
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0331TS168_1
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS168_1.T0331.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    E       2      -       -           -
LGA    L       3      -       -           -
LGA    K       4      -       -           -
LGA    D       5      -       -           -
LGA    I       6      -       -           -
LGA    M       7      -       -           -
LGA    H       8      -       -           -
LGA    I       9      -       -           -
LGA    L      10      -       -           -
LGA    E      11      -       -           -
LGA    D      12      M       1          4.178
LGA    M      13      E       2          1.657
LGA    K      14      L       3          3.609
LGA    V      15      K       4          4.173
LGA    G      16      D       5          2.385
LGA    -       -      I       6           -
LGA    -       -      M       7           -
LGA    V      17      H       8          3.690
LGA    F      18      I       9           -
LGA    A      19      L      10          3.154
LGA    T      20      E      11          4.677
LGA    L      21      D      12           -
LGA    -       -      M      13           -
LGA    -       -      K      14           -
LGA    D      22      V      15          2.733
LGA    E      23      G      16          4.498
LGA    Y      24      -       -           -
LGA    G      25      -       -           -
LGA    N      26      V      17          2.674
LGA    P      27      -       -           -
LGA    H      28      -       -           -
LGA    A      29      -       -           -
LGA    R      30      -       -           -
LGA    H      31      -       -           -
LGA    A      32      -       -           -
LGA    H      33      -       -           -
LGA    I      34      -       -           -
LGA    T      35      -       -           -
LGA    A      36      -       -           -
LGA    A      37      -       -           -
LGA    N      38      -       -           -
LGA    E      39      -       -           -
LGA    E      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    F      43      -       -           -
LGA    F      44      -       -           -
LGA    M      45      -       -           -
LGA    T      46      F      18          2.068
LGA    S      47      A      19          5.211
LGA    P      48      -       -           -
LGA    E      49      -       -           -
LGA    T      50      -       -           -
LGA    H      51      -       -           -
LGA    F      52      T      20          0.486
LGA    Y      53      L      21          3.191
LGA    D      54      D      22           -
LGA    Q      55      E      23           -
LGA    L      56      Y      24           -
LGA    M      57      G      25           -
LGA    G      58      N      26           -
LGA    D      59      P      27           -
LGA    Q      60      H      28           -
LGA    R      61      A      29           -
LGA    V      62      R      30           -
LGA    A      63      H      31           -
LGA    M      64      A      32           -
LGA    -       -      H      33           -
LGA    -       -      I      34           -
LGA    -       -      T      35           -
LGA    -       -      A      36           -
LGA    -       -      A      37           -
LGA    -       -      N      38           -
LGA    -       -      E      39           -
LGA    T      65      E      40          3.122
LGA    A      66      G      41          4.285
LGA    I      67      -       -           -
LGA    S      68      -       -           -
LGA    E      69      -       -           -
LGA    E      70      -       -           -
LGA    G      71      -       -           -
LGA    Y      72      -       -           -
LGA    L      73      -       -           -
LGA    I      74      -       -           -
LGA    Q      75      I      42          2.114
LGA    V      76      F      43          3.241
LGA    V      77      -       -           -
LGA    R      78      -       -           -
LGA    V      79      F      44          4.856
LGA    E      80      M      45          4.460
LGA    G      81      -       -           -
LGA    T      82      T      46          4.006
LGA    A      83      S      47          4.109
LGA    R      84      -       -           -
LGA    P      85      -       -           -
LGA    V      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    D      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    K      92      -       -           -
LGA    T      93      -       -           -
LGA    V      94      -       -           -
LGA    F      95      -       -           -
LGA    A      96      -       -           -
LGA    D      97      P      48          2.850
LGA    N      98      E      49          2.923
LGA    P      99      T      50          1.131
LGA    Y     100      H      51          1.782
LGA    Y     101      F      52          2.759
LGA    Q     102      Y      53          1.742
LGA    H     103      D      54          2.060
LGA    I     104      Q      55          3.446
LGA    Y     105      L      56          1.740
LGA    K     106      M      57          4.338
LGA    D     107      G      58          1.643
LGA    E     108      D      59           #
LGA    S     109      -       -           -
LGA    S     110      -       -           -
LGA    D     111      -       -           -
LGA    T     112      -       -           -
LGA    M     113      Q      60           #
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      M      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      I      67           -
LGA    -       -      S      68           -
LGA    -       -      E      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      V      77           -
LGA    -       -      R      78           -
LGA    -       -      V      79           -
LGA    -       -      E      80           -
LGA    -       -      G      81           -
LGA    -       -      T      82           -
LGA    -       -      A      83           -
LGA    -       -      R      84           -
LGA    Q     114      P      85          2.787
LGA    -       -      V      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      D      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      K      92           -
LGA    -       -      T      93           -
LGA    -       -      V      94           -
LGA    -       -      F      95           -
LGA    -       -      A      96           -
LGA    -       -      D      97           -
LGA    -       -      N      98           -
LGA    -       -      P      99           -
LGA    -       -      Y     100           -
LGA    -       -      Y     101           -
LGA    -       -      Q     102           -
LGA    -       -      H     103           -
LGA    -       -      I     104           -
LGA    -       -      Y     105           -
LGA    -       -      K     106           -
LGA    -       -      T     112           -
LGA    -       -      M     113           -
LGA    -       -      Q     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    V     115      Q     117          1.418
LGA    F     116      I     118           #
LGA    Q     117      Y     119           -
LGA    I     118      A     120           -
LGA    Y     119      G     121           -
LGA    A     120      H     122           -
LGA    G     121      G     123           -
LGA    H     122      F     124           -
LGA    G     123      Y     125           -
LGA    F     124      H     126           -
LGA    Y     125      S     127           -
LGA    H     126      L     128           -
LGA    S     127      T     129           -
LGA    L     128      Q     130           -
LGA    T     129      G     131           -
LGA    Q     130      H     132           -
LGA    G     131      K     133           -
LGA    H     132      Y     134           -
LGA    K     133      I     135           -
LGA    Y     134      F     136           -
LGA    I     135      S     137           -
LGA    F     136      I     138           -
LGA    S     137      G     139           -
LGA    I     138      E     145           -
LGA    G     139      V     146           -
LGA    Q     140      R     147           -
LGA    G     141      A     148           -
LGA    E     142      L     149           -
LGA    H     143      -       -           -
LGA    S     144      -       -           -
LGA    E     145      -       -           -
LGA    V     146      -       -           -
LGA    R     147      -       -           -
LGA    A     148      -       -           -
LGA    L     149      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  139    5.0     36    3.25     2.78     14.141     1.075

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.677776 * X  +  -0.725766 * Y  +   0.117830 * Z  +  17.202272
  Y_new =  -0.019278 * X  +   0.177741 * Y  +   0.983889 * Z  +  39.660767
  Z_new =  -0.735016 * X  +   0.664584 * Y  +  -0.134460 * Z  +  27.816174 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.770423   -1.371170  [ DEG:   101.4378    -78.5622 ]
  Theta =   0.825690    2.315903  [ DEG:    47.3085    132.6915 ]
  Phi   =  -3.113157    0.028435  [ DEG:  -178.3708      1.6292 ]
 
# 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: T0331TS168_1                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS168_1.T0331.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  139   5.0   36   3.25    2.78  14.141
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS168_1
PFRMAT TS
TARGET T0331
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -5.831  31.158  12.749  1.00 25.00           C
ATOM      2  CA  GLU     2      -5.930  32.725  16.219  1.00 25.00           C
ATOM      3  CA  LEU     3      -2.619  33.878  17.653  1.00 25.00           C
ATOM      4  CA  LYS     4      -0.753  36.438  15.601  1.00 25.00           C
ATOM      5  CA  ASP     5       0.681  38.336  12.599  1.00 25.00           C
ATOM      6  CA  ILE     6       3.836  39.173  14.604  1.00 25.00           C
ATOM      7  CA  MET     7       4.212  35.493  15.595  1.00 25.00           C
ATOM      8  CA  HIS     8       3.834  34.442  11.932  1.00 25.00           C
ATOM      9  CA  ILE     9       6.495  36.997  10.899  1.00 25.00           C
ATOM     10  CA  LEU    10       8.856  35.669  13.607  1.00 25.00           C
ATOM     11  CA  GLU    11       8.282  32.085  12.386  1.00 25.00           C
ATOM     12  CA  ASP    12       9.027  33.166   8.787  1.00 25.00           C
ATOM     13  CA  MET    13      11.960  35.544   9.471  1.00 25.00           C
ATOM     14  CA  LYS    14      15.070  33.844  10.999  1.00 25.00           C
ATOM     15  CA  VAL    15      14.152  33.701  14.727  1.00 25.00           C
ATOM     16  CA  GLY    16      11.472  32.510  17.196  1.00 25.00           C
ATOM     17  CA  VAL    17      11.237  35.758  19.121  1.00 25.00           C
ATOM     18  CA  PHE    18      11.594  35.792  22.913  1.00 25.00           C
ATOM     19  CA  ALA    19      14.513  33.368  22.402  1.00 25.00           C
ATOM     20  CA  THR    20      16.798  32.752  25.373  1.00 25.00           C
ATOM     21  CA  LEU    21      18.854  33.102  28.597  1.00 25.00           C
ATOM     22  CA  ASP    22      19.437  29.637  30.094  1.00 25.00           C
ATOM     23  CA  GLU    23      21.816  30.358  32.970  1.00 25.00           C
ATOM     24  CA  TYR    24      23.038  27.693  35.319  1.00 25.00           C
ATOM     25  CA  GLY    25      24.224  25.423  32.558  1.00 25.00           C
ATOM     26  CA  ASN    26      26.229  28.461  31.443  1.00 25.00           C
ATOM     27  CA  PRO    27      29.935  29.160  30.938  1.00 25.00           C
ATOM     28  CA  HIS    28      29.186  28.730  27.282  1.00 25.00           C
ATOM     29  CA  ALA    29      26.420  31.378  27.366  1.00 25.00           C
ATOM     30  CA  ARG    30      26.032  31.127  23.564  1.00 25.00           C
ATOM     31  CA  HIS    31      25.793  27.313  23.815  1.00 25.00           C
ATOM     32  CA  ALA    32      23.126  27.635  26.544  1.00 25.00           C
ATOM     33  CA  HIS    33      21.151  30.084  24.360  1.00 25.00           C
ATOM     34  CA  ILE    34      21.365  27.659  21.404  1.00 25.00           C
ATOM     35  CA  THR    35      20.125  24.799  23.629  1.00 25.00           C
ATOM     36  CA  ALA    36      17.203  26.964  24.826  1.00 25.00           C
ATOM     37  CA  ALA    37      16.318  27.819  21.200  1.00 25.00           C
ATOM     38  CA  ASN    38      17.619  24.979  18.955  1.00 25.00           C
ATOM     39  CA  GLU    39      20.653  24.970  16.618  1.00 25.00           C
ATOM     40  CA  GLU    40      19.939  28.748  16.478  1.00 25.00           C
ATOM     41  CA  GLY    41      18.086  31.942  17.264  1.00 25.00           C
ATOM     42  CA  ILE    42      21.154  34.180  17.954  1.00 25.00           C
ATOM     43  CA  PHE    43      19.647  34.670  21.446  1.00 25.00           C
ATOM     44  CA  PHE    44      22.166  35.019  24.199  1.00 25.00           C
ATOM     45  CA  MET    45      23.934  35.950  27.487  1.00 25.00           C
ATOM     46  CA  THR    46      24.180  34.285  30.897  1.00 25.00           C
ATOM     47  CA  SER    47      25.845  33.595  34.247  1.00 25.00           C
ATOM     48  CA  PRO    48      28.475  31.200  35.425  1.00 25.00           C
ATOM     49  CA  GLU    49      31.062  28.473  35.877  1.00 25.00           C
ATOM     50  CA  THR    50      33.698  30.556  34.037  1.00 25.00           C
ATOM     51  CA  HIS    51      32.557  33.789  32.349  1.00 25.00           C
ATOM     52  CA  PHE    52      29.986  36.460  31.389  1.00 25.00           C
ATOM     53  CA  TYR    53      32.715  38.494  29.634  1.00 25.00           C
ATOM     54  CA  ASP    54      33.848  35.371  27.727  1.00 25.00           C
ATOM     55  CA  GLN    55      30.234  34.677  26.667  1.00 25.00           C
ATOM     56  CA  LEU    56      29.866  38.295  25.465  1.00 25.00           C
ATOM     57  CA  MET    57      32.998  40.097  24.105  1.00 25.00           C
ATOM     58  CA  GLY    58      30.424  42.648  22.923  1.00 25.00           C
ATOM     59  CA  ASP    59      27.805  41.449  20.434  1.00 25.00           C
ATOM     60  CA  GLN    60      29.938  38.337  20.157  1.00 25.00           C
ATOM     61  CA  ARG    61      27.798  35.270  20.923  1.00 25.00           C
ATOM     62  CA  VAL    62      24.649  37.254  20.211  1.00 25.00           C
ATOM     63  CA  ALA    63      21.649  39.525  19.548  1.00 25.00           C
ATOM     64  CA  MET    64      19.965  42.659  21.024  1.00 25.00           C
ATOM     65  CA  THR    65      16.579  43.216  22.743  1.00 25.00           C
ATOM     66  CA  ALA    66      13.091  42.097  23.806  1.00 25.00           C
ATOM     67  CA  ILE    67      10.548  41.792  20.941  1.00 25.00           C
ATOM     68  CA  SER    68      12.129  45.028  19.717  1.00 25.00           C
ATOM     69  CA  GLU    69      14.300  45.872  16.702  1.00 25.00           C
ATOM     70  CA  GLU    70      12.405  45.249  13.496  1.00 25.00           C
ATOM     71  CA  GLY    71      11.830  41.557  13.055  1.00 25.00           C
ATOM     72  CA  TYR    72      11.794  40.022  16.521  1.00 25.00           C
ATOM     73  CA  LEU    73      15.151  38.475  15.773  1.00 25.00           C
ATOM     74  CA  ILE    74      16.598  38.262  19.327  1.00 25.00           C
ATOM     75  CA  GLN    75      16.109  38.082  23.130  1.00 25.00           C
ATOM     76  CA  VAL    76      17.963  37.575  26.413  1.00 25.00           C
ATOM     77  CA  VAL    77      20.798  40.061  25.729  1.00 25.00           C
ATOM     78  CA  ARG    78      21.893  40.173  29.377  1.00 25.00           C
ATOM     79  CA  VAL    79      21.587  38.633  32.810  1.00 25.00           C
ATOM     80  CA  GLU    80      20.463  35.560  34.845  1.00 25.00           C
ATOM     81  CA  GLY    81      19.840  34.237  38.350  1.00 25.00           C
ATOM     82  CA  THR    82      16.443  35.860  38.918  1.00 25.00           C
ATOM     83  CA  ALA    83      17.564  36.551  42.540  1.00 25.00           C
ATOM     84  CA  ARG    84      14.192  38.272  42.970  1.00 25.00           C
ATOM     85  CA  PRO    85      10.431  38.714  42.927  1.00 25.00           C
ATOM     86  CA  VAL    86      10.870  39.025  46.679  1.00 25.00           C
ATOM     87  CA  GLU    87       8.399  41.871  47.097  1.00 25.00           C
ATOM     88  CA  ASN    88       8.246  44.582  44.466  1.00 25.00           C
ATOM     89  CA  ASP    89      10.013  47.471  42.678  1.00 25.00           C
ATOM     90  CA  TYR    90      11.920  48.323  45.890  1.00 25.00           C
ATOM     91  CA  LEU    91      12.966  44.659  46.270  1.00 25.00           C
ATOM     92  CA  LYS    92      14.172  44.600  42.636  1.00 25.00           C
ATOM     93  CA  THR    93      16.184  47.805  43.226  1.00 25.00           C
ATOM     94  CA  VAL    94      17.755  46.271  46.364  1.00 25.00           C
ATOM     95  CA  PHE    95      18.673  43.119  44.393  1.00 25.00           C
ATOM     96  CA  ALA    96      20.260  45.269  41.649  1.00 25.00           C
ATOM     97  CA  ASP    97      23.892  44.884  42.744  1.00 25.00           C
ATOM     98  CA  ASN    98      23.187  41.174  42.634  1.00 25.00           C
ATOM     99  CA  PRO    99      24.944  37.948  43.792  1.00 25.00           C
ATOM    100  CA  TYR   100      26.908  38.492  40.596  1.00 25.00           C
ATOM    101  CA  TYR   101      24.025  38.581  38.076  1.00 25.00           C
ATOM    102  CA  GLN   102      24.283  42.397  37.879  1.00 25.00           C
ATOM    103  CA  HIS   103      28.058  42.136  37.288  1.00 25.00           C
ATOM    104  CA  ILE   104      27.470  39.564  34.512  1.00 25.00           C
ATOM    105  CA  TYR   105      27.427  42.546  32.091  1.00 25.00           C
ATOM    106  CA  LYS   106      30.879  43.738  33.295  1.00 25.00           C
ATOM    107  CA  ASP   107      32.223  45.431  36.384  1.00 25.00           C
ATOM    108  CA  GLU   108      33.269  49.054  35.709  1.00 25.00           C
ATOM    109  CA  SER   109      32.991  49.314  31.957  1.00 25.00           C
ATOM    110  CA  SER   110      31.259  52.524  30.939  1.00 25.00           C
ATOM    111  CA  ASP   111      28.378  50.410  29.588  1.00 25.00           C
ATOM    112  CA  THR   112      25.574  47.876  30.246  1.00 25.00           C
ATOM    113  CA  MET   113      22.474  45.636  30.420  1.00 25.00           C
ATOM    114  CA  GLN   114      19.371  43.949  31.843  1.00 25.00           C
ATOM    115  CA  VAL   115      17.803  43.232  28.434  1.00 25.00           C
ATOM    116  CA  PHE   116      15.802  40.588  30.413  1.00 25.00           C
ATOM    117  CA  GLN   117      16.705  36.984  31.299  1.00 25.00           C
ATOM    118  CA  ILE   118      14.145  34.444  32.568  1.00 25.00           C
ATOM    119  CA  TYR   119      16.467  31.742  33.902  1.00 25.00           C
ATOM    120  CA  ALA   120      14.657  28.688  32.538  1.00 25.00           C
ATOM    121  CA  GLY   121      11.474  29.466  34.409  1.00 25.00           C
ATOM    122  CA  HIS   122      10.339  30.829  31.095  1.00 25.00           C
ATOM    123  CA  GLY   123      12.982  31.754  28.450  1.00 25.00           C
ATOM    124  CA  PHE   124      12.831  35.408  27.571  1.00 25.00           C
ATOM    125  CA  TYR   125      11.153  38.639  28.661  1.00 25.00           C
ATOM    126  CA  HIS   126      10.515  42.397  28.892  1.00 25.00           C
ATOM    127  CA  SER   127       9.021  45.770  29.481  1.00 25.00           C
ATOM    128  CA  LEU   128       5.526  44.634  28.606  1.00 25.00           C
ATOM    129  CA  THR   129       4.030  47.771  30.095  1.00 25.00           C
ATOM    130  CA  GLN   130       0.349  46.694  30.077  1.00 25.00           C
ATOM    131  CA  GLY   131       0.895  43.885  32.566  1.00 25.00           C
ATOM    132  CA  HIS   132       4.058  41.822  33.023  1.00 25.00           C
ATOM    133  CA  LYS   133       6.725  41.088  35.555  1.00 25.00           C
ATOM    134  CA  TYR   134      10.272  41.264  34.333  1.00 25.00           C
ATOM    135  CA  ILE   135      13.061  43.665  33.377  1.00 25.00           C
ATOM    136  CA  PHE   136      14.143  47.233  32.636  1.00 25.00           C
ATOM    137  CA  SER   137      13.068  50.251  30.566  1.00 25.00           C
ATOM    138  CA  ILE   138      14.116  53.575  31.942  1.00 25.00           C
ATOM    139  CA  GLY   139      12.262  56.862  31.549  1.00 25.00           C
ATOM    140  CA  GLN   140      12.341  60.556  30.502  1.00 25.00           C
ATOM    141  CA  GLY   141      12.813  64.124  29.139  1.00 25.00           C
ATOM    142  CA  GLU   142      14.604  66.396  26.672  1.00 25.00           C
ATOM    143  CA  HIS   143      13.303  65.174  23.316  1.00 25.00           C
ATOM    144  CA  SER   144       9.809  63.763  23.099  1.00 25.00           C
ATOM    145  CA  GLU   145       6.351  65.181  23.754  1.00 25.00           C
ATOM    146  CA  VAL   146       4.882  64.879  20.260  1.00 25.00           C
ATOM    147  CA  ARG   147       4.662  64.092  16.558  1.00 25.00           C
ATOM    148  CA  ALA   148       3.328  60.656  17.454  1.00 25.00           C
ATOM    149  CA  LEU   149       1.457  57.844  15.566  1.00 25.00           C
TER
END
