
#######################################################
#                                                     #
#                        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  147 (  147),  selected  147 , name T0303TS393_2-D1
# Molecule2: number of CA atoms  147 ( 1151),  selected  147 , name T0303_D1.pdb
# PARAMETERS: T0303TS393_2-D1.T0303_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.461
LGA    T       2      T       2          4.796
LGA    Q       3      Q       3          1.771
LGA    F       4      F       4          2.496
LGA    K       5      K       5           -
LGA    L       6      L       6          5.092
LGA    I       7      I       7          3.734
LGA    G       8      G       8          3.876
LGA    F       9      F       9          3.292
LGA    D      10      D      10          2.260
LGA    L      11      L      11          1.086
LGA    D      12      D      12          4.157
LGA    G      13      G      13          2.348
LGA    T      14      T      14          1.224
LGA    L      15      L      15          1.133
LGA    V      16      V      16          1.575
LGA    N      17      N      17           -
LGA    R      95      R      95          3.149
LGA    L      96      L      96          3.918
LGA    Y      97      Y      97          3.978
LGA    P      98      P      98          3.965
LGA    N      99      N      99          3.129
LGA    V     100      V     100          1.807
LGA    K     101      K     101          2.086
LGA    E     102      E     102          1.950
LGA    T     103      T     103          1.724
LGA    L     104      L     104          1.261
LGA    E     105      E     105          1.094
LGA    A     106      A     106          1.330
LGA    L     107      L     107          1.069
LGA    K     108      K     108          0.620
LGA    A     109      A     109          1.089
LGA    Q     110      Q     110          2.219
LGA    G     111      G     111          0.959
LGA    Y     112      Y     112          2.290
LGA    I     113      I     113          4.132
LGA    L     114      L     114          2.708
LGA    A     115      A     115          2.039
LGA    V     116      V     116          2.594
LGA    V     117      V     117          3.399
LGA    T     118      T     118          2.391
LGA    N     119      N     119           #
LGA    K     120      K     120           -
LGA    P     121      P     121           #
LGA    T     122      T     122          4.020
LGA    K     123      K     123          3.700
LGA    H     124      H     124          2.407
LGA    V     125      V     125          2.036
LGA    Q     126      Q     126          2.002
LGA    P     127      P     127          1.607
LGA    I     128      I     128          2.368
LGA    L     129      L     129          3.136
LGA    T     130      T     130          2.508
LGA    A     131      A     131          1.824
LGA    F     132      F     132          1.318
LGA    G     133      G     133          1.159
LGA    I     134      I     134          0.584
LGA    D     135      D     135          4.663
LGA    H     136      H     136          4.554
LGA    L     137      L     137          4.407
LGA    F     138      F     138          4.628
LGA    S     139      S     139           #
LGA    E     140      E     140          3.186
LGA    M     141      M     141          1.386
LGA    L     142      L     142          4.317
LGA    G     143      G     143          2.682
LGA    G     144      G     144          1.646
LGA    Q     145      Q     145          2.511
LGA    S     146      S     146          2.416
LGA    L     147      L     147          0.700
LGA    P     148      P     148          0.816
LGA    E     149      E     149          2.112
LGA    I     150      I     150          2.279
LGA    K     151      K     151          4.436
LGA    P     152      P     152          0.778
LGA    H     153      H     153          2.596
LGA    P     154      P     154          2.011
LGA    A     155      A     155          1.880
LGA    P     156      P     156          2.147
LGA    F     157      F     157          2.416
LGA    Y     158      Y     158          1.771
LGA    Y     159      Y     159          1.863
LGA    L     160      L     160          3.035
LGA    C     161      C     161          2.852
LGA    G     162      G     162          2.617
LGA    K     163      K     163          3.415
LGA    F     164      F     164          3.640
LGA    G     165      G     165          4.926
LGA    L     166      L     166          4.715
LGA    Y     167      Y     167          4.337
LGA    P     168      P     168          2.695
LGA    K     169      K     169          2.598
LGA    Q     170      Q     170          2.294
LGA    I     171      I     171          1.727
LGA    L     172      L     172          1.718
LGA    F     173      F     173          1.250
LGA    V     174      V     174          0.918
LGA    G     175      G     175          1.479
LGA    D     176      D     176          1.408
LGA    S     177      S     177          1.418
LGA    Q     178      Q     178          0.854
LGA    N     179      N     179          1.491
LGA    D     180      D     180          1.238
LGA    I     181      I     181          0.401
LGA    F     182      F     182          2.324
LGA    A     183      A     183          2.873
LGA    A     184      A     184          1.471
LGA    H     185      H     185          1.774
LGA    S     186      S     186          3.788
LGA    A     187      A     187          3.345
LGA    G     188      G     188          1.602
LGA    C     189      C     189          2.488
LGA    A     190      A     190          2.202
LGA    V     191      V     191          1.289
LGA    V     192      V     192          1.909
LGA    G     193      G     193          1.465
LGA    L     194      L     194          1.064
LGA    T     195      T     195           #
LGA    Y     196      Y     196          4.801
LGA    G     197      G     197          2.434
LGA    Y     198      Y     198          2.550
LGA    N     199      N     199          4.039
LGA    Y     200      Y     200           -
LGA    N     201      N     201           -
LGA    I     202      -       -           -
LGA    P     203      I     202          5.131
LGA    -       -      P     203           -
LGA    I     204      I     204          1.615
LGA    A     205      A     205          1.862
LGA    Q     206      Q     206          2.906
LGA    S     207      S     207          1.632
LGA    K     208      K     208          3.475
LGA    P     209      P     209          1.954
LGA    D     210      D     210          2.130
LGA    W     211      W     211          2.776
LGA    I     212      I     212          1.390
LGA    F     213      F     213          4.481
LGA    -       -      D     214           -
LGA    -       -      D     215           -
LGA    -       -      F     216           -
LGA    -       -      A     217           -
LGA    D     214      D     218          5.077
LGA    D     215      I     219          3.570
LGA    -       -      L     220           -
LGA    F     216      K     221           #
LGA    A     217      I     222           -
LGA    D     218      T     223           -
LGA    I     219      Q     224           -
LGA    L     220      -       -           -
LGA    K     221      -       -           -
LGA    I     222      -       -           -
LGA    T     223      -       -           -
LGA    Q     224      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  147  147    5.0    128    2.76    98.44     53.787     4.480

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.651682 * X  +  -0.751554 * Y  +  -0.102359 * Z  +  -8.858995
  Y_new =  -0.052662 * X  +   0.179457 * Y  +  -0.982355 * Z  +  79.382042
  Z_new =   0.756662 * X  +  -0.634793 * Y  +  -0.156527 * Z  +  17.964737 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.812553    1.329040  [ DEG:  -103.8516     76.1484 ]
  Theta =  -0.858192   -2.283401  [ DEG:   -49.1708   -130.8292 ]
  Phi   =  -3.060959    0.080634  [ DEG:  -175.3800      4.6200 ]
 
# 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: T0303TS393_2-D1                               
REMARK     2: T0303_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS393_2-D1.T0303_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  147  147   5.0  128   2.76   98.44  53.787
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS393_2-D1
PFRMAT TS
TARGET T0303
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -21.544  53.667   4.957  1.00 25.00           C
ATOM      2  CA  THR     2     -17.903  53.703   6.031  1.00 25.00           C
ATOM      3  CA  GLN     3     -15.130  55.920   7.298  1.00 25.00           C
ATOM      4  CA  PHE     4     -17.806  58.297   8.553  1.00 25.00           C
ATOM      5  CA  LYS     5     -18.953  61.925   7.921  1.00 25.00           C
ATOM      6  CA  LEU     6     -16.508  62.651  10.783  1.00 25.00           C
ATOM      7  CA  ILE     7     -16.669  66.298  11.721  1.00 25.00           C
ATOM      8  CA  GLY     8     -15.089  68.723  14.205  1.00 25.00           C
ATOM      9  CA  PHE     9     -14.754  70.554  17.512  1.00 25.00           C
ATOM     10  CA  ASP    10     -11.567  72.281  16.285  1.00 25.00           C
ATOM     11  CA  LEU    11     -10.545  75.060  18.572  1.00 25.00           C
ATOM     12  CA  ASP    12      -7.880  76.933  16.708  1.00 25.00           C
ATOM     13  CA  GLY    13     -10.405  79.597  15.771  1.00 25.00           C
ATOM     14  CA  THR    14     -13.810  77.939  16.101  1.00 25.00           C
ATOM     15  CA  LEU    15     -15.497  76.837  19.340  1.00 25.00           C
ATOM     16  CA  VAL    16     -14.062  79.824  21.172  1.00 25.00           C
ATOM     17  CA  ASN    17     -11.973  78.476  24.050  1.00 25.00           C
ATOM     95  CA  ARG    95     -18.230  83.471  26.031  1.00 25.00           C
ATOM     96  CA  LEU    96     -17.782  79.939  24.573  1.00 25.00           C
ATOM     97  CA  TYR    97     -19.726  80.295  21.325  1.00 25.00           C
ATOM     98  CA  PRO    98     -23.308  80.727  20.117  1.00 25.00           C
ATOM     99  CA  ASN    99     -23.172  77.133  19.068  1.00 25.00           C
ATOM    100  CA  VAL   100     -20.111  75.081  18.197  1.00 25.00           C
ATOM    101  CA  LYS   101     -21.125  73.172  21.358  1.00 25.00           C
ATOM    102  CA  GLU   102     -24.467  72.227  19.746  1.00 25.00           C
ATOM    103  CA  THR   103     -22.637  71.001  16.613  1.00 25.00           C
ATOM    104  CA  LEU   104     -20.274  68.909  18.781  1.00 25.00           C
ATOM    105  CA  GLU   105     -23.269  67.398  20.628  1.00 25.00           C
ATOM    106  CA  ALA   106     -24.934  66.551  17.286  1.00 25.00           C
ATOM    107  CA  LEU   107     -21.705  64.893  16.067  1.00 25.00           C
ATOM    108  CA  LYS   108     -21.504  62.852  19.301  1.00 25.00           C
ATOM    109  CA  ALA   109     -25.147  61.755  18.865  1.00 25.00           C
ATOM    110  CA  GLN   110     -24.351  58.121  17.952  1.00 25.00           C
ATOM    111  CA  GLY   111     -20.654  57.273  17.495  1.00 25.00           C
ATOM    112  CA  TYR   112     -17.380  59.175  18.256  1.00 25.00           C
ATOM    113  CA  ILE   113     -18.000  61.981  15.752  1.00 25.00           C
ATOM    114  CA  LEU   114     -14.773  63.928  16.278  1.00 25.00           C
ATOM    115  CA  ALA   115     -11.962  66.153  17.489  1.00 25.00           C
ATOM    116  CA  VAL   116      -8.770  68.231  17.752  1.00 25.00           C
ATOM    117  CA  VAL   117      -7.174  69.808  14.698  1.00 25.00           C
ATOM    118  CA  THR   118      -5.095  72.407  16.574  1.00 25.00           C
ATOM    119  CA  ASN   119      -3.255  69.991  18.945  1.00 25.00           C
ATOM    120  CA  LYS   120      -2.147  70.131  22.618  1.00 25.00           C
ATOM    121  CA  PRO   121      -1.286  71.929  25.869  1.00 25.00           C
ATOM    122  CA  THR   122      -4.188  69.928  27.400  1.00 25.00           C
ATOM    123  CA  LYS   123      -4.762  71.736  30.726  1.00 25.00           C
ATOM    124  CA  HIS   124      -6.317  74.705  28.872  1.00 25.00           C
ATOM    125  CA  VAL   125      -8.611  72.327  26.937  1.00 25.00           C
ATOM    126  CA  GLN   126      -9.669  70.645  30.212  1.00 25.00           C
ATOM    127  CA  PRO   127     -10.418  74.068  31.756  1.00 25.00           C
ATOM    128  CA  ILE   128     -12.509  75.021  28.693  1.00 25.00           C
ATOM    129  CA  LEU   129     -14.444  71.728  28.959  1.00 25.00           C
ATOM    130  CA  THR   130     -15.090  72.379  32.677  1.00 25.00           C
ATOM    131  CA  ALA   131     -16.340  75.907  31.868  1.00 25.00           C
ATOM    132  CA  PHE   132     -17.713  76.947  28.475  1.00 25.00           C
ATOM    133  CA  GLY   133     -20.374  74.271  27.945  1.00 25.00           C
ATOM    134  CA  ILE   134     -19.174  71.035  26.415  1.00 25.00           C
ATOM    135  CA  ASP   135     -19.062  67.428  25.350  1.00 25.00           C
ATOM    136  CA  HIS   136     -16.459  64.833  24.272  1.00 25.00           C
ATOM    137  CA  LEU   137     -15.469  67.027  21.294  1.00 25.00           C
ATOM    138  CA  PHE   138     -15.110  70.054  23.612  1.00 25.00           C
ATOM    139  CA  SER   139     -12.919  68.003  25.992  1.00 25.00           C
ATOM    140  CA  GLU   140     -10.733  66.884  23.054  1.00 25.00           C
ATOM    141  CA  MET   141      -7.492  68.823  22.741  1.00 25.00           C
ATOM    142  CA  LEU   142      -7.086  72.257  21.238  1.00 25.00           C
ATOM    143  CA  GLY   143      -4.088  74.632  21.627  1.00 25.00           C
ATOM    144  CA  GLY   144      -0.636  74.321  19.979  1.00 25.00           C
ATOM    145  CA  GLN   145       2.371  72.562  21.508  1.00 25.00           C
ATOM    146  CA  SER   146       2.942  69.732  24.028  1.00 25.00           C
ATOM    147  CA  LEU   147       3.658  67.285  21.195  1.00 25.00           C
ATOM    148  CA  PRO   148       6.123  69.186  19.059  1.00 25.00           C
ATOM    149  CA  GLU   149       6.528  70.963  15.663  1.00 25.00           C
ATOM    150  CA  ILE   150       3.356  73.051  15.653  1.00 25.00           C
ATOM    151  CA  LYS   151       3.062  75.114  12.467  1.00 25.00           C
ATOM    152  CA  PRO   152       0.897  73.112   9.985  1.00 25.00           C
ATOM    153  CA  HIS   153       2.648  70.400   7.960  1.00 25.00           C
ATOM    154  CA  PRO   154       1.892  67.813  10.621  1.00 25.00           C
ATOM    155  CA  ALA   155       3.032  66.345  13.969  1.00 25.00           C
ATOM    156  CA  PRO   156      -0.098  67.743  15.675  1.00 25.00           C
ATOM    157  CA  PHE   157      -2.302  66.213  12.942  1.00 25.00           C
ATOM    158  CA  TYR   158      -0.556  62.834  13.394  1.00 25.00           C
ATOM    159  CA  TYR   159      -1.110  63.025  17.178  1.00 25.00           C
ATOM    160  CA  LEU   160      -4.814  63.825  16.621  1.00 25.00           C
ATOM    161  CA  CYS   161      -5.124  60.843  14.238  1.00 25.00           C
ATOM    162  CA  GLY   162      -3.463  58.566  16.831  1.00 25.00           C
ATOM    163  CA  LYS   163      -5.880  59.826  19.521  1.00 25.00           C
ATOM    164  CA  PHE   164      -8.852  59.153  17.201  1.00 25.00           C
ATOM    165  CA  GLY   165     -10.363  55.704  17.623  1.00 25.00           C
ATOM    166  CA  LEU   166     -11.914  55.849  14.166  1.00 25.00           C
ATOM    167  CA  TYR   167      -8.379  55.473  12.876  1.00 25.00           C
ATOM    168  CA  PRO   168      -7.241  57.986  10.245  1.00 25.00           C
ATOM    169  CA  LYS   169     -10.172  57.672   7.799  1.00 25.00           C
ATOM    170  CA  GLN   170     -12.374  59.766  10.130  1.00 25.00           C
ATOM    171  CA  ILE   171     -11.103  63.207  11.029  1.00 25.00           C
ATOM    172  CA  LEU   172     -12.359  66.110   8.829  1.00 25.00           C
ATOM    173  CA  PHE   173     -10.786  68.672  11.138  1.00 25.00           C
ATOM    174  CA  VAL   174     -12.716  71.988  10.942  1.00 25.00           C
ATOM    175  CA  GLY   175     -11.094  75.222  12.242  1.00 25.00           C
ATOM    176  CA  ASP   176     -10.204  78.618  10.864  1.00 25.00           C
ATOM    177  CA  SER   177      -6.779  79.723   9.548  1.00 25.00           C
ATOM    178  CA  GLN   178      -4.888  77.460   7.198  1.00 25.00           C
ATOM    179  CA  ASN   179      -4.098  75.393  10.325  1.00 25.00           C
ATOM    180  CA  ASP   180      -7.359  73.433   9.882  1.00 25.00           C
ATOM    181  CA  ILE   181      -6.491  72.770   6.212  1.00 25.00           C
ATOM    182  CA  PHE   182      -3.006  71.550   7.232  1.00 25.00           C
ATOM    183  CA  ALA   183      -4.559  69.226   9.850  1.00 25.00           C
ATOM    184  CA  ALA   184      -6.978  67.842   7.223  1.00 25.00           C
ATOM    185  CA  HIS   185      -4.060  67.235   4.819  1.00 25.00           C
ATOM    186  CA  SER   186      -2.129  65.419   7.583  1.00 25.00           C
ATOM    187  CA  ALA   187      -5.036  63.079   8.223  1.00 25.00           C
ATOM    188  CA  GLY   188      -6.513  62.724   4.718  1.00 25.00           C
ATOM    189  CA  CYS   189     -10.271  63.037   5.416  1.00 25.00           C
ATOM    190  CA  ALA   190      -9.959  65.917   2.912  1.00 25.00           C
ATOM    191  CA  VAL   191     -11.695  68.825   4.653  1.00 25.00           C
ATOM    192  CA  VAL   192     -12.974  72.361   5.323  1.00 25.00           C
ATOM    193  CA  GLY   193     -12.221  75.787   6.938  1.00 25.00           C
ATOM    194  CA  LEU   194     -14.889  78.424   7.659  1.00 25.00           C
ATOM    195  CA  THR   195     -17.135  76.855  10.324  1.00 25.00           C
ATOM    196  CA  TYR   196     -17.808  79.470  13.002  1.00 25.00           C
ATOM    197  CA  GLY   197     -15.359  82.077  11.709  1.00 25.00           C
ATOM    198  CA  TYR   198     -11.895  83.522  11.316  1.00 25.00           C
ATOM    199  CA  ASN   199     -11.245  83.949   7.638  1.00 25.00           C
ATOM    200  CA  TYR   200     -14.975  83.549   6.762  1.00 25.00           C
ATOM    201  CA  ASN   201     -13.626  82.281   3.487  1.00 25.00           C
ATOM    202  CA  ILE   202     -13.181  82.127  -0.313  1.00 25.00           C
ATOM    203  CA  PRO   203      -9.375  82.123   0.107  1.00 25.00           C
ATOM    204  CA  ILE   204      -9.635  79.290   2.670  1.00 25.00           C
ATOM    205  CA  ALA   205     -11.846  77.288   0.268  1.00 25.00           C
ATOM    206  CA  GLN   206      -9.313  77.828  -2.553  1.00 25.00           C
ATOM    207  CA  SER   207      -6.026  77.574  -0.664  1.00 25.00           C
ATOM    208  CA  LYS   208      -6.014  73.847   0.168  1.00 25.00           C
ATOM    209  CA  PRO   209      -9.060  72.274   1.652  1.00 25.00           C
ATOM    210  CA  ASP   210     -11.422  70.091  -0.333  1.00 25.00           C
ATOM    211  CA  TRP   211     -14.069  72.680   0.433  1.00 25.00           C
ATOM    212  CA  ILE   212     -16.891  74.283   2.474  1.00 25.00           C
ATOM    213  CA  PHE   213     -19.539  72.122   4.119  1.00 25.00           C
ATOM    214  CA  ASP   214     -22.767  70.147   3.738  1.00 25.00           C
ATOM    215  CA  ASP   215     -23.817  71.353   7.130  1.00 25.00           C
ATOM    216  CA  PHE   216     -21.597  74.164   8.262  1.00 25.00           C
ATOM    217  CA  ALA   217     -23.436  76.617   5.967  1.00 25.00           C
ATOM    218  CA  ASP   218     -25.475  77.908   8.941  1.00 25.00           C
ATOM    219  CA  ILE   219     -22.262  78.377  10.972  1.00 25.00           C
ATOM    220  CA  LEU   220     -20.673  80.294   8.062  1.00 25.00           C
ATOM    221  CA  LYS   221     -23.773  82.530   7.811  1.00 25.00           C
ATOM    222  CA  ILE   222     -23.620  83.207  11.577  1.00 25.00           C
ATOM    223  CA  THR   223     -19.908  84.107  11.289  1.00 25.00           C
ATOM    224  CA  GLN   224     -17.163  86.610  10.394  1.00 25.00           C
TER
END
