
#######################################################
#                                                     #
#                        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  141 (  141),  selected  141 , name T0329TS393_4-D1
# Molecule2: number of CA atoms  141 ( 1070),  selected  141 , name T0329_D1.pdb
# PARAMETERS: T0329TS393_4-D1.T0329_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          5.020
LGA    K       2      K       2          1.706
LGA    Y       3      Y       3          2.353
LGA    K       4      K       4          2.874
LGA    -       -      A       5           -
LGA    A       5      A       6          3.780
LGA    A       6      I       7           #
LGA    I       7      F       8          2.294
LGA    F       8      D       9           #
LGA    D       9      M      10          3.625
LGA    M      10      -       -           -
LGA    D      11      -       -           -
LGA    G      12      D      11          1.445
LGA    T      13      G      12          0.987
LGA    I      14      T      13          1.556
LGA    L      15      I      14          3.337
LGA    -       -      L      15           -
LGA    D      16      D      16          4.563
LGA    G     109      -       -           -
LGA    P     110      G     109          2.334
LGA    F     111      P     110          2.782
LGA    P     112      F     111           #
LGA    G     113      P     112          4.696
LGA    -       -      G     113           -
LGA    I     114      I     114          2.073
LGA    L     115      L     115          2.571
LGA    D     116      D     116          2.182
LGA    L     117      L     117          1.379
LGA    M     118      M     118          1.641
LGA    K     119      K     119          1.629
LGA    N     120      N     120          1.479
LGA    L     121      L     121          1.583
LGA    R     122      R     122          1.571
LGA    Q     123      Q     123          1.594
LGA    K     124      K     124          1.256
LGA    G     125      G     125          1.522
LGA    V     126      V     126          1.891
LGA    K     127      K     127          2.149
LGA    L     128      L     128          2.070
LGA    A     129      A     129          2.839
LGA    V     130      V     130          3.044
LGA    V     131      V     131          3.652
LGA    S     132      S     132          2.051
LGA    N     133      N     133          3.300
LGA    K     134      K     134          3.903
LGA    P     135      P     135          3.623
LGA    N     136      N     136          2.031
LGA    E     137      E     137          1.142
LGA    A     138      A     138          1.406
LGA    V     139      V     139          2.054
LGA    Q     140      Q     140          2.375
LGA    V     141      V     141          2.574
LGA    L     142      L     142          3.307
LGA    V     143      V     143          3.551
LGA    E     144      E     144          3.233
LGA    E     145      E     145          4.448
LGA    L     146      L     146           #
LGA    F     147      F     147          4.372
LGA    P     148      P     148          1.365
LGA    G     149      G     149           #
LGA    S     150      S     150          2.754
LGA    F     151      F     151          3.210
LGA    D     152      D     152          1.969
LGA    F     153      F     153          2.637
LGA    A     154      A     154          1.701
LGA    L     155      L     155          2.463
LGA    G     156      G     156          3.539
LGA    R     163      R     163          3.321
LGA    K     164      K     164          4.454
LGA    P     165      P     165          2.565
LGA    A     166      A     166          2.838
LGA    P     167      P     167          2.700
LGA    D     168      D     168          1.472
LGA    M     169      M     169          0.572
LGA    T     170      T     170          1.285
LGA    S     171      S     171          2.035
LGA    E     172      E     172          1.403
LGA    C     173      C     173          0.714
LGA    V     174      V     174          2.104
LGA    K     175      K     175          1.985
LGA    V     176      V     176          0.423
LGA    L     177      L     177          1.254
LGA    G     178      G     178          2.136
LGA    V     179      V     179          0.740
LGA    P     180      P     180          1.383
LGA    R     181      R     181          2.683
LGA    D     182      D     182          3.596
LGA    K     183      K     183           #
LGA    C     184      C     184          4.515
LGA    V     185      V     185          2.710
LGA    Y     186      Y     186          2.138
LGA    I     187      I     187          3.190
LGA    G     188      G     188          1.801
LGA    D     189      D     189          3.108
LGA    S     190      S     190          2.674
LGA    E     191      E     191          2.229
LGA    I     192      I     192          1.939
LGA    D     193      D     193          0.690
LGA    I     194      I     194          1.227
LGA    Q     195      Q     195          1.629
LGA    T     196      T     196          1.553
LGA    A     197      A     197          1.313
LGA    R     198      R     198          0.892
LGA    N     199      N     199          1.548
LGA    S     200      S     200          1.306
LGA    E     201      E     201          2.595
LGA    M     202      M     202          2.589
LGA    D     203      D     203          2.284
LGA    E     204      E     204          1.358
LGA    I     205      I     205          2.750
LGA    A     206      A     206          4.492
LGA    V     207      V     207          3.183
LGA    N     208      N     208          4.408
LGA    W     209      W     209          3.602
LGA    G     210      G     210          2.990
LGA    F     211      F     211          3.127
LGA    R     212      R     212          0.537
LGA    S     213      S     213          1.618
LGA    V     214      V     214          2.875
LGA    P     215      P     215          2.298
LGA    F     216      F     216          2.404
LGA    L     217      L     217          3.731
LGA    Q     218      Q     218          4.500
LGA    K     219      K     219          4.714
LGA    H     220      H     220          1.582
LGA    G     221      G     221          2.031
LGA    A     222      A     222          3.994
LGA    T     223      T     223          3.205
LGA    V     224      -       -           -
LGA    I     225      V     224          3.435
LGA    V     226      I     225          2.359
LGA    D     227      V     226          2.745
LGA    T     228      D     227           -
LGA    A     229      -       -           -
LGA    E     230      -       -           -
LGA    K     231      -       -           -
LGA    L     232      T     228          4.259
LGA    E     233      A     229          5.275
LGA    E     234      E     230          3.542
LGA    A     235      K     231           #
LGA    I     236      L     232           -
LGA    L     237      E     233           -
LGA    G     238      E     234           -
LGA    E     239      A     235           -
LGA    -       -      I     236           -
LGA    -       -      L     237           -
LGA    -       -      G     238           -
LGA    -       -      E     239           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  141    5.0    122    2.73    88.52     50.797     4.311

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.680587 * X  +   0.394726 * Y  +   0.617246 * Z  +  -4.482078
  Y_new =   0.112695 * X  +   0.888837 * Y  +  -0.444149 * Z  +   9.324808
  Z_new =  -0.723948 * X  +  -0.232721 * Y  +  -0.649415 * Z  +  40.672432 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.797494    0.344099  [ DEG:  -160.2846     19.7154 ]
  Theta =   0.809509    2.332084  [ DEG:    46.3814    133.6186 ]
  Phi   =   2.977497   -0.164096  [ DEG:   170.5980     -9.4020 ]
 
# 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: T0329TS393_4-D1                               
REMARK     2: T0329_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS393_4-D1.T0329_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  141  141   5.0  122   2.73   88.52  50.797
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS393_4-D1
PFRMAT TS
TARGET T0329
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      19.741  -4.565  29.893  1.00 25.00           C
ATOM      2  CA  LYS     2      16.965  -2.637  31.552  1.00 25.00           C
ATOM      3  CA  TYR     3      15.028   0.589  31.758  1.00 25.00           C
ATOM      4  CA  LYS     4      16.402   1.938  35.019  1.00 25.00           C
ATOM      5  CA  ALA     5      13.227   1.236  36.936  1.00 25.00           C
ATOM      6  CA  ALA     6      10.656   3.406  38.785  1.00 25.00           C
ATOM      7  CA  ILE     7       7.527   5.627  38.376  1.00 25.00           C
ATOM      8  CA  PHE     8       5.727   5.606  41.772  1.00 25.00           C
ATOM      9  CA  ASP     9       5.226   9.389  41.411  1.00 25.00           C
ATOM     10  CA  MET    10       2.484  11.349  43.128  1.00 25.00           C
ATOM     11  CA  ASP    11      -0.864  12.728  41.944  1.00 25.00           C
ATOM     12  CA  GLY    12      -1.961  10.321  39.177  1.00 25.00           C
ATOM     13  CA  THR    13      -2.845   6.839  40.409  1.00 25.00           C
ATOM     14  CA  ILE    14       0.882   6.816  41.338  1.00 25.00           C
ATOM     15  CA  LEU    15       0.053   7.135  45.051  1.00 25.00           C
ATOM     16  CA  ASP    16      -1.552   3.809  45.949  1.00 25.00           C
ATOM    109  CA  GLY   109      -1.018  13.541  53.619  1.00 25.00           C
ATOM    110  CA  PRO   110      -0.239   9.795  53.254  1.00 25.00           C
ATOM    111  CA  PHE   111       0.959   9.998  49.650  1.00 25.00           C
ATOM    112  CA  PRO   112       4.326   9.211  51.254  1.00 25.00           C
ATOM    113  CA  GLY   113       3.705   5.705  50.002  1.00 25.00           C
ATOM    114  CA  ILE   114       5.448   4.932  46.757  1.00 25.00           C
ATOM    115  CA  LEU   115       8.402   6.868  48.238  1.00 25.00           C
ATOM    116  CA  ASP   116       9.739   3.653  49.835  1.00 25.00           C
ATOM    117  CA  LEU   117       9.427   1.829  46.481  1.00 25.00           C
ATOM    118  CA  MET   118      11.305   4.672  44.732  1.00 25.00           C
ATOM    119  CA  LYS   119      14.072   4.503  47.375  1.00 25.00           C
ATOM    120  CA  ASN   120      14.340   0.714  46.889  1.00 25.00           C
ATOM    121  CA  LEU   121      14.587   1.193  43.097  1.00 25.00           C
ATOM    122  CA  ARG   122      17.339   3.811  43.583  1.00 25.00           C
ATOM    123  CA  GLN   123      19.243   1.417  45.888  1.00 25.00           C
ATOM    124  CA  LYS   124      21.508   1.064  42.870  1.00 25.00           C
ATOM    125  CA  GLY   125      21.938   4.642  41.756  1.00 25.00           C
ATOM    126  CA  VAL   126      19.167   5.550  39.251  1.00 25.00           C
ATOM    127  CA  LYS   127      15.727   7.247  39.386  1.00 25.00           C
ATOM    128  CA  LEU   128      12.066   8.228  39.059  1.00 25.00           C
ATOM    129  CA  ALA   129       9.822   9.591  36.267  1.00 25.00           C
ATOM    130  CA  VAL   130       6.080  10.261  36.527  1.00 25.00           C
ATOM    131  CA  VAL   131       4.386  13.271  38.051  1.00 25.00           C
ATOM    132  CA  SER   132       1.615  11.933  35.732  1.00 25.00           C
ATOM    133  CA  ASN   133       0.829  13.081  32.199  1.00 25.00           C
ATOM    134  CA  LYS   134      -1.748  15.251  33.973  1.00 25.00           C
ATOM    135  CA  PRO   135       0.601  18.090  35.105  1.00 25.00           C
ATOM    136  CA  ASN   136       1.177  21.345  37.001  1.00 25.00           C
ATOM    137  CA  GLU   137       1.880  22.774  40.484  1.00 25.00           C
ATOM    138  CA  ALA   138       0.452  19.608  42.097  1.00 25.00           C
ATOM    139  CA  VAL   139       2.655  17.435  39.842  1.00 25.00           C
ATOM    140  CA  GLN   140       5.727  19.513  40.798  1.00 25.00           C
ATOM    141  CA  VAL   141       4.867  19.120  44.508  1.00 25.00           C
ATOM    142  CA  LEU   142       4.503  15.335  44.050  1.00 25.00           C
ATOM    143  CA  VAL   143       7.900  15.198  42.284  1.00 25.00           C
ATOM    144  CA  GLU   144       9.493  17.187  45.143  1.00 25.00           C
ATOM    145  CA  GLU   145       7.953  14.790  47.703  1.00 25.00           C
ATOM    146  CA  LEU   146       9.304  11.790  45.742  1.00 25.00           C
ATOM    147  CA  PHE   147      12.785  13.386  45.649  1.00 25.00           C
ATOM    148  CA  PRO   148      12.635  13.987  49.429  1.00 25.00           C
ATOM    149  CA  GLY   149      11.616  10.340  49.995  1.00 25.00           C
ATOM    150  CA  SER   150      14.529   9.161  47.805  1.00 25.00           C
ATOM    151  CA  PHE   151      15.169  10.109  44.195  1.00 25.00           C
ATOM    152  CA  ASP   152      15.638  12.106  41.009  1.00 25.00           C
ATOM    153  CA  PHE   153      12.416  13.510  39.587  1.00 25.00           C
ATOM    154  CA  ALA   154       9.545  14.867  37.532  1.00 25.00           C
ATOM    155  CA  LEU   155       8.816  16.902  34.391  1.00 25.00           C
ATOM    156  CA  GLY   156       5.186  16.335  33.519  1.00 25.00           C
ATOM    163  CA  ARG   163      -2.604  17.692  26.682  1.00 25.00           C
ATOM    164  CA  LYS   164      -3.202  14.916  29.188  1.00 25.00           C
ATOM    165  CA  PRO   165      -1.075  13.265  26.477  1.00 25.00           C
ATOM    166  CA  ALA   166       2.415  14.858  26.454  1.00 25.00           C
ATOM    167  CA  PRO   167       5.244  12.286  26.672  1.00 25.00           C
ATOM    168  CA  ASP   168       7.538  15.157  25.597  1.00 25.00           C
ATOM    169  CA  MET   169       7.858  16.297  29.239  1.00 25.00           C
ATOM    170  CA  THR   170       8.728  12.723  30.307  1.00 25.00           C
ATOM    171  CA  SER   171      11.379  12.518  27.551  1.00 25.00           C
ATOM    172  CA  GLU   172      12.865  15.857  28.698  1.00 25.00           C
ATOM    173  CA  CYS   173      12.971  14.596  32.312  1.00 25.00           C
ATOM    174  CA  VAL   174      14.724  11.389  31.167  1.00 25.00           C
ATOM    175  CA  LYS   175      17.283  13.458  29.207  1.00 25.00           C
ATOM    176  CA  VAL   176      17.916  15.640  32.291  1.00 25.00           C
ATOM    177  CA  LEU   177      18.411  12.507  34.437  1.00 25.00           C
ATOM    178  CA  GLY   178      21.240  11.184  32.259  1.00 25.00           C
ATOM    179  CA  VAL   179      19.386   8.728  29.996  1.00 25.00           C
ATOM    180  CA  PRO   180      19.556   7.733  26.269  1.00 25.00           C
ATOM    181  CA  ARG   181      15.799   8.415  26.407  1.00 25.00           C
ATOM    182  CA  ASP   182      15.434   4.878  27.828  1.00 25.00           C
ATOM    183  CA  LYS   183      15.083   6.308  31.363  1.00 25.00           C
ATOM    184  CA  CYS   184      13.175   5.743  34.627  1.00 25.00           C
ATOM    185  CA  VAL   185       9.800   4.325  33.594  1.00 25.00           C
ATOM    186  CA  TYR   186       6.533   6.197  33.053  1.00 25.00           C
ATOM    187  CA  ILE   187       3.405   5.841  35.133  1.00 25.00           C
ATOM    188  CA  GLY   188       0.727   3.986  37.010  1.00 25.00           C
ATOM    189  CA  ASP   189      -1.702   6.110  34.907  1.00 25.00           C
ATOM    190  CA  SER   190      -4.458   6.826  32.449  1.00 25.00           C
ATOM    191  CA  GLU   191      -3.705   6.276  28.766  1.00 25.00           C
ATOM    192  CA  ILE   192      -0.960   8.882  29.356  1.00 25.00           C
ATOM    193  CA  ASP   193       1.447   6.126  30.487  1.00 25.00           C
ATOM    194  CA  ILE   194       0.625   4.086  27.351  1.00 25.00           C
ATOM    195  CA  GLN   195       1.261   7.159  25.155  1.00 25.00           C
ATOM    196  CA  THR   196       4.621   7.742  26.900  1.00 25.00           C
ATOM    197  CA  ALA   197       5.576   4.075  26.336  1.00 25.00           C
ATOM    198  CA  ARG   198       4.643   4.376  22.634  1.00 25.00           C
ATOM    199  CA  ASN   199       6.769   7.546  22.330  1.00 25.00           C
ATOM    200  CA  SER   200       9.319   8.776  24.893  1.00 25.00           C
ATOM    201  CA  GLU   201      11.593   5.833  24.535  1.00 25.00           C
ATOM    202  CA  MET   202      10.389   4.979  28.014  1.00 25.00           C
ATOM    203  CA  ASP   203      10.824   1.337  28.936  1.00 25.00           C
ATOM    204  CA  GLU   204       7.218   1.384  30.242  1.00 25.00           C
ATOM    205  CA  ILE   205       4.159   1.270  32.480  1.00 25.00           C
ATOM    206  CA  ALA   206       5.149   1.160  36.151  1.00 25.00           C
ATOM    207  CA  VAL   207       3.022   0.517  39.170  1.00 25.00           C
ATOM    208  CA  ASN   208      -0.276   0.844  40.939  1.00 25.00           C
ATOM    209  CA  TRP   209      -2.705  -1.729  39.548  1.00 25.00           C
ATOM    210  CA  GLY   210      -5.260   0.428  41.357  1.00 25.00           C
ATOM    211  CA  PHE   211      -4.945   2.779  38.370  1.00 25.00           C
ATOM    212  CA  ARG   212      -7.733   2.413  35.894  1.00 25.00           C
ATOM    213  CA  SER   213      -9.410  -0.628  37.423  1.00 25.00           C
ATOM    214  CA  VAL   214      -7.376  -3.854  37.884  1.00 25.00           C
ATOM    215  CA  PRO   215      -8.216  -5.154  34.380  1.00 25.00           C
ATOM    216  CA  PHE   216      -7.501  -1.696  32.899  1.00 25.00           C
ATOM    217  CA  LEU   217      -4.144  -1.575  34.738  1.00 25.00           C
ATOM    218  CA  GLN   218      -3.259  -5.053  33.401  1.00 25.00           C
ATOM    219  CA  LYS   219      -4.157  -3.943  29.848  1.00 25.00           C
ATOM    220  CA  HIS   220      -6.160  -1.911  27.266  1.00 25.00           C
ATOM    221  CA  GLY   221      -2.738  -0.600  26.250  1.00 25.00           C
ATOM    222  CA  ALA   222       0.976  -1.273  25.804  1.00 25.00           C
ATOM    223  CA  THR   223       3.186  -3.051  28.293  1.00 25.00           C
ATOM    224  CA  VAL   224       0.413  -1.765  30.542  1.00 25.00           C
ATOM    225  CA  ILE   225       1.797  -3.286  33.740  1.00 25.00           C
ATOM    226  CA  VAL   226       1.336  -4.315  37.359  1.00 25.00           C
ATOM    227  CA  ASP   227       2.765  -7.821  37.590  1.00 25.00           C
ATOM    228  CA  THR   228       6.094  -8.589  35.818  1.00 25.00           C
ATOM    229  CA  ALA   229       7.662  -6.433  38.530  1.00 25.00           C
ATOM    230  CA  GLU   230       7.799  -8.844  41.503  1.00 25.00           C
ATOM    231  CA  LYS   231       8.966  -6.000  43.787  1.00 25.00           C
ATOM    232  CA  LEU   232       6.096  -3.791  42.543  1.00 25.00           C
ATOM    233  CA  GLU   233       3.598  -6.616  43.212  1.00 25.00           C
ATOM    234  CA  GLU   234       5.007  -7.059  46.745  1.00 25.00           C
ATOM    235  CA  ALA   235       4.687  -3.293  47.371  1.00 25.00           C
ATOM    236  CA  ILE   236       1.061  -3.373  46.142  1.00 25.00           C
ATOM    237  CA  LEU   237      -0.015  -3.797  49.777  1.00 25.00           C
ATOM    238  CA  GLY   238      -2.835  -1.786  51.300  1.00 25.00           C
ATOM    239  CA  GLU   239      -4.957   1.144  50.126  1.00 25.00           C
TER
END
