
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS168_2.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      -       -           -
LGA    G      16      -       -           -
LGA    V      17      -       -           -
LGA    F      18      -       -           -
LGA    A      19      -       -           -
LGA    T      20      -       -           -
LGA    L      21      -       -           -
LGA    D      22      -       -           -
LGA    E      23      V      15          3.268
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          4.992
LGA    H      33      V      17          1.484
LGA    I      34      F      18           #
LGA    T      35      -       -           -
LGA    A      36      -       -           -
LGA    A      37      -       -           -
LGA    N      38      -       -           -
LGA    E      39      -       -           -
LGA    E      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      A      19          3.626
LGA    F      43      T      20          3.900
LGA    F      44      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    M      45      R      30           #
LGA    T      46      H      31           #
LGA    S      47      -       -           -
LGA    P      48      A      32           #
LGA    E      49      H      33           #
LGA    T      50      I      34           -
LGA    H      51      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    F      52      T      46          3.726
LGA    Y      53      S      47          2.462
LGA    D      54      -       -           -
LGA    Q      55      -       -           -
LGA    L      56      P      48          3.113
LGA    M      57      E      49          2.221
LGA    G      58      T      50          2.303
LGA    D      59      H      51          3.580
LGA    Q      60      F      52          1.688
LGA    -       -      Y      53           -
LGA    R      61      D      54          3.198
LGA    V      62      Q      55          1.209
LGA    A      63      L      56          3.000
LGA    M      64      M      57          3.094
LGA    -       -      G      58           -
LGA    T      65      D      59           #
LGA    A      66      Q      60          4.061
LGA    I      67      -       -           -
LGA    S      68      -       -           -
LGA    E      69      -       -           -
LGA    E      70      -       -           -
LGA    G      71      -       -           -
LGA    Y      72      R      61          2.826
LGA    L      73      V      62          5.310
LGA    I      74      A      63          5.068
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    Q      75      T      82          4.157
LGA    V      76      A      83          3.627
LGA    V      77      R      84           #
LGA    R      78      P      85          4.445
LGA    V      79      V      86           #
LGA    E      80      E      87           -
LGA    -       -      N      88           -
LGA    -       -      D      89           -
LGA    -       -      Y      90           -
LGA    G      81      L      91           #
LGA    T      82      K      92           -
LGA    A      83      -       -           -
LGA    R      84      -       -           -
LGA    P      85      -       -           -
LGA    V      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    D      89      -       -           -
LGA    Y      90      T      93           #
LGA    L      91      -       -           -
LGA    K      92      V      94          5.164
LGA    T      93      F      95          2.271
LGA    V      94      A      96          1.700
LGA    -       -      D      97           -
LGA    F      95      N      98          1.775
LGA    -       -      P      99           -
LGA    A      96      Y     100           #
LGA    D      97      Y     101          4.454
LGA    N      98      Q     102          2.050
LGA    P      99      H     103          0.598
LGA    Y     100      -       -           -
LGA    Y     101      I     104          1.981
LGA    Q     102      Y     105          0.887
LGA    H     103      K     106          1.676
LGA    I     104      T     112           #
LGA    Y     105      M     113          2.933
LGA    K     106      -       -           -
LGA    D     107      -       -           -
LGA    E     108      -       -           -
LGA    S     109      -       -           -
LGA    S     110      -       -           -
LGA    D     111      -       -           -
LGA    T     112      Q     114           #
LGA    M     113      V     115          4.223
LGA    Q     114      -       -           -
LGA    V     115      F     116          3.971
LGA    F     116      Q     117          1.524
LGA    Q     117      I     118          1.185
LGA    I     118      -       -           -
LGA    Y     119      -       -           -
LGA    A     120      -       -           -
LGA    G     121      -       -           -
LGA    H     122      -       -           -
LGA    G     123      -       -           -
LGA    F     124      -       -           -
LGA    Y     125      -       -           -
LGA    H     126      -       -           -
LGA    S     127      -       -           -
LGA    L     128      -       -           -
LGA    T     129      -       -           -
LGA    Q     130      -       -           -
LGA    G     131      -       -           -
LGA    H     132      -       -           -
LGA    K     133      Y     119           #
LGA    Y     134      A     120          4.151
LGA    -       -      G     121           -
LGA    -       -      H     122           -
LGA    -       -      G     123           -
LGA    -       -      F     124           -
LGA    -       -      Y     125           -
LGA    -       -      H     126           -
LGA    -       -      S     127           -
LGA    -       -      L     128           -
LGA    -       -      T     129           -
LGA    -       -      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    -       -      Y     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    I     135      S     137           #
LGA    F     136      I     138          4.228
LGA    S     137      G     139           -
LGA    I     138      E     145           #
LGA    G     139      V     146          2.292
LGA    Q     140      R     147          1.363
LGA    G     141      A     148          3.507
LGA    E     142      -       -           -
LGA    H     143      -       -           -
LGA    S     144      -       -           -
LGA    E     145      L     149          5.058
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     44    3.29     2.27     17.699     1.298

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.714142 * X  +  -0.356052 * Y  +  -0.602684 * Z  +  21.386000
  Y_new =  -0.687240 * X  +   0.520266 * Y  +   0.506975 * Z  +  38.349701
  Z_new =   0.133046 * X  +   0.776241 * Y  +  -0.616238 * Z  +  27.612991 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.241791   -0.899802  [ DEG:   128.4452    -51.5548 ]
  Theta =  -0.133442   -3.008151  [ DEG:    -7.6457   -172.3543 ]
  Phi   =  -2.375389    0.766204  [ DEG:  -136.0997     43.9002 ]
 
# 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_2                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS168_2.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   44   3.29    2.27  17.699
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS168_2
PFRMAT TS
TARGET T0331
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      50.695  31.565  33.061  1.00 25.00           C
ATOM      2  CA  GLU     2      49.021  34.945  33.503  1.00 25.00           C
ATOM      3  CA  LEU     3      46.788  34.242  30.503  1.00 25.00           C
ATOM      4  CA  LYS     4      44.426  36.994  31.441  1.00 25.00           C
ATOM      5  CA  ASP     5      41.899  34.135  31.767  1.00 25.00           C
ATOM      6  CA  ILE     6      39.095  36.441  30.549  1.00 25.00           C
ATOM      7  CA  MET     7      41.235  37.504  27.555  1.00 25.00           C
ATOM      8  CA  HIS     8      41.934  33.832  26.723  1.00 25.00           C
ATOM      9  CA  ILE     9      38.191  33.049  26.915  1.00 25.00           C
ATOM     10  CA  LEU    10      37.430  35.996  24.591  1.00 25.00           C
ATOM     11  CA  GLU    11      40.077  34.760  22.116  1.00 25.00           C
ATOM     12  CA  ASP    12      38.557  31.245  22.208  1.00 25.00           C
ATOM     13  CA  MET    13      34.847  31.998  22.226  1.00 25.00           C
ATOM     14  CA  LYS    14      35.644  34.039  19.083  1.00 25.00           C
ATOM     15  CA  VAL    15      33.651  37.007  20.429  1.00 25.00           C
ATOM     16  CA  GLY    16      29.920  36.019  20.561  1.00 25.00           C
ATOM     17  CA  VAL    17      29.497  38.708  23.231  1.00 25.00           C
ATOM     18  CA  PHE    18      26.267  36.803  23.886  1.00 25.00           C
ATOM     19  CA  ALA    19      24.973  37.030  27.432  1.00 25.00           C
ATOM     20  CA  THR    20      22.631  35.791  30.181  1.00 25.00           C
ATOM     21  CA  LEU    21      19.025  36.876  30.605  1.00 25.00           C
ATOM     22  CA  ASP    22      17.543  33.449  31.415  1.00 25.00           C
ATOM     23  CA  GLU    23      15.333  30.376  32.122  1.00 25.00           C
ATOM     24  CA  TYR    24      15.000  29.767  35.898  1.00 25.00           C
ATOM     25  CA  GLY    25      17.264  27.235  37.631  1.00 25.00           C
ATOM     26  CA  ASN    26      18.114  30.257  39.848  1.00 25.00           C
ATOM     27  CA  PRO    27      20.960  32.160  41.506  1.00 25.00           C
ATOM     28  CA  HIS    28      22.812  31.393  38.264  1.00 25.00           C
ATOM     29  CA  ALA    29      25.105  28.947  36.414  1.00 25.00           C
ATOM     30  CA  ARG    30      22.057  26.984  35.181  1.00 25.00           C
ATOM     31  CA  HIS    31      20.429  30.229  33.963  1.00 25.00           C
ATOM     32  CA  ALA    32      23.649  31.183  32.122  1.00 25.00           C
ATOM     33  CA  HIS    33      23.765  27.724  30.482  1.00 25.00           C
ATOM     34  CA  ILE    34      20.111  28.089  29.396  1.00 25.00           C
ATOM     35  CA  THR    35      20.870  31.540  27.916  1.00 25.00           C
ATOM     36  CA  ALA    36      23.867  30.093  26.019  1.00 25.00           C
ATOM     37  CA  ALA    37      21.673  27.264  24.661  1.00 25.00           C
ATOM     38  CA  ASN    38      24.409  24.839  25.603  1.00 25.00           C
ATOM     39  CA  GLU    39      27.401  25.294  27.839  1.00 25.00           C
ATOM     40  CA  GLU    40      28.778  28.522  26.411  1.00 25.00           C
ATOM     41  CA  GLY    41      28.474  31.272  23.846  1.00 25.00           C
ATOM     42  CA  ILE    42      29.595  33.683  26.622  1.00 25.00           C
ATOM     43  CA  PHE    43      27.968  33.994  30.085  1.00 25.00           C
ATOM     44  CA  PHE    44      26.873  36.019  33.112  1.00 25.00           C
ATOM     45  CA  MET    45      23.894  37.696  34.845  1.00 25.00           C
ATOM     46  CA  THR    46      20.827  35.447  35.058  1.00 25.00           C
ATOM     47  CA  SER    47      17.903  37.824  35.286  1.00 25.00           C
ATOM     48  CA  PRO    48      15.333  35.151  36.333  1.00 25.00           C
ATOM     49  CA  GLU    49      12.061  33.710  37.614  1.00 25.00           C
ATOM     50  CA  THR    50      13.589  32.212  40.763  1.00 25.00           C
ATOM     51  CA  HIS    51      15.095  35.717  41.316  1.00 25.00           C
ATOM     52  CA  PHE    52      16.259  39.094  39.935  1.00 25.00           C
ATOM     53  CA  TYR    53      17.978  39.890  43.263  1.00 25.00           C
ATOM     54  CA  ASP    54      19.719  36.479  43.208  1.00 25.00           C
ATOM     55  CA  GLN    55      20.896  37.110  39.619  1.00 25.00           C
ATOM     56  CA  LEU    56      22.249  40.544  40.641  1.00 25.00           C
ATOM     57  CA  MET    57      23.540  40.011  44.187  1.00 25.00           C
ATOM     58  CA  GLY    58      27.168  38.934  44.240  1.00 25.00           C
ATOM     59  CA  ASP    59      26.242  35.683  42.528  1.00 25.00           C
ATOM     60  CA  GLN    60      26.166  37.681  39.307  1.00 25.00           C
ATOM     61  CA  ARG    61      29.473  39.450  39.790  1.00 25.00           C
ATOM     62  CA  VAL    62      29.034  40.430  36.131  1.00 25.00           C
ATOM     63  CA  ALA    63      30.222  41.667  32.766  1.00 25.00           C
ATOM     64  CA  MET    64      29.122  45.358  32.706  1.00 25.00           C
ATOM     65  CA  THR    65      26.729  46.375  29.947  1.00 25.00           C
ATOM     66  CA  ALA    66      26.730  46.099  26.116  1.00 25.00           C
ATOM     67  CA  ILE    67      26.460  48.056  22.818  1.00 25.00           C
ATOM     68  CA  SER    68      29.439  45.963  21.835  1.00 25.00           C
ATOM     69  CA  GLU    69      32.449  46.306  19.489  1.00 25.00           C
ATOM     70  CA  GLU    70      34.306  43.150  20.389  1.00 25.00           C
ATOM     71  CA  GLY    71      34.611  44.780  23.794  1.00 25.00           C
ATOM     72  CA  TYR    72      31.549  43.196  25.440  1.00 25.00           C
ATOM     73  CA  LEU    73      32.968  40.490  27.759  1.00 25.00           C
ATOM     74  CA  ILE    74      29.677  38.594  28.244  1.00 25.00           C
ATOM     75  CA  GLN    75      27.214  41.464  28.680  1.00 25.00           C
ATOM     76  CA  VAL    76      24.040  40.965  30.749  1.00 25.00           C
ATOM     77  CA  VAL    77      24.547  43.054  33.956  1.00 25.00           C
ATOM     78  CA  ARG    78      20.802  42.407  34.353  1.00 25.00           C
ATOM     79  CA  VAL    79      17.347  41.793  32.838  1.00 25.00           C
ATOM     80  CA  GLU    80      14.055  39.923  32.473  1.00 25.00           C
ATOM     81  CA  GLY    81      11.650  38.967  29.686  1.00 25.00           C
ATOM     82  CA  THR    82       9.100  36.514  28.372  1.00 25.00           C
ATOM     83  CA  ALA    83       5.940  36.641  26.338  1.00 25.00           C
ATOM     84  CA  ARG    84       7.022  38.482  23.133  1.00 25.00           C
ATOM     85  CA  PRO    85       8.304  40.088  19.982  1.00 25.00           C
ATOM     86  CA  VAL    86       5.855  38.401  17.618  1.00 25.00           C
ATOM     87  CA  GLU    87       3.202  41.128  17.952  1.00 25.00           C
ATOM     88  CA  ASN    88       3.752  44.540  16.530  1.00 25.00           C
ATOM     89  CA  ASP    89       6.471  46.151  18.691  1.00 25.00           C
ATOM     90  CA  TYR    90       3.806  48.084  20.647  1.00 25.00           C
ATOM     91  CA  LEU    91       1.827  44.851  21.192  1.00 25.00           C
ATOM     92  CA  LYS    92       4.994  43.091  22.431  1.00 25.00           C
ATOM     93  CA  THR    93       5.687  45.985  24.842  1.00 25.00           C
ATOM     94  CA  VAL    94       2.093  45.790  26.150  1.00 25.00           C
ATOM     95  CA  PHE    95       2.462  42.014  26.671  1.00 25.00           C
ATOM     96  CA  ALA    96       5.743  42.570  28.567  1.00 25.00           C
ATOM     97  CA  ASP    97       4.602  43.186  32.117  1.00 25.00           C
ATOM     98  CA  ASN    98       3.800  39.502  32.410  1.00 25.00           C
ATOM     99  CA  PRO    99       6.256  39.483  35.355  1.00 25.00           C
ATOM    100  CA  TYR   100      10.009  39.600  35.895  1.00 25.00           C
ATOM    101  CA  TYR   101      10.031  42.793  33.781  1.00 25.00           C
ATOM    102  CA  GLN   102       7.796  44.541  36.353  1.00 25.00           C
ATOM    103  CA  HIS   103      10.141  43.442  39.175  1.00 25.00           C
ATOM    104  CA  ILE   104      13.154  44.778  37.223  1.00 25.00           C
ATOM    105  CA  TYR   105      15.217  44.335  40.388  1.00 25.00           C
ATOM    106  CA  LYS   106      12.931  46.403  42.521  1.00 25.00           C
ATOM    107  CA  ASP   107      13.618  48.078  45.812  1.00 25.00           C
ATOM    108  CA  GLU   108      11.271  50.852  44.694  1.00 25.00           C
ATOM    109  CA  SER   109      13.374  52.053  41.765  1.00 25.00           C
ATOM    110  CA  SER   110      16.201  54.610  41.909  1.00 25.00           C
ATOM    111  CA  ASP   111      18.305  52.233  39.919  1.00 25.00           C
ATOM    112  CA  THR   112      18.414  49.476  37.315  1.00 25.00           C
ATOM    113  CA  MET   113      17.696  46.520  34.969  1.00 25.00           C
ATOM    114  CA  GLN   114      14.903  46.217  32.340  1.00 25.00           C
ATOM    115  CA  VAL   115      17.487  45.670  29.606  1.00 25.00           C
ATOM    116  CA  PHE   116      20.099  43.214  28.345  1.00 25.00           C
ATOM    117  CA  GLN   117      22.077  41.977  25.378  1.00 25.00           C
ATOM    118  CA  ILE   118      20.401  38.660  26.145  1.00 25.00           C
ATOM    119  CA  TYR   119      21.293  36.700  23.011  1.00 25.00           C
ATOM    120  CA  ALA   120      19.792  33.222  23.146  1.00 25.00           C
ATOM    121  CA  GLY   121      16.678  31.058  23.033  1.00 25.00           C
ATOM    122  CA  HIS   122      14.697  33.823  21.234  1.00 25.00           C
ATOM    123  CA  GLY   123      15.981  36.449  23.666  1.00 25.00           C
ATOM    124  CA  PHE   124      15.201  39.516  25.798  1.00 25.00           C
ATOM    125  CA  TYR   125      16.538  42.880  24.696  1.00 25.00           C
ATOM    126  CA  HIS   126      16.275  46.617  23.900  1.00 25.00           C
ATOM    127  CA  SER   127      15.248  49.357  21.468  1.00 25.00           C
ATOM    128  CA  LEU   128      18.142  51.599  22.466  1.00 25.00           C
ATOM    129  CA  THR   129      19.018  54.673  20.523  1.00 25.00           C
ATOM    130  CA  GLN   130      17.385  54.157  17.142  1.00 25.00           C
ATOM    131  CA  GLY   131      17.477  51.166  14.853  1.00 25.00           C
ATOM    132  CA  HIS   132      18.889  49.306  17.935  1.00 25.00           C
ATOM    133  CA  LYS   133      17.029  46.033  18.178  1.00 25.00           C
ATOM    134  CA  TYR   134      19.047  43.821  20.433  1.00 25.00           C
ATOM    135  CA  ILE   135      18.362  40.035  20.328  1.00 25.00           C
ATOM    136  CA  PHE   136      18.963  37.184  17.861  1.00 25.00           C
ATOM    137  CA  SER   137      18.406  33.843  16.040  1.00 25.00           C
ATOM    138  CA  ILE   138      18.266  34.496  12.339  1.00 25.00           C
ATOM    139  CA  GLY   139      18.319  33.652   8.678  1.00 25.00           C
ATOM    140  CA  GLN   140      20.516  33.463   5.529  1.00 25.00           C
ATOM    141  CA  GLY   141      19.954  30.891   2.771  1.00 25.00           C
ATOM    142  CA  GLU   142      21.195  32.555  -0.416  1.00 25.00           C
ATOM    143  CA  HIS   143      24.926  32.808   0.192  1.00 25.00           C
ATOM    144  CA  SER   144      28.097  30.782   0.781  1.00 25.00           C
ATOM    145  CA  GLU   145      27.038  27.364   1.940  1.00 25.00           C
ATOM    146  CA  VAL   146      28.300  23.837   1.843  1.00 25.00           C
ATOM    147  CA  ARG   147      30.772  23.221   4.658  1.00 25.00           C
ATOM    148  CA  ALA   148      34.355  23.685   5.978  1.00 25.00           C
ATOM    149  CA  LEU   149      36.891  24.170   8.766  1.00 25.00           C
TER
END
