103  CA  ALA    14      -5.008  -2.869  -3.623  1.00   .00
ATOM    104  C   ALA    14      -5.984  -3.228  -2.340  1.00   .00
ATOM    105  O   ALA    14      -6.549  -2.308  -1.722  1.00   .00
ATOM    106  CB  ALA    14      -5.628  -3.272  -4.989  1.00   .00
ATOM    107  N   ALA    15      -6.112  -4.570  -1.935  1.00   .00
ATOM    108  CA  ALA    15      -6.947  -4.968  -0.683  1.00   .00
ATOM    109  C   ALA    15      -6.385  -4.269   0.705  1.00   .00
ATOM    110  O   ALA    15      -7.176  -3.684   1.460  1.00   .00
ATOM    111  CB  ALA    15      -6.963  -6.522  -0.626  1.00   .00
ATOM    112  N   LYS    16      -5.006  -4.312   0.963  1.00   .00
ATOM    113  CA  LYS    16      -4.381  -3.597   2.219  1.00   .00
ATOM    114  C   LYS    16      -4.591  -1.952   2.214  1.00   .00
ATOM    115  O   LYS    16      -4.797  -1.324   3.268  1.00   .00
ATOM    116  CB  LYS    16      -2.867  -4.012   2.241  1.00   .00
ATOM    121  N   ALA    17      -4.553  -1.308   0.987  1.00   .00
ATOM    122  CA  ALA    17      -4.819   0.206   0.837  1.00   .00
ATOM    123  C   ALA    17      -6.432   0.525   1.051  1.00   .00
ATOM    124  O   ALA    17      -6.794   1.403   1.843  1.00   .00
ATOM    125  CB  ALA    17      -4.297   0.603  -0.579  1.00   .00
ATOM    126  N   LYS    18      -7.364  -0.258   0.343  1.00   .00
ATOM    127  CA  LYS    18      -8.911  -0.094   0.523  1.00   .00
ATOM    128  C   LYS    18      -9.435  -0.440   2.050  1.00   .00
ATOM    129  O   LYS    18     -10.244   0.301   2.596  1.00   .00
ATOM    130  CB  LYS    18      -9.548  -1.010  -0.565  1.00   .00
ATOM    135  N   ALA    19      -8.918  -1.558   2.686  1.00   .00
ATOM    136  CA  ALA    19      -9.321  -1.928   4.146  1.00   .00
ATOM    137  C   ALA    19      -8.636  -1.002   5.322  1.00   .00
ATOM    138  O   ALA    19      -9.142  -0.973   6.448  1.00   .00
ATOM    139  CB  ALA    19      -8.905  -3.428   4.319  1.00   .00
ATOM    140  N   GLY    20      -7.494  -0.280   5.014  1.00   .00
ATOM    141  CA  GLY    20      -6.755   0.589   6.072  1.00   .00
ATOM    142  C   GLY    20      -5.751  -0.287   6.907  1.00   .00
ATOM    143  O   GLY    20      -6.002  -0.572   8.071  1.00   .00
ATOM    144  N   VAL    21      -4.594  -0.732   6.269  1.00   .00
ATOM    145  CA  VAL    21      -3.525  -1.661   6.978  1.00   .00
ATOM    146  C   VAL    21      -3.159  -1.432   8.596  1.00   .00
ATOM    147  O   VAL    21      -2.903  -2.398   9.338  1.00   .00
ATOM    148  CB  VAL    21      -2.261  -1.572   6.063  1.00   .00
ATOM    151  N   ILE    22      -3.176  -0.154   9.057  1.00   .00
ATOM    152  CA  ILE    22      -2.946   0.217  10.537  1.00   .00
ATOM    153  C   ILE    22      -4.008   1.418  10.856  1.00   .00
ATOM    154  O   ILE    22      -3.943   2.489  10.235  1.00   .00
ATOM    155  CB  ILE    22      -1.442   0.618  10.746  1.00   .00
ATOM    159  N   THR    23      -4.978   1.209  11.801  1.00   .00
ATOM    160  CA  THR    23      -6.038   2.294  12.136  1.00   .00
ATOM    161  C   THR    23      -5.428   3.634  12.832  1.00   .00
ATOM    162  O   THR    23      -4.713   3.563  13.855  1.00   .00
ATOM    163  CB  THR    23      -7.121   1.615  13.022  1.00   .00
ATOM    166  N   GLU    24      -5.721   4.841  12.227  1.00   .00
ATOM    167  CA  GLU    24      -5.181   6.150  12.790  1.00   .00
ATOM    168  C   GLU    24      -5.871   6.616  14.212  1.00   .00
ATOM    169  O   GLU    24      -7.097   6.733  14.336  1.00   .00
ATOM    170  CB  GLU    24      -5.318   7.230  11.680  1.00   .00
ATOM    175  N   GLU    25      -5.024   6.870  15.223  1.00   .00
ATOM    176  CA  GLU    25      -5.505   7.340  16.618  1.00   .00
ATOM    177  C   GLU    25      -4.759   8.743  17.025  1.00   .00
ATOM    178  O   GLU    25      -3.829   9.217  16.347  1.00   .00
ATOM    179  CB  GLU    25      -5.213   6.156  17.628  1.00   .00
ATOM    184  N   GLU    26      -5.172   9.400  18.170  1.00   .00
ATOM    185  CA  GLU    26      -4.478  10.737  18.621  1.00   .00
ATOM    186  C   GLU    26      -2.979  10.479  19.320  1.00   .00
ATOM    187  O   GLU    26      -2.718  10.835  20.484  1.00   .00
ATOM    188  CB  GLU    26      -5.499  11.430  19.585  1.00   .00
ATOM    193  N   LYS    27      -2.060   9.833  18.526  1.00   .00
ATOM    194  CA  LYS    27      -0.647   9.485  18.993  1.00   .00
ATOM    195  C   LYS    27       0.425   9.549  17.787  1.00   .00
ATOM    196  O   LYS    27       0.211   8.992  16.700  1.00   .00
ATOM    197  CB  LYS    27      -0.713   8.020  19.592  1.00   .00
ATOM    202  N   ALA    28       1.611  10.227  17.991  1.00   .00
ATOM    203  CA  ALA    28       2.717  10.313  16.863  1.00   .00
ATOM    204  C   ALA    28       3.573   8.872  16.585  1.00   .00
ATOM    205  O   ALA    28       4.796   8.809  16.504  1.00   .00
ATOM    206  CB  ALA    28       3.624  11.512  17.270  1.00   .00
ATOM    207  N   GLU    29       2.774   7.813  16.452  1.00   .00
ATOM    208  CA  GLU    29       3.231   6.365  16.169  1.00   .00
ATOM    209  C   GLU    29       1.992   5.718  15.308  1.00   .00
ATOM    210  O   GLU    29       2.154   5.395  14.132  1.00   .00
ATOM    211  CB  GLU    29       3.587   5.657  17.527  1.00   .00
ATOM    216  N   GLN    30       0.721   5.642  15.922  1.00   .00
ATOM    217  CA  GLN    30      -0.563   5.177  15.125  1.00   .00
ATOM    218  C   GLN    30      -1.132   6.419  14.137  1.00   .00
ATOM    219  O   GLN    30      -2.273   6.875  14.197  1.00   .00
ATOM    220  CB  GLN    30      -1.597   4.720  16.185  1.00   .00
ATOM    225  N   GLN    31      -0.201   6.866  13.275  1.00   .00
ATOM    226  CA  GLN    31      -0.370   8.011  12.239  1.00   .00
ATOM    227  C   GLN    31       0.891   7.793  11.197  1.00   .00
ATOM    228  O   GLN    31       0.694   7.514  10.006  1.00   .00
ATOM    229  CB  GLN    31      -0.386   9.419  12.976  1.00   .00
ATOM    234  N   LYS    32       2.207   7.873  11.747  1.00   .00
ATOM    235  CA  LYS    32       3.463   7.558  10.908  1.00   .00
ATOM    236  C   LYS    32       3.453   6.004  10.349  1.00   .00
ATOM    237  O   LYS    32       3.717   5.777   9.171  1.00   .00
ATOM    238  CB  LYS    32       4.692   7.863  11.840  1.00   .00
ATOM    243  N   LEU    33       3.082   4.970  11.238  1.00   .00
ATOM    244  CA  LEU    33       2.945   3.485  10.779  1.00   .00
ATOM    245  C   LEU    33       1.821   3.287   9.598  1.00   .00
ATOM    246  O   LEU    33       2.081   2.598   8.603  1.00   .00
ATOM    247  CB  LEU    33       2.644   2.653  12.078  1.00   .00
ATOM    251  N   ARG    34       0.617   3.984   9.726  1.00   .00
ATOM    252  CA  ARG    34      -0.463   3.974   8.611  1.00   .00
ATOM    253  C   ARG    34       0.102   4.703   7.229  1.00   .00
ATOM    254  O   ARG    34       0.002   4.138   6.125  1.00   .00
ATOM    255  CB  ARG    34      -1.719   4.682   9.204  1.00   .00
ATOM    262  N   GLN    35       0.742   5.943   7.360  1.00   .00
ATOM    263  CA  GLN    35       1.400   6.666   6.152  1.00   .00
ATOM    264  C   GLN    35       2.618   5.750   5.488  1.00   .00
ATOM    265  O   GLN    35       2.654   5.558   4.262  1.00   .00
ATOM    266  CB  GLN    35       1.882   8.066   6.693  1.00   .00
ATOM    271  N   GLU    36       3.564   5.168   6.356  1.00   .00
ATOM    272  CA  GLU    36       4.686   4.224   5.817  1.00   .00
ATOM    273  C   GLU    36       4.068   2.863   5.108  1.00   .00
ATOM    274  O   GLU    36       4.473   2.501   3.996  1.00   .00
ATOM    275  CB  GLU    36       5.609   3.927   7.035  1.00   .00
ATOM    280  N   TYR    37       3.040   2.181   5.787  1.00   .00
ATOM    281  CA  TYR    37       2.329   0.940   5.179  1.00   .00
ATOM    282  C   TYR    37       1.569   1.298   3.757  1.00   .00
ATOM    283  O   TYR    37       1.728   0.568   2.761  1.00   .00
ATOM    284  CB  TYR    37       1.389   0.379   6.273  1.00   .00
ATOM    292  N   LEU    38       0.812   2.478   3.690  1.00   .00
ATOM    293  CA  LEU    38       0.152   2.969   2.377  1.00   .00
ATOM    294  C   LEU    38       1.284   3.311   1.205  1.00   .00
ATOM    295  O   LEU    38       1.144   2.882   0.052  1.00   .00
ATOM    296  CB  LEU    38      -0.697   4.197   2.762  1.00   .00
ATOM    300  N   LYS    39       2.430   4.038   1.595  1.00   .00
ATOM    301  CA  LYS    39       3.605   4.326   0.623  1.00   .00
ATOM    302  C   LYS    39       4.336   2.941   0.110  1.00   .00
ATOM    303  O   LYS    39       4.552   2.761  -1.100  1.00   .00
ATOM    304  CB  LYS    39       4.566   5.288   1.366  1.00   .00
ATOM    309  N   GLY    40       4.654   1.962   1.073  1.00   .00
ATOM    310  CA  GLY    40       5.255   0.554   0.648  1.00   .00
ATOM    311  C   GLY    40       4.292  -0.258  -0.352  1.00   .00
ATOM    312  O   GLY    40       4.753  -0.747  -1.380  1.00   .00
TER   
END
