
#######################################################
#                                                     #
#                        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 T0331TS393_5
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS393_5.T0331.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    E       2      E       2           -
LGA    L       3      L       3           -
LGA    K       4      K       4           -
LGA    D       5      D       5           -
LGA    I       6      I       6           -
LGA    M       7      M       7           -
LGA    H       8      H       8           -
LGA    I       9      I       9           -
LGA    L      10      L      10           -
LGA    E      11      E      11           -
LGA    D      12      D      12           -
LGA    M      13      M      13           -
LGA    K      14      K      14           -
LGA    V      15      V      15           -
LGA    G      16      -       -           -
LGA    V      17      -       -           -
LGA    F      18      -       -           -
LGA    A      19      -       -           -
LGA    T      20      -       -           -
LGA    L      21      -       -           -
LGA    D      22      -       -           -
LGA    E      23      -       -           -
LGA    Y      24      -       -           -
LGA    G      25      -       -           -
LGA    N      26      -       -           -
LGA    P      27      -       -           -
LGA    H      28      -       -           -
LGA    A      29      -       -           -
LGA    R      30      -       -           -
LGA    H      31      -       -           -
LGA    A      32      G      16           #
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      V      17           #
LGA    F      44      F      18          4.218
LGA    M      45      A      19          3.370
LGA    -       -      T      20           -
LGA    -       -      L      21           -
LGA    -       -      D      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      G      25           -
LGA    -       -      N      26           -
LGA    -       -      P      27           -
LGA    -       -      H      28           -
LGA    -       -      A      29           -
LGA    T      46      R      30          1.996
LGA    S      47      H      31          1.446
LGA    P      48      A      32           #
LGA    E      49      -       -           -
LGA    T      50      -       -           -
LGA    H      51      H      33           #
LGA    F      52      -       -           -
LGA    Y      53      -       -           -
LGA    D      54      -       -           -
LGA    Q      55      -       -           -
LGA    L      56      -       -           -
LGA    M      57      -       -           -
LGA    G      58      -       -           -
LGA    D      59      -       -           -
LGA    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      I      34          1.639
LGA    A      83      T      35          3.678
LGA    R      84      A      36          2.057
LGA    P      85      A      37          1.397
LGA    V      86      N      38          3.138
LGA    E      87      -       -           -
LGA    N      88      E      39          2.149
LGA    D      89      E      40          0.875
LGA    Y      90      G      41           -
LGA    L      91      I      42           -
LGA    K      92      F      43          5.338
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      F      44          2.679
LGA    Q     102      M      45          2.252
LGA    H     103      -       -           -
LGA    I     104      T      46          1.612
LGA    Y     105      -       -           -
LGA    K     106      S      47          2.399
LGA    D     107      P      48          3.747
LGA    E     108      E      49           -
LGA    S     109      T      50           -
LGA    S     110      H      51           -
LGA    D     111      F      52           -
LGA    T     112      Y      53          3.580
LGA    M     113      D      54          4.372
LGA    Q     114      Q      55           #
LGA    V     115      L      56          4.443
LGA    F     116      M      57           -
LGA    -       -      G      58           -
LGA    -       -      D      59           -
LGA    -       -      Q      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    Q     117      A      63          1.394
LGA    I     118      M      64          1.157
LGA    Y     119      T      65          2.358
LGA    A     120      A      66          0.609
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    G     121      V      76          3.896
LGA    H     122      V      77          3.247
LGA    G     123      R      78          3.310
LGA    F     124      V      79          2.908
LGA    Y     125      E      80          1.653
LGA    H     126      G      81          1.118
LGA    -       -      T      82           -
LGA    -       -      A      83           -
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           -
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    -       -      Q     117           -
LGA    -       -      I     118           -
LGA    S     127      Y     119          5.308
LGA    L     128      -       -           -
LGA    T     129      -       -           -
LGA    Q     130      -       -           -
LGA    G     131      -       -           -
LGA    H     132      A     120          3.347
LGA    K     133      G     121          2.745
LGA    Y     134      H     122           #
LGA    I     135      G     123          4.838
LGA    F     136      F     124          3.494
LGA    S     137      Y     125          2.387
LGA    I     138      H     126          4.613
LGA    -       -      S     127           -
LGA    -       -      L     128           -
LGA    -       -      T     129           -
LGA    -       -      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    G     139      Y     134          1.606
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      S     137           -
LGA    -       -      I     138           -
LGA    -       -      G     139           -
LGA    -       -      E     145           -
LGA    -       -      V     146           -
LGA    -       -      R     147           -
LGA    Q     140      A     148          1.349
LGA    G     141      L     149          4.523
LGA    E     142      -       -           -
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     40    3.08     7.50     16.449     1.256

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.037791 * X  +   0.276841 * Y  +  -0.960172 * Z  +  27.650785
  Y_new =   0.493567 * X  +   0.830303 * Y  +   0.258822 * Z  +  32.372322
  Z_new =   0.868887 * X  +  -0.483690 * Y  +  -0.105262 * Z  +  27.710752 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.785077    1.356515  [ DEG:  -102.2774     77.7226 ]
  Theta =  -1.052948   -2.088644  [ DEG:   -60.3295   -119.6705 ]
  Phi   =   1.494379   -1.647214  [ DEG:    85.6216    -94.3784 ]
 
# 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: T0331TS393_5                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS393_5.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   40   3.08    7.50  16.449
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS393_5
PFRMAT TS
TARGET T0331
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      54.213  20.597  29.658  1.00 25.00           C
ATOM      2  CA  GLU     2      52.616  22.467  32.545  1.00 25.00           C
ATOM      3  CA  LEU     3      51.877  25.474  30.424  1.00 25.00           C
ATOM      4  CA  LYS     4      48.828  27.374  31.623  1.00 25.00           C
ATOM      5  CA  ASP     5      46.736  24.294  30.725  1.00 25.00           C
ATOM      6  CA  ILE     6      43.622  26.491  30.337  1.00 25.00           C
ATOM      7  CA  MET     7      45.567  28.889  28.071  1.00 25.00           C
ATOM      8  CA  HIS     8      46.776  25.940  25.947  1.00 25.00           C
ATOM      9  CA  ILE     9      43.184  24.648  25.652  1.00 25.00           C
ATOM     10  CA  LEU    10      41.994  28.127  24.580  1.00 25.00           C
ATOM     11  CA  GLU    11      44.771  28.292  21.949  1.00 25.00           C
ATOM     12  CA  ASP    12      43.768  24.838  20.636  1.00 25.00           C
ATOM     13  CA  MET    13      41.450  26.459  18.096  1.00 25.00           C
ATOM     14  CA  LYS    14      41.523  29.662  16.025  1.00 25.00           C
ATOM     15  CA  VAL    15      40.379  31.228  19.278  1.00 25.00           C
ATOM     16  CA  GLY    16      37.335  28.960  19.508  1.00 25.00           C
ATOM     17  CA  VAL    17      34.895  29.889  22.225  1.00 25.00           C
ATOM     18  CA  PHE    18      35.583  28.217  25.553  1.00 25.00           C
ATOM     19  CA  ALA    19      34.656  29.242  29.066  1.00 25.00           C
ATOM     20  CA  THR    20      33.308  28.635  32.609  1.00 25.00           C
ATOM     21  CA  LEU    21      29.666  29.740  33.252  1.00 25.00           C
ATOM     22  CA  ASP    22      29.575  29.363  37.076  1.00 25.00           C
ATOM     23  CA  GLU    23      29.629  27.052  40.134  1.00 25.00           C
ATOM     24  CA  TYR    24      32.696  25.674  38.400  1.00 25.00           C
ATOM     25  CA  GLY    25      32.668  22.499  36.295  1.00 25.00           C
ATOM     26  CA  ASN    26      29.974  21.492  38.821  1.00 25.00           C
ATOM     27  CA  PRO    27      26.671  23.013  39.921  1.00 25.00           C
ATOM     28  CA  HIS    28      25.014  25.107  37.160  1.00 25.00           C
ATOM     29  CA  ALA    29      28.306  24.742  35.238  1.00 25.00           C
ATOM     30  CA  ARG    30      27.456  21.095  34.429  1.00 25.00           C
ATOM     31  CA  HIS    31      23.990  22.151  33.191  1.00 25.00           C
ATOM     32  CA  ALA    32      25.572  24.855  30.988  1.00 25.00           C
ATOM     33  CA  HIS    33      28.020  22.283  29.549  1.00 25.00           C
ATOM     34  CA  ILE    34      25.116  19.898  28.811  1.00 25.00           C
ATOM     35  CA  THR    35      23.208  22.721  27.065  1.00 25.00           C
ATOM     36  CA  ALA    36      26.304  23.551  24.968  1.00 25.00           C
ATOM     37  CA  ALA    37      26.668  19.863  24.001  1.00 25.00           C
ATOM     38  CA  ASN    38      29.082  17.814  26.134  1.00 25.00           C
ATOM     39  CA  GLU    39      31.901  18.679  28.531  1.00 25.00           C
ATOM     40  CA  GLU    40      33.578  20.331  25.604  1.00 25.00           C
ATOM     41  CA  GLY    41      32.215  23.524  27.065  1.00 25.00           C
ATOM     42  CA  ILE    42      31.095  25.475  23.996  1.00 25.00           C
ATOM     43  CA  PHE    43      30.608  28.605  26.104  1.00 25.00           C
ATOM     44  CA  PHE    44      28.087  30.019  28.502  1.00 25.00           C
ATOM     45  CA  MET    45      25.936  32.396  30.626  1.00 25.00           C
ATOM     46  CA  THR    46      24.617  30.139  33.425  1.00 25.00           C
ATOM     47  CA  SER    47      22.007  27.333  33.764  1.00 25.00           C
ATOM     48  CA  PRO    48      20.564  27.420  37.252  1.00 25.00           C
ATOM     49  CA  GLU    49      19.546  26.073  40.722  1.00 25.00           C
ATOM     50  CA  THR    50      21.791  28.083  43.094  1.00 25.00           C
ATOM     51  CA  HIS    51      21.200  31.120  40.979  1.00 25.00           C
ATOM     52  CA  PHE    52      24.553  30.318  39.310  1.00 25.00           C
ATOM     53  CA  TYR    53      25.794  33.866  40.041  1.00 25.00           C
ATOM     54  CA  ASP    54      24.723  33.513  43.701  1.00 25.00           C
ATOM     55  CA  GLN    55      26.564  30.164  43.943  1.00 25.00           C
ATOM     56  CA  LEU    56      29.708  31.755  42.444  1.00 25.00           C
ATOM     57  CA  MET    57      33.218  32.441  43.863  1.00 25.00           C
ATOM     58  CA  GLY    58      33.585  36.224  43.979  1.00 25.00           C
ATOM     59  CA  ASP    59      32.212  37.654  40.730  1.00 25.00           C
ATOM     60  CA  GLN    60      34.962  37.683  38.186  1.00 25.00           C
ATOM     61  CA  ARG    61      35.803  34.285  39.626  1.00 25.00           C
ATOM     62  CA  VAL    62      35.999  33.337  35.919  1.00 25.00           C
ATOM     63  CA  ALA    63      35.877  33.485  32.103  1.00 25.00           C
ATOM     64  CA  MET    64      35.715  37.240  31.215  1.00 25.00           C
ATOM     65  CA  THR    65      34.333  38.471  27.882  1.00 25.00           C
ATOM     66  CA  ALA    66      33.017  38.886  24.337  1.00 25.00           C
ATOM     67  CA  ILE    67      32.627  39.292  20.595  1.00 25.00           C
ATOM     68  CA  SER    68      35.597  36.893  20.532  1.00 25.00           C
ATOM     69  CA  GLU    69      36.989  34.640  17.822  1.00 25.00           C
ATOM     70  CA  GLU    70      40.147  36.692  18.469  1.00 25.00           C
ATOM     71  CA  GLY    71      40.929  36.495  22.235  1.00 25.00           C
ATOM     72  CA  TYR    72      38.182  37.229  24.814  1.00 25.00           C
ATOM     73  CA  LEU    73      38.997  33.736  26.111  1.00 25.00           C
ATOM     74  CA  ILE    74      35.176  33.374  26.288  1.00 25.00           C
ATOM     75  CA  GLN    75      31.854  33.305  28.142  1.00 25.00           C
ATOM     76  CA  VAL    76      31.086  35.262  31.320  1.00 25.00           C
ATOM     77  CA  VAL    77      31.056  36.299  34.950  1.00 25.00           C
ATOM     78  CA  ARG    78      27.931  34.203  35.058  1.00 25.00           C
ATOM     79  CA  VAL    79      24.353  35.374  34.628  1.00 25.00           C
ATOM     80  CA  GLU    80      21.344  33.979  32.832  1.00 25.00           C
ATOM     81  CA  GLY    81      18.373  34.347  30.423  1.00 25.00           C
ATOM     82  CA  THR    82      15.826  31.707  29.292  1.00 25.00           C
ATOM     83  CA  ALA    83      12.236  32.661  28.472  1.00 25.00           C
ATOM     84  CA  ARG    84      13.107  35.427  25.966  1.00 25.00           C
ATOM     85  CA  PRO    85      13.612  36.422  22.322  1.00 25.00           C
ATOM     86  CA  VAL    86       9.949  37.334  22.431  1.00 25.00           C
ATOM     87  CA  GLU    87       9.146  38.519  18.853  1.00 25.00           C
ATOM     88  CA  ASN    88      11.504  41.450  18.333  1.00 25.00           C
ATOM     89  CA  ASP    89      14.232  43.720  19.776  1.00 25.00           C
ATOM     90  CA  TYR    90      11.599  45.649  21.780  1.00 25.00           C
ATOM     91  CA  LEU    91      10.173  42.359  23.124  1.00 25.00           C
ATOM     92  CA  LYS    92      13.687  41.221  24.134  1.00 25.00           C
ATOM     93  CA  THR    93      14.280  44.556  25.922  1.00 25.00           C
ATOM     94  CA  VAL    94      10.946  44.185  27.772  1.00 25.00           C
ATOM     95  CA  PHE    95      11.899  40.628  28.824  1.00 25.00           C
ATOM     96  CA  ALA    96      15.287  41.883  30.091  1.00 25.00           C
ATOM     97  CA  ASP    97      13.597  42.078  33.497  1.00 25.00           C
ATOM     98  CA  ASN    98      11.877  38.630  33.414  1.00 25.00           C
ATOM     99  CA  PRO    99      13.145  35.486  35.155  1.00 25.00           C
ATOM    100  CA  TYR   100      16.722  34.241  35.219  1.00 25.00           C
ATOM    101  CA  TYR   101      17.922  37.742  34.229  1.00 25.00           C
ATOM    102  CA  GLN   102      15.891  39.274  37.092  1.00 25.00           C
ATOM    103  CA  HIS   103      17.409  36.756  39.548  1.00 25.00           C
ATOM    104  CA  ILE   104      20.923  37.613  38.293  1.00 25.00           C
ATOM    105  CA  TYR   105      23.961  39.318  39.786  1.00 25.00           C
ATOM    106  CA  LYS   106      21.758  41.027  42.356  1.00 25.00           C
ATOM    107  CA  ASP   107      19.431  41.577  45.286  1.00 25.00           C
ATOM    108  CA  GLU   108      19.356  45.367  44.871  1.00 25.00           C
ATOM    109  CA  SER   109      23.066  45.230  45.566  1.00 25.00           C
ATOM    110  CA  SER   110      24.073  47.907  42.985  1.00 25.00           C
ATOM    111  CA  ASP   111      26.380  46.563  40.295  1.00 25.00           C
ATOM    112  CA  THR   112      26.787  44.015  37.448  1.00 25.00           C
ATOM    113  CA  MET   113      26.913  40.625  35.639  1.00 25.00           C
ATOM    114  CA  GLN   114      24.372  40.184  32.887  1.00 25.00           C
ATOM    115  CA  VAL   115      27.343  38.888  30.841  1.00 25.00           C
ATOM    116  CA  PHE   116      24.921  37.330  28.406  1.00 25.00           C
ATOM    117  CA  GLN   117      27.257  35.024  26.517  1.00 25.00           C
ATOM    118  CA  ILE   118      24.037  33.052  25.936  1.00 25.00           C
ATOM    119  CA  TYR   119      23.357  29.402  26.898  1.00 25.00           C
ATOM    120  CA  ALA   120      20.781  26.904  25.559  1.00 25.00           C
ATOM    121  CA  GLY   121      20.073  27.787  21.924  1.00 25.00           C
ATOM    122  CA  HIS   122      23.861  28.285  21.862  1.00 25.00           C
ATOM    123  CA  GLY   123      26.999  30.343  22.765  1.00 25.00           C
ATOM    124  CA  PHE   124      27.552  33.936  21.593  1.00 25.00           C
ATOM    125  CA  TYR   125      28.466  37.588  22.263  1.00 25.00           C
ATOM    126  CA  HIS   126      27.099  41.136  22.156  1.00 25.00           C
ATOM    127  CA  SER   127      25.723  44.676  21.964  1.00 25.00           C
ATOM    128  CA  LEU   128      29.227  45.876  22.690  1.00 25.00           C
ATOM    129  CA  THR   129      28.631  48.469  20.034  1.00 25.00           C
ATOM    130  CA  GLN   130      25.850  49.176  17.464  1.00 25.00           C
ATOM    131  CA  GLY   131      25.077  45.961  15.673  1.00 25.00           C
ATOM    132  CA  HIS   132      24.613  42.612  17.406  1.00 25.00           C
ATOM    133  CA  LYS   133      22.403  40.576  19.762  1.00 25.00           C
ATOM    134  CA  TYR   134      22.900  38.142  22.552  1.00 25.00           C
ATOM    135  CA  ILE   135      22.427  34.593  21.342  1.00 25.00           C
ATOM    136  CA  PHE   136      23.174  32.328  18.408  1.00 25.00           C
ATOM    137  CA  SER   137      22.619  28.915  16.749  1.00 25.00           C
ATOM    138  CA  ILE   138      21.384  29.079  13.167  1.00 25.00           C
ATOM    139  CA  GLY   139      20.791  28.401   9.471  1.00 25.00           C
ATOM    140  CA  GLN   140      20.752  28.611   5.729  1.00 25.00           C
ATOM    141  CA  GLY   141      21.181  27.426   2.190  1.00 25.00           C
ATOM    142  CA  GLU   142      24.690  26.637   0.959  1.00 25.00           C
ATOM    143  CA  HIS   143      28.256  27.364   2.057  1.00 25.00           C
ATOM    144  CA  SER   144      30.690  24.448   2.397  1.00 25.00           C
ATOM    145  CA  GLU   145      29.553  21.419   0.506  1.00 25.00           C
ATOM    146  CA  VAL   146      28.733  17.741   0.951  1.00 25.00           C
ATOM    147  CA  ARG   147      30.592  15.999   3.825  1.00 25.00           C
ATOM    148  CA  ALA   148      34.013  15.207   5.396  1.00 25.00           C
ATOM    149  CA  LEU   149      36.571  16.563   7.891  1.00 25.00           C
TER
END
