
#######################################################
#                                                     #
#                        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  144 (  144),  selected  144 , name T0370TS168_2-D1
# Molecule2: number of CA atoms  144 ( 1104),  selected  144 , name T0370_D1.pdb
# PARAMETERS: T0370TS168_2-D1.T0370_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       8           -
LGA    -       -      A       9           -
LGA    -       -      K      10           -
LGA    T       8      Q      11          1.212
LGA    A       9      R      12          1.946
LGA    K      10      I      13          2.912
LGA    Q      11      Q      14          1.263
LGA    R      12      D      15          1.858
LGA    I      13      T      16          3.122
LGA    Q      14      L      17          1.320
LGA    D      15      N      18          2.371
LGA    T      16      -       -           -
LGA    L      17      R      19          3.334
LGA    N      18      L      20           #
LGA    R      19      -       -           -
LGA    L      20      -       -           -
LGA    E      21      E      21          5.129
LGA    L      22      L      22          3.970
LGA    D      23      D      23          1.623
LGA    V      24      V      24          4.380
LGA    D      25      D      25          4.188
LGA    A      26      A      26          2.831
LGA    W      27      -       -           -
LGA    V      28      -       -           -
LGA    S      29      -       -           -
LGA    T      30      W      27           #
LGA    A      31      -       -           -
LGA    G      32      -       -           -
LGA    A      33      -       -           -
LGA    D      34      -       -           -
LGA    G      35      -       -           -
LGA    G      36      -       -           -
LGA    A      37      -       -           -
LGA    P      38      -       -           -
LGA    Y      39      -       -           -
LGA    L      40      -       -           -
LGA    V      41      -       -           -
LGA    P      42      -       -           -
LGA    L      43      -       -           -
LGA    S      44      -       -           -
LGA    Y      45      -       -           -
LGA    L      46      -       -           -
LGA    W      47      -       -           -
LGA    D      48      -       -           -
LGA    G      49      -       -           -
LGA    E      50      -       -           -
LGA    T      51      -       -           -
LGA    F      52      -       -           -
LGA    L      53      -       -           -
LGA    V      54      V      28           #
LGA    A      55      S      29           -
LGA    T      56      -       -           -
LGA    P      57      T      30           #
LGA    -       -      A      31           -
LGA    A      58      G      32           #
LGA    A      59      A      33           -
LGA    S      60      D      34           -
LGA    P      61      G      35           -
LGA    T      62      G      36           -
LGA    G      63      -       -           -
LGA    R      64      A      37          4.185
LGA    N      65      P      38          3.452
LGA    L      66      Y      39          3.882
LGA    S      67      L      40          3.752
LGA    E      68      V      41          3.026
LGA    T      69      P      42          4.106
LGA    G      70      L      43          3.714
LGA    R      71      S      44          2.370
LGA    V      72      Y      45          1.283
LGA    R      73      L      46          3.873
LGA    L      74      W      47          3.989
LGA    G      75      D      48           -
LGA    I      76      -       -           -
LGA    G      77      -       -           -
LGA    P      78      -       -           -
LGA    T      79      -       -           -
LGA    R      80      -       -           -
LGA    D      81      -       -           -
LGA    L      82      -       -           -
LGA    V      83      -       -           -
LGA    L      84      -       -           -
LGA    V      85      -       -           -
LGA    E      86      -       -           -
LGA    G      87      -       -           -
LGA    T      88      -       -           -
LGA    A      89      G      49          1.734
LGA    L      90      -       -           -
LGA    P      91      -       -           -
LGA    L      92      -       -           -
LGA    E      93      -       -           -
LGA    P      94      -       -           -
LGA    A      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    P      98      -       -           -
LGA    D      99      -       -           -
LGA    G     100      -       -           -
LGA    V     101      -       -           -
LGA    G     102      -       -           -
LGA    D     103      -       -           -
LGA    T     104      E      50          1.928
LGA    F     105      T      51          2.336
LGA    A     106      F      52           #
LGA    -       -      L      53           -
LGA    -       -      V      54           -
LGA    -       -      A      55           -
LGA    -       -      T      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      A      59           -
LGA    -       -      S      60           -
LGA    -       -      P      61           -
LGA    -       -      T      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      S      67           -
LGA    -       -      E      68           -
LGA    -       -      T      69           -
LGA    -       -      G      70           -
LGA    -       -      R      71           -
LGA    E     107      V      72           #
LGA    K     108      R      73           -
LGA    T     109      L      74           -
LGA    G     110      G      75           -
LGA    F     111      I      76           -
LGA    D     112      G      77           -
LGA    P     113      P      78           -
LGA    R     114      T      79           -
LGA    R     115      R      80           -
LGA    L     116      D      81           -
LGA    -       -      L      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      V      85           -
LGA    T     117      E      86           #
LGA    T     118      G      87          3.893
LGA    S     119      T      88           #
LGA    Y     120      -       -           -
LGA    L     121      -       -           -
LGA    Y     122      -       -           -
LGA    F     123      -       -           -
LGA    R     124      A      89           #
LGA    I     125      L      90          2.357
LGA    S     126      P      91          2.315
LGA    P     127      -       -           -
LGA    R     128      -       -           -
LGA    R     129      -       -           -
LGA    V     130      L      92          2.182
LGA    Q     131      E      93          1.643
LGA    A     132      -       -           -
LGA    W     133      P      94          4.129
LGA    R     134      A      95          4.522
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      P      98           -
LGA    -       -      D      99           -
LGA    -       -      G     100           -
LGA    E     135      V     101           #
LGA    A     136      G     102          1.905
LGA    N     137      -       -           -
LGA    E     138      -       -           -
LGA    L     139      -       -           -
LGA    S     140      D     103          3.354
LGA    G     141      T     104           -
LGA    R     142      F     105           -
LGA    E     143      -       -           -
LGA    L     144      -       -           -
LGA    M     145      A     106          5.450
LGA    R     146      -       -           -
LGA    D     147      -       -           -
LGA    G     148      -       -           -
LGA    E     149      E     107          2.559
LGA    W     150      K     108          2.732
LGA    L     151      T     109          3.185
LGA    -       -      G     110           -
LGA    -       -      F     111           -
LGA    -       -      D     112           -
LGA    -       -      P     113           -
LGA    -       -      R     114           -
LGA    -       -      R     115           -
LGA    -       -      L     116           -
LGA    -       -      T     117           -
LGA    -       -      T     118           -
LGA    -       -      S     119           -
LGA    -       -      Y     120           -
LGA    -       -      L     121           -
LGA    -       -      Y     122           -
LGA    -       -      F     123           -
LGA    -       -      R     124           -
LGA    -       -      I     125           -
LGA    -       -      S     126           -
LGA    -       -      P     127           -
LGA    -       -      R     128           -
LGA    -       -      R     129           -
LGA    -       -      V     130           -
LGA    -       -      Q     131           -
LGA    -       -      A     132           -
LGA    -       -      W     133           -
LGA    -       -      R     134           -
LGA    -       -      E     135           -
LGA    -       -      A     136           -
LGA    -       -      N     137           -
LGA    -       -      E     138           -
LGA    -       -      L     139           -
LGA    -       -      S     140           -
LGA    -       -      G     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      M     145           -
LGA    -       -      R     146           -
LGA    -       -      D     147           -
LGA    -       -      G     148           -
LGA    -       -      E     149           -
LGA    -       -      W     150           -
LGA    -       -      L     151           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0     42    3.18    19.05     16.362     1.280

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.140902 * X  +   0.357916 * Y  +  -0.923061 * Z  +   3.548071
  Y_new =  -0.989559 * X  +   0.079467 * Y  +  -0.120239 * Z  +  33.875751
  Z_new =   0.030318 * X  +   0.930366 * Y  +   0.365377 * Z  +  20.961784 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.196579   -1.945014  [ DEG:    68.5589   -111.4411 ]
  Theta =  -0.030322   -3.111270  [ DEG:    -1.7373   -178.2627 ]
  Phi   =  -1.429358    1.712234  [ DEG:   -81.8962     98.1038 ]
 
# 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: T0370TS168_2-D1                               
REMARK     2: T0370_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0370TS168_2-D1.T0370_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  144  144   5.0   42   3.18   19.05  16.362
REMARK  ---------------------------------------------------------- 
MOLECULE T0370TS168_2-D1
PFRMAT TS
TARGET T0370
MODEL 2
PARENT N/A
ATOM      8  CA  THR     8      24.100  33.155  25.046  1.00 25.00           C
ATOM      9  CA  ALA     9      23.240  34.111  21.439  1.00 25.00           C
ATOM     10  CA  LYS    10      19.664  32.828  21.926  1.00 25.00           C
ATOM     11  CA  GLN    11      19.346  34.865  25.153  1.00 25.00           C
ATOM     12  CA  ARG    12      20.611  37.989  23.335  1.00 25.00           C
ATOM     13  CA  ILE    13      18.069  37.415  20.528  1.00 25.00           C
ATOM     14  CA  GLN    14      15.266  37.038  23.110  1.00 25.00           C
ATOM     15  CA  ASP    15      16.361  40.291  24.810  1.00 25.00           C
ATOM     16  CA  THR    16      16.363  42.086  21.427  1.00 25.00           C
ATOM     17  CA  LEU    17      12.846  40.758  20.692  1.00 25.00           C
ATOM     18  CA  ASN    18      11.644  41.972  24.120  1.00 25.00           C
ATOM     19  CA  ARG    19      13.157  45.427  23.453  1.00 25.00           C
ATOM     20  CA  LEU    20      11.413  45.560  20.047  1.00 25.00           C
ATOM     21  CA  GLU    21       8.085  44.607  21.685  1.00 25.00           C
ATOM     22  CA  LEU    22       7.677  41.402  19.744  1.00 25.00           C
ATOM     23  CA  ASP    23       9.969  42.106  16.813  1.00 25.00           C
ATOM     24  CA  VAL    24       9.656  38.367  16.399  1.00 25.00           C
ATOM     25  CA  ASP    25       9.858  37.285  12.731  1.00 25.00           C
ATOM     26  CA  ALA    26       6.036  37.142  12.536  1.00 25.00           C
ATOM     27  CA  TRP    27       5.804  40.650  14.056  1.00 25.00           C
ATOM     28  CA  VAL    28       8.349  41.950  11.507  1.00 25.00           C
ATOM     29  CA  SER    29       6.339  40.367   8.657  1.00 25.00           C
ATOM     30  CA  THR    30       3.135  41.992   9.980  1.00 25.00           C
ATOM     31  CA  ALA    31       5.081  45.281   9.607  1.00 25.00           C
ATOM     32  CA  GLY    32       6.977  44.998   6.258  1.00 25.00           C
ATOM     33  CA  ALA    33       5.496  42.321   3.932  1.00 25.00           C
ATOM     34  CA  ASP    34       1.938  41.494   5.093  1.00 25.00           C
ATOM     35  CA  GLY    35      -1.740  42.146   5.687  1.00 25.00           C
ATOM     36  CA  GLY    36      -2.677  40.760   9.110  1.00 25.00           C
ATOM     37  CA  ALA    37      -2.090  38.496  12.141  1.00 25.00           C
ATOM     38  CA  PRO    38      -5.117  38.166  14.413  1.00 25.00           C
ATOM     39  CA  TYR    39      -4.843  35.880  17.487  1.00 25.00           C
ATOM     40  CA  LEU    40      -1.801  37.642  18.978  1.00 25.00           C
ATOM     41  CA  VAL    41      -2.630  40.502  21.341  1.00 25.00           C
ATOM     42  CA  PRO    42      -0.436  40.853  24.370  1.00 25.00           C
ATOM     43  CA  LEU    43       1.849  38.676  22.313  1.00 25.00           C
ATOM     44  CA  SER    44       5.236  38.529  24.041  1.00 25.00           C
ATOM     45  CA  TYR    45       3.485  37.947  27.370  1.00 25.00           C
ATOM     46  CA  LEU    46       0.584  39.419  29.246  1.00 25.00           C
ATOM     47  CA  TRP    47      -0.988  37.810  32.366  1.00 25.00           C
ATOM     48  CA  ASP    48      -3.999  39.501  34.024  1.00 25.00           C
ATOM     49  CA  GLY    49      -6.739  37.140  32.709  1.00 25.00           C
ATOM     50  CA  GLU    50      -5.116  37.761  29.358  1.00 25.00           C
ATOM     51  CA  THR    51      -2.490  36.440  26.857  1.00 25.00           C
ATOM     52  CA  PHE    52      -2.009  34.913  23.371  1.00 25.00           C
ATOM     53  CA  LEU    53      -1.378  33.240  20.077  1.00 25.00           C
ATOM     54  CA  VAL    54       0.275  32.077  16.804  1.00 25.00           C
ATOM     55  CA  ALA    55      -1.993  32.416  13.770  1.00 25.00           C
ATOM     56  CA  THR    56      -5.699  31.782  14.355  1.00 25.00           C
ATOM     57  CA  PRO    57      -5.270  28.509  12.581  1.00 25.00           C
ATOM     58  CA  ALA    58      -7.565  25.513  12.294  1.00 25.00           C
ATOM     59  CA  ALA    59      -9.229  26.413   8.963  1.00 25.00           C
ATOM     60  CA  SER    60      -6.309  26.158   6.512  1.00 25.00           C
ATOM     61  CA  PRO    61      -9.159  26.328   3.913  1.00 25.00           C
ATOM     62  CA  THR    62      -6.442  25.263   1.460  1.00 25.00           C
ATOM     63  CA  GLY    63      -2.764  24.289   1.529  1.00 25.00           C
ATOM     64  CA  ARG    64      -3.179  21.916   4.445  1.00 25.00           C
ATOM     65  CA  ASN    65      -0.953  22.279   7.527  1.00 25.00           C
ATOM     66  CA  LEU    66      -1.024  25.642   9.271  1.00 25.00           C
ATOM     67  CA  SER    67      -1.251  27.149   5.768  1.00 25.00           C
ATOM     68  CA  GLU    68       2.346  28.503   6.019  1.00 25.00           C
ATOM     69  CA  THR    69       3.078  30.206   9.381  1.00 25.00           C
ATOM     70  CA  GLY    70       3.077  32.476  12.447  1.00 25.00           C
ATOM     71  CA  ARG    71       1.833  35.824  13.862  1.00 25.00           C
ATOM     72  CA  VAL    72       3.445  36.212  17.286  1.00 25.00           C
ATOM     73  CA  ARG    73       3.753  34.349  20.596  1.00 25.00           C
ATOM     74  CA  LEU    74       2.915  33.988  24.259  1.00 25.00           C
ATOM     75  CA  GLY    75       0.678  31.340  25.725  1.00 25.00           C
ATOM     76  CA  ILE    76      -0.381  32.299  29.235  1.00 25.00           C
ATOM     77  CA  GLY    77      -3.800  30.714  29.109  1.00 25.00           C
ATOM     78  CA  PRO    78      -6.013  27.728  30.087  1.00 25.00           C
ATOM     79  CA  THR    79      -4.121  24.614  28.883  1.00 25.00           C
ATOM     80  CA  ARG    80      -1.157  26.688  27.707  1.00 25.00           C
ATOM     81  CA  ASP    81       0.589  26.482  24.302  1.00 25.00           C
ATOM     82  CA  LEU    82      -0.244  28.966  21.535  1.00 25.00           C
ATOM     83  CA  VAL    83       3.482  29.324  21.032  1.00 25.00           C
ATOM     84  CA  LEU    84       4.883  30.729  17.730  1.00 25.00           C
ATOM     85  CA  VAL    85       7.300  33.194  16.145  1.00 25.00           C
ATOM     86  CA  GLU    86       9.823  31.436  18.391  1.00 25.00           C
ATOM     87  CA  GLY    87       7.853  31.706  21.693  1.00 25.00           C
ATOM     88  CA  THR    88       8.475  34.274  24.439  1.00 25.00           C
ATOM     89  CA  ALA    89       8.707  36.697  27.340  1.00 25.00           C
ATOM     90  CA  LEU    90       8.116  38.883  30.380  1.00 25.00           C
ATOM     91  CA  PRO    91       9.418  37.443  33.637  1.00 25.00           C
ATOM     92  CA  LEU    92       6.924  38.170  36.384  1.00 25.00           C
ATOM     93  CA  GLU    93       6.371  36.803  39.901  1.00 25.00           C
ATOM     94  CA  PRO    94       9.923  35.587  40.307  1.00 25.00           C
ATOM     95  CA  ALA    95       9.278  31.813  39.880  1.00 25.00           C
ATOM     96  CA  GLY    96       8.066  28.688  38.110  1.00 25.00           C
ATOM     97  CA  LEU    97       4.690  29.589  36.514  1.00 25.00           C
ATOM     98  CA  PRO    98       2.681  27.934  39.344  1.00 25.00           C
ATOM     99  CA  ASP    99       3.756  24.682  37.764  1.00 25.00           C
ATOM    100  CA  GLY   100       6.139  24.792  34.765  1.00 25.00           C
ATOM    101  CA  VAL   101       6.081  27.125  31.805  1.00 25.00           C
ATOM    102  CA  GLY   102       9.615  28.390  31.306  1.00 25.00           C
ATOM    103  CA  ASP   103       8.193  31.685  32.617  1.00 25.00           C
ATOM    104  CA  THR   104       5.633  32.016  29.780  1.00 25.00           C
ATOM    105  CA  PHE   105       6.063  29.749  26.724  1.00 25.00           C
ATOM    106  CA  ALA   106       6.120  26.697  24.448  1.00 25.00           C
ATOM    107  CA  GLU   107       6.138  23.106  23.143  1.00 25.00           C
ATOM    108  CA  LYS   108       6.350  19.546  24.623  1.00 25.00           C
ATOM    109  CA  THR   109      10.035  20.485  24.984  1.00 25.00           C
ATOM    110  CA  GLY   110      10.182  18.347  28.150  1.00 25.00           C
ATOM    111  CA  PHE   111       9.313  15.539  25.736  1.00 25.00           C
ATOM    112  CA  ASP   112      10.741  15.625  22.212  1.00 25.00           C
ATOM    113  CA  PRO   113      12.364  18.699  20.745  1.00 25.00           C
ATOM    114  CA  ARG   114      13.643  16.796  17.678  1.00 25.00           C
ATOM    115  CA  ARG   115      11.765  19.206  15.369  1.00 25.00           C
ATOM    116  CA  LEU   116       8.725  17.012  15.666  1.00 25.00           C
ATOM    117  CA  THR   117       7.574  18.382  19.077  1.00 25.00           C
ATOM    118  CA  THR   118       7.424  21.882  17.705  1.00 25.00           C
ATOM    119  CA  SER   119       6.350  25.511  18.041  1.00 25.00           C
ATOM    120  CA  TYR   120       8.077  27.371  15.188  1.00 25.00           C
ATOM    121  CA  LEU   121       4.628  27.592  13.769  1.00 25.00           C
ATOM    122  CA  TYR   122       1.553  27.186  15.925  1.00 25.00           C
ATOM    123  CA  PHE   123      -2.120  27.474  16.781  1.00 25.00           C
ATOM    124  CA  ARG   124      -4.663  29.561  18.752  1.00 25.00           C
ATOM    125  CA  ILE   125      -4.754  26.715  21.258  1.00 25.00           C
ATOM    126  CA  SER   126      -8.456  25.881  21.513  1.00 25.00           C
ATOM    127  CA  PRO   127     -11.395  26.332  23.797  1.00 25.00           C
ATOM    128  CA  ARG   128      -9.990  27.962  26.965  1.00 25.00           C
ATOM    129  CA  ARG   129      -7.045  29.373  24.965  1.00 25.00           C
ATOM    130  CA  VAL   130      -9.462  30.771  22.344  1.00 25.00           C
ATOM    131  CA  GLN   131     -11.558  32.392  25.109  1.00 25.00           C
ATOM    132  CA  ALA   132      -8.404  33.949  26.623  1.00 25.00           C
ATOM    133  CA  TRP   133      -7.394  35.304  23.186  1.00 25.00           C
ATOM    134  CA  ARG   134     -10.889  36.795  22.720  1.00 25.00           C
ATOM    135  CA  GLU   135     -10.676  38.440  26.172  1.00 25.00           C
ATOM    136  CA  ALA   136      -7.245  39.895  25.293  1.00 25.00           C
ATOM    137  CA  ASN   137      -8.641  41.263  22.000  1.00 25.00           C
ATOM    138  CA  GLU   138     -11.578  42.850  23.875  1.00 25.00           C
ATOM    139  CA  LEU   139      -9.152  44.450  26.371  1.00 25.00           C
ATOM    140  CA  SER   140      -7.048  45.825  23.482  1.00 25.00           C
ATOM    141  CA  GLY   141     -10.195  47.266  21.844  1.00 25.00           C
ATOM    142  CA  ARG   142     -11.197  48.908  25.156  1.00 25.00           C
ATOM    143  CA  GLU   143      -7.692  50.414  25.497  1.00 25.00           C
ATOM    144  CA  LEU   144      -7.898  51.767  21.920  1.00 25.00           C
ATOM    145  CA  MET   145      -5.346  49.499  20.353  1.00 25.00           C
ATOM    146  CA  ARG   146      -3.219  52.651  20.315  1.00 25.00           C
ATOM    147  CA  ASP   147      -1.278  52.880  23.575  1.00 25.00           C
ATOM    148  CA  GLY   148       1.859  51.114  22.316  1.00 25.00           C
ATOM    149  CA  GLU   149       1.810  47.371  22.136  1.00 25.00           C
ATOM    150  CA  TRP   150       4.173  44.420  21.811  1.00 25.00           C
ATOM    151  CA  LEU   151       2.617  42.476  18.887  1.00 25.00           C
TER
END
