
#######################################################
#                                                     #
#                        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  156 (  156),  selected  156 , name T0364TS393_1
# Molecule2: number of CA atoms  153 ( 1220),  selected  153 , name T0364.pdb
# PARAMETERS: T0364TS393_1.T0364.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    P       2      M       1           #
LGA    A       3      P       2          5.396
LGA    L       4      A       3          3.572
LGA    I       5      L       4          1.723
LGA    T       6      I       5          0.848
LGA    Y       7      T       6          3.429
LGA    -       -      Y       7           -
LGA    R       8      R       8          0.908
LGA    T       9      T       9          2.500
LGA    T      10      T      10          3.728
LGA    V      11      V      11          3.845
LGA    Q      12      Q      12          2.597
LGA    E      13      E      13          0.992
LGA    D      14      D      14           -
LGA    W      15      W      15          5.380
LGA    V      16      V      16          1.843
LGA    D      17      D      17          2.937
LGA    -       -      Y      18           -
LGA    Y      18      N      19           #
LGA    N      19      G      20           -
LGA    G      20      H      21           -
LGA    H      21      L      22           #
LGA    L      22      R      23          1.637
LGA    R      23      -       -           -
LGA    D      24      D      24          2.303
LGA    A      25      A      25          2.285
LGA    F      26      F      26          2.673
LGA    Y      27      Y      27          2.602
LGA    L      28      L      28          2.113
LGA    L      29      L      29          1.928
LGA    I      30      I      30          2.584
LGA    F      31      F      31          2.292
LGA    S      32      S      32          1.481
LGA    Y      33      Y      33          2.331
LGA    A      34      A      34          3.083
LGA    T      35      T      35          2.806
LGA    D      36      D      36          2.490
LGA    A      37      A      37          3.468
LGA    L      38      L      38          3.993
LGA    M      39      M      39          3.618
LGA    D      40      D      40          3.436
LGA    R      41      -       -           -
LGA    I      42      R      41          1.896
LGA    G      43      I      42          2.355
LGA    L      44      -       -           -
LGA    D      45      -       -           -
LGA    A      46      -       -           -
LGA    D      47      -       -           -
LGA    S      48      G      43          3.487
LGA    R      49      L      44          3.198
LGA    G      50      D      45          4.854
LGA    Q      51      A      46          4.443
LGA    S      52      D      47           #
LGA    G      53      S      48          2.590
LGA    -       -      R      49           -
LGA    N      54      G      50          2.069
LGA    S      55      Q      51          1.662
LGA    -       -      S      52           -
LGA    L      56      G      53          1.741
LGA    F      57      N      54          2.900
LGA    T      58      S      55           #
LGA    -       -      L      56           -
LGA    L      59      F      57          2.089
LGA    E      60      T      58          2.151
LGA    -       -      L      59           -
LGA    A      61      E      60          4.522
LGA    H      62      A      61          2.670
LGA    I      63      H      62          4.647
LGA    N      64      I      63          1.976
LGA    Y      65      N      64          3.659
LGA    L      66      Y      65          1.274
LGA    H      67      L      66          3.487
LGA    E      68      H      67          3.142
LGA    -       -      E      68           -
LGA    V      69      V      69          2.555
LGA    K      70      K      70           #
LGA    L      71      L      71           -
LGA    G      72      G      72          3.817
LGA    T      73      T      73          3.864
LGA    E      74      E      74          4.702
LGA    V      75      V      75          4.154
LGA    W      76      W      76          3.048
LGA    V      77      V      77          2.489
LGA    Q      78      Q      78          3.363
LGA    T      79      T      79          3.127
LGA    Q      80      Q      80          4.807
LGA    I      81      I      81          1.922
LGA    L      82      L      82          4.517
LGA    G      83      G      83          2.077
LGA    F      84      F      84          2.130
LGA    D      85      D      85          2.471
LGA    R      86      R      86          2.602
LGA    K      87      K      87          3.182
LGA    R      88      R      88          2.227
LGA    L      89      L      89          1.273
LGA    H      90      H      90          0.634
LGA    V      91      V      91          1.384
LGA    Y      92      Y      92          0.952
LGA    H      93      H      93          2.715
LGA    S      94      S      94          1.916
LGA    L      95      L      95          2.677
LGA    H      96      H      96          1.744
LGA    -       -      R      97           -
LGA    -       -      A      98           -
LGA    R      97      G      99           #
LGA    A      98      F     100          2.189
LGA    G      99      D     101          4.721
LGA    F     100      -       -           -
LGA    D     101      E     102          2.181
LGA    E     102      V     103          3.119
LGA    V     103      L     104          2.366
LGA    L     104      A     105          2.090
LGA    A     105      A     106          4.776
LGA    A     106      S     107          3.570
LGA    S     107      E     108          5.130
LGA    E     108      Q     109          5.379
LGA    Q     109      -       -           -
LGA    M     110      -       -           -
LGA    L     111      M     110           #
LGA    L     112      L     111          2.664
LGA    H     113      L     112          3.841
LGA    -       -      H     113           -
LGA    V     114      V     114          1.535
LGA    D     115      D     115          2.274
LGA    L     116      L     116          1.121
LGA    A     117      Q     120           #
LGA    G     118      S     121           -
LGA    P     119      -       -           -
LGA    Q     120      -       -           -
LGA    S     121      -       -           -
LGA    A     122      A     122           #
LGA    P     123      P     123           #
LGA    F     124      F     124          3.312
LGA    G     125      G     125          2.122
LGA    H     126      H     126          2.029
LGA    T     127      T     127          1.849
LGA    T     128      T     128          1.639
LGA    V     129      V     129          2.604
LGA    C     130      C     130          2.846
LGA    R     131      R     131          2.268
LGA    L     132      L     132          3.003
LGA    N     133      N     133          3.933
LGA    H     134      H     134          3.535
LGA    L     135      L     135          3.359
LGA    V     136      V     136          4.568
LGA    E     137      E     137           #
LGA    Q     138      -       -           -
LGA    Q     139      -       -           -
LGA    E     140      Q     138          5.499
LGA    G     141      Q     139           -
LGA    A     142      E     140           -
LGA    Q     143      G     141           -
LGA    A     144      A     142           -
LGA    P     145      Q     143           -
LGA    Q     146      A     144           -
LGA    Y     147      P     145           -
LGA    M     148      Q     146           -
LGA    G     149      Y     147           -
LGA    R     150      M     148           -
LGA    T     151      G     149           -
LGA    I     152      R     150           -
LGA    K     153      T     151           -
LGA    L     154      I     152           -
LGA    P     155      K     153           -
LGA    A     156      L     154           -
LGA    -       -      P     155           -
LGA    -       -      A     156           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  156  153    5.0    108    3.06    64.81     38.472     3.416

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.092764 * X  +   0.990985 * Y  +  -0.096666 * Z  +  44.920578
  Y_new =  -0.470534 * X  +   0.041929 * Y  +   0.881385 * Z  +  11.537995
  Z_new =   0.877492 * X  +   0.127246 * Y  +   0.462402 * Z  +   5.454704 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.268538   -2.873055  [ DEG:    15.3861   -164.6139 ]
  Theta =  -1.070608   -2.070984  [ DEG:   -61.3413   -118.6587 ]
  Phi   =  -1.765447    1.376145  [ DEG:  -101.1527     78.8473 ]
 
# 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: T0364TS393_1                                  
REMARK     2: T0364.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0364TS393_1.T0364.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  156  153   5.0  108   3.06   64.81  38.472
REMARK  ---------------------------------------------------------- 
MOLECULE T0364TS393_1
PFRMAT TS
TARGET T0364
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      28.069   7.133  13.909  1.00 25.00           C
ATOM      2  CA  PRO     2      30.507   9.660  12.416  1.00 25.00           C
ATOM      3  CA  ALA     3      33.853  11.389  12.395  1.00 25.00           C
ATOM      4  CA  LEU     4      36.951  11.681  10.203  1.00 25.00           C
ATOM      5  CA  ILE     5      37.950  12.509   6.627  1.00 25.00           C
ATOM      6  CA  THR     6      37.519   9.789   4.073  1.00 25.00           C
ATOM      7  CA  TYR     7      39.749   8.398   1.264  1.00 25.00           C
ATOM      8  CA  ARG     8      38.869   5.803  -1.411  1.00 25.00           C
ATOM      9  CA  THR     9      40.896   2.665  -2.332  1.00 25.00           C
ATOM     10  CA  THR    10      43.110   1.437  -5.134  1.00 25.00           C
ATOM     11  CA  VAL    11      45.896  -1.232  -5.212  1.00 25.00           C
ATOM     12  CA  GLN    12      46.505  -4.065  -7.725  1.00 25.00           C
ATOM     13  CA  GLU    13      44.957  -6.736  -9.850  1.00 25.00           C
ATOM     14  CA  ASP    14      42.531  -8.859  -7.783  1.00 25.00           C
ATOM     15  CA  TRP    15      44.398  -7.914  -4.575  1.00 25.00           C
ATOM     16  CA  VAL    16      47.545  -9.585  -6.023  1.00 25.00           C
ATOM     17  CA  ASP    17      50.064 -12.247  -7.042  1.00 25.00           C
ATOM     18  CA  TYR    18      53.203 -14.338  -7.543  1.00 25.00           C
ATOM     19  CA  ASN    19      53.032 -15.922  -4.152  1.00 25.00           C
ATOM     20  CA  GLY    20      53.765 -13.672  -1.197  1.00 25.00           C
ATOM     21  CA  HIS    21      51.234 -10.796  -1.276  1.00 25.00           C
ATOM     22  CA  LEU    22      48.626  -8.146  -0.396  1.00 25.00           C
ATOM     23  CA  ARG    23      50.123  -8.595   3.135  1.00 25.00           C
ATOM     24  CA  ASP    24      52.775  -5.978   3.938  1.00 25.00           C
ATOM     25  CA  ALA    25      54.694  -3.557   1.673  1.00 25.00           C
ATOM     26  CA  PHE    26      51.708  -3.389  -0.719  1.00 25.00           C
ATOM     27  CA  TYR    27      49.362  -2.670   2.221  1.00 25.00           C
ATOM     28  CA  LEU    28      51.699   0.111   3.437  1.00 25.00           C
ATOM     29  CA  LEU    29      51.768   1.623  -0.080  1.00 25.00           C
ATOM     30  CA  ILE    30      47.943   1.516  -0.230  1.00 25.00           C
ATOM     31  CA  PHE    31      47.737   3.238   3.185  1.00 25.00           C
ATOM     32  CA  SER    32      50.170   5.947   1.994  1.00 25.00           C
ATOM     33  CA  TYR    33      48.067   6.482  -1.162  1.00 25.00           C
ATOM     34  CA  ALA    34      44.900   6.786   0.970  1.00 25.00           C
ATOM     35  CA  THR    35      46.638   9.343   3.231  1.00 25.00           C
ATOM     36  CA  ASP    36      47.737  11.348   0.159  1.00 25.00           C
ATOM     37  CA  ALA    37      44.152  11.293  -1.190  1.00 25.00           C
ATOM     38  CA  LEU    38      42.835  12.505   2.196  1.00 25.00           C
ATOM     39  CA  MET    39      45.412  15.338   2.213  1.00 25.00           C
ATOM     40  CA  ASP    40      44.370  16.340  -1.333  1.00 25.00           C
ATOM     41  CA  ARG    41      40.690  16.358  -0.274  1.00 25.00           C
ATOM     42  CA  ILE    42      41.545  18.548   2.751  1.00 25.00           C
ATOM     43  CA  GLY    43      44.838  20.452   2.640  1.00 25.00           C
ATOM     44  CA  LEU    44      45.952  18.838   5.874  1.00 25.00           C
ATOM     45  CA  ASP    45      47.985  18.122   9.026  1.00 25.00           C
ATOM     46  CA  ALA    46      50.473  20.779   7.972  1.00 25.00           C
ATOM     47  CA  ASP    47      52.845  21.284   5.009  1.00 25.00           C
ATOM     48  CA  SER    48      49.880  22.184   2.758  1.00 25.00           C
ATOM     49  CA  ARG    49      48.632  24.697   5.365  1.00 25.00           C
ATOM     50  CA  GLY    50      52.124  26.254   5.573  1.00 25.00           C
ATOM     51  CA  GLN    51      52.255  26.532   1.755  1.00 25.00           C
ATOM     52  CA  SER    52      56.059  26.460   2.091  1.00 25.00           C
ATOM     53  CA  GLY    53      56.314  24.169  -0.994  1.00 25.00           C
ATOM     54  CA  ASN    54      56.605  21.262   1.497  1.00 25.00           C
ATOM     55  CA  SER    55      53.511  19.825  -0.209  1.00 25.00           C
ATOM     56  CA  LEU    56      53.483  16.885   2.265  1.00 25.00           C
ATOM     57  CA  PHE    57      55.963  14.023   1.922  1.00 25.00           C
ATOM     58  CA  THR    58      56.078  11.306   4.593  1.00 25.00           C
ATOM     59  CA  LEU    59      58.711  10.792   7.250  1.00 25.00           C
ATOM     60  CA  GLU    60      56.850   9.778  10.360  1.00 25.00           C
ATOM     61  CA  ALA    61      53.572   7.875  10.338  1.00 25.00           C
ATOM     62  CA  HIS    62      51.427   5.054  11.626  1.00 25.00           C
ATOM     63  CA  ILE    63      51.132   2.182   9.090  1.00 25.00           C
ATOM     64  CA  ASN    64      50.661  -1.528   9.956  1.00 25.00           C
ATOM     65  CA  TYR    65      47.714  -3.659   8.842  1.00 25.00           C
ATOM     66  CA  LEU    66      45.421  -6.714   9.137  1.00 25.00           C
ATOM     67  CA  HIS    67      42.380  -8.407   7.585  1.00 25.00           C
ATOM     68  CA  GLU    68      40.613  -7.899   4.286  1.00 25.00           C
ATOM     69  CA  VAL    69      38.910  -5.959   1.425  1.00 25.00           C
ATOM     70  CA  LYS    70      35.406  -6.467   0.052  1.00 25.00           C
ATOM     71  CA  LEU    71      32.898  -5.254  -2.544  1.00 25.00           C
ATOM     72  CA  GLY    72      35.753  -3.777  -4.670  1.00 25.00           C
ATOM     73  CA  THR    73      35.605  -1.004  -2.061  1.00 25.00           C
ATOM     74  CA  GLU    74      37.728  -0.780   1.067  1.00 25.00           C
ATOM     75  CA  VAL    75      40.620   0.903   2.847  1.00 25.00           C
ATOM     76  CA  TRP    76      39.135   4.062   4.327  1.00 25.00           C
ATOM     77  CA  VAL    77      42.610   5.451   4.876  1.00 25.00           C
ATOM     78  CA  GLN    78      41.969   8.910   6.348  1.00 25.00           C
ATOM     79  CA  THR    79      43.834  11.776   7.949  1.00 25.00           C
ATOM     80  CA  GLN    80      42.106  15.042   9.036  1.00 25.00           C
ATOM     81  CA  ILE    81      43.918  15.487  12.336  1.00 25.00           C
ATOM     82  CA  LEU    82      45.994  16.927  15.230  1.00 25.00           C
ATOM     83  CA  GLY    83      49.175  16.776  17.383  1.00 25.00           C
ATOM     84  CA  PHE    84      50.035  20.235  16.147  1.00 25.00           C
ATOM     85  CA  ASP    85      51.347  21.225  19.608  1.00 25.00           C
ATOM     86  CA  ARG    86      54.880  21.685  18.369  1.00 25.00           C
ATOM     87  CA  LYS    87      55.355  18.805  15.958  1.00 25.00           C
ATOM     88  CA  ARG    88      53.328  18.258  12.765  1.00 25.00           C
ATOM     89  CA  LEU    89      51.003  15.311  11.978  1.00 25.00           C
ATOM     90  CA  HIS    90      50.064  12.490  14.393  1.00 25.00           C
ATOM     91  CA  VAL    91      47.807  11.448  11.509  1.00 25.00           C
ATOM     92  CA  TYR    92      45.407   8.750  12.756  1.00 25.00           C
ATOM     93  CA  HIS    93      42.196   7.423  11.073  1.00 25.00           C
ATOM     94  CA  SER    94      40.060   4.861   9.211  1.00 25.00           C
ATOM     95  CA  LEU    95      39.691   1.116   8.542  1.00 25.00           C
ATOM     96  CA  HIS    96      37.035  -0.511   6.357  1.00 25.00           C
ATOM     97  CA  ARG    97      33.605  -2.071   6.876  1.00 25.00           C
ATOM     98  CA  ALA    98      30.251  -3.245   8.144  1.00 25.00           C
ATOM     99  CA  GLY    99      29.601  -6.731   9.394  1.00 25.00           C
ATOM    100  CA  PHE   100      30.621  -6.467  13.098  1.00 25.00           C
ATOM    101  CA  ASP   101      33.775  -4.642  12.164  1.00 25.00           C
ATOM    102  CA  GLU   102      36.881  -4.536   9.980  1.00 25.00           C
ATOM    103  CA  VAL   103      40.672  -4.159   9.705  1.00 25.00           C
ATOM    104  CA  LEU   104      42.720  -2.764   6.908  1.00 25.00           C
ATOM    105  CA  ALA   105      45.205   0.031   6.377  1.00 25.00           C
ATOM    106  CA  ALA   106      44.659   1.017   9.986  1.00 25.00           C
ATOM    107  CA  SER   107      46.570   4.276   9.324  1.00 25.00           C
ATOM    108  CA  GLU   108      48.122   7.568   8.260  1.00 25.00           C
ATOM    109  CA  GLN   109      50.582   9.677   6.268  1.00 25.00           C
ATOM    110  CA  MET   110      49.383  13.230   6.303  1.00 25.00           C
ATOM    111  CA  LEU   111      52.880  13.898   7.503  1.00 25.00           C
ATOM    112  CA  LEU   112      55.897  14.940   9.567  1.00 25.00           C
ATOM    113  CA  HIS   113      56.473  18.551   8.532  1.00 25.00           C
ATOM    114  CA  VAL   114      59.981  17.840   7.214  1.00 25.00           C
ATOM    115  CA  ASP   115      60.268  21.054   5.310  1.00 25.00           C
ATOM    116  CA  LEU   116      62.394  22.431   2.485  1.00 25.00           C
ATOM    117  CA  ALA   117      65.921  23.778   1.779  1.00 25.00           C
ATOM    118  CA  GLY   118      68.114  26.360   3.601  1.00 25.00           C
ATOM    119  CA  PRO   119      67.197  26.221   7.289  1.00 25.00           C
ATOM    120  CA  GLN   120      65.604  28.223  10.099  1.00 25.00           C
ATOM    121  CA  SER   121      62.568  28.631  12.304  1.00 25.00           C
ATOM    122  CA  ALA   122      59.980  27.334  14.758  1.00 25.00           C
ATOM    123  CA  PRO   123      56.389  27.716  15.949  1.00 25.00           C
ATOM    124  CA  PHE   124      53.521  26.095  14.076  1.00 25.00           C
ATOM    125  CA  GLY   125      52.230  29.109  12.167  1.00 25.00           C
ATOM    126  CA  HIS   126      50.009  32.045  11.045  1.00 25.00           C
ATOM    127  CA  THR   127      47.905  30.807   8.095  1.00 25.00           C
ATOM    128  CA  THR   128      48.382  27.184   9.242  1.00 25.00           C
ATOM    129  CA  VAL   129      47.316  28.142  12.793  1.00 25.00           C
ATOM    130  CA  CYS   130      44.202  29.894  11.412  1.00 25.00           C
ATOM    131  CA  ARG   131      43.344  26.790   9.340  1.00 25.00           C
ATOM    132  CA  LEU   132      43.750  24.578  12.440  1.00 25.00           C
ATOM    133  CA  ASN   133      41.462  26.913  14.435  1.00 25.00           C
ATOM    134  CA  HIS   134      38.846  26.776  11.642  1.00 25.00           C
ATOM    135  CA  LEU   135      39.037  22.951  11.616  1.00 25.00           C
ATOM    136  CA  VAL   136      38.581  22.878  15.418  1.00 25.00           C
ATOM    137  CA  GLU   137      35.542  25.190  15.123  1.00 25.00           C
ATOM    138  CA  GLN   138      34.049  22.922  12.423  1.00 25.00           C
ATOM    139  CA  GLN   139      34.600  19.860  14.655  1.00 25.00           C
ATOM    140  CA  GLU   140      32.556  21.748  17.247  1.00 25.00           C
ATOM    141  CA  GLY   141      29.263  23.394  16.245  1.00 25.00           C
ATOM    142  CA  ALA   142      26.953  25.681  14.307  1.00 25.00           C
ATOM    143  CA  GLN   143      23.352  25.020  13.181  1.00 25.00           C
ATOM    144  CA  ALA   144      23.035  27.109  10.018  1.00 25.00           C
ATOM    145  CA  PRO   145      24.762  28.397   6.895  1.00 25.00           C
ATOM    146  CA  GLN   146      23.784  25.399   4.882  1.00 25.00           C
ATOM    147  CA  TYR   147      23.888  24.389   1.231  1.00 25.00           C
ATOM    148  CA  MET   148      22.999  27.942   0.350  1.00 25.00           C
ATOM    149  CA  GLY   149      25.276  28.677  -2.686  1.00 25.00           C
ATOM    150  CA  ARG   150      27.953  30.363  -4.742  1.00 25.00           C
ATOM    151  CA  THR   151      31.548  29.933  -5.710  1.00 25.00           C
ATOM    152  CA  ILE   152      32.937  26.918  -7.658  1.00 25.00           C
ATOM    153  CA  LYS   153      33.641  24.188 -10.232  1.00 25.00           C
ATOM    154  CA  LEU   154      36.070  21.698  -8.591  1.00 25.00           C
ATOM    155  CA  PRO   155      38.362  20.890 -11.462  1.00 25.00           C
ATOM    156  CA  ALA   156      40.521  17.877 -12.362  1.00 25.00           C
TER
END
