
#######################################################
#                                                     #
#                        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  142 (  142),  selected  142 , name T0378TS393_5-D2
# Molecule2: number of CA atoms  142 ( 1079),  selected  142 , name T0378_D2.pdb
# PARAMETERS: T0378TS393_5-D2.T0378_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     100      G     100          1.103
LGA    L     101      L     101          0.573
LGA    T     102      T     102          3.077
LGA    L     103      L     103          3.165
LGA    L     104      L     104          2.627
LGA    L     105      L     105          1.403
LGA    D     106      D     106          1.561
LGA    G     107      G     107          1.409
LGA    V     108      V     108          0.674
LGA    Q     109      Q     109          2.277
LGA    D     110      D     110          1.112
LGA    P     111      P     111          2.157
LGA    G     112      G     112          2.050
LGA    N     113      N     113          1.968
LGA    V     114      V     114          1.943
LGA    G     115      G     115          2.010
LGA    T     116      T     116          2.137
LGA    I     117      I     117          2.069
LGA    L     118      L     118          2.021
LGA    R     119      R     119          2.263
LGA    T     120      T     120          2.488
LGA    A     121      A     121          2.342
LGA    D     122      D     122          2.498
LGA    W     123      W     123          3.040
LGA    F     124      F     124          1.946
LGA    G     125      G     125          2.644
LGA    I     126      I     126          2.718
LGA    R     127      R     127          1.125
LGA    H     128      H     128          1.539
LGA    V     129      V     129          1.985
LGA    W     130      W     130          0.958
LGA    L     131      L     131          1.714
LGA    G     132      G     132          1.632
LGA    T     133      T     133          1.806
LGA    G     134      G     134          2.186
LGA    S     135      S     135          3.936
LGA    A     136      A     136          2.735
LGA    D     137      D     137          2.806
LGA    V     138      V     138          3.097
LGA    F     139      F     139          2.639
LGA    S     140      S     140          1.608
LGA    P     141      P     141          1.449
LGA    K     142      K     142          1.148
LGA    V     143      V     143          1.159
LGA    V     144      V     144          1.064
LGA    Q     145      Q     145          1.878
LGA    A     146      A     146          1.921
LGA    S     147      S     147          0.917
LGA    M     148      M     148          1.552
LGA    G     149      G     149          0.932
LGA    A     150      A     150          2.025
LGA    L     151      L     151          2.260
LGA    A     152      A     152          4.135
LGA    R     153      R     153          1.648
LGA    V     154      V     154          0.605
LGA    Q     155      Q     155          0.884
LGA    P     156      P     156          0.646
LGA    T     157      T     157          1.005
LGA    P     158      P     158          1.515
LGA    L     159      L     159          0.441
LGA    K     160      K     160          1.155
LGA    N     161      N     161          0.705
LGA    T     162      T     162          0.841
LGA    V     163      V     163          1.825
LGA    D     164      D     164          1.738
LGA    T     165      T     165          1.409
LGA    L     166      L     166          1.698
LGA    A     167      A     167          3.470
LGA    Y     168      Y     168          3.829
LGA    F     169      F     169          3.105
LGA    R     170      R     170          4.046
LGA    R     171      R     171           #
LGA    Q     172      Q     172          3.937
LGA    G     173      G     173          4.060
LGA    I     174      I     174          2.333
LGA    P     175      P     175          3.075
LGA    V     176      V     176          1.381
LGA    Y     177      Y     177          1.617
LGA    G     178      G     178          2.281
LGA    A     179      A     179          2.208
LGA    F     180      F     180          3.952
LGA    L     181      L     181          3.338
LGA    D     182      D     182          2.340
LGA    G     183      -       -           -
LGA    Q     184      G     183          2.262
LGA    S     185      Q     184          2.123
LGA    L     186      S     185          1.605
LGA    Y     187      L     186          1.489
LGA    E     188      Y     187          2.467
LGA    A     189      -       -           -
LGA    P     190      E     188          3.194
LGA    L     191      A     189          2.561
LGA    P     192      P     190          2.889
LGA    N     193      L     191          3.536
LGA    F     194      P     192          2.068
LGA    T     195      N     193          2.099
LGA    -       -      F     194           -
LGA    -       -      T     195           -
LGA    E     196      E     196          3.818
LGA    P     197      P     197          5.108
LGA    A     198      A     198          1.399
LGA    I     199      I     199          2.048
LGA    L     200      L     200          2.096
LGA    V     201      V     201          1.367
LGA    L     202      L     202          1.432
LGA    G     203      G     203          2.987
LGA    S     204      S     204          0.707
LGA    E     205      E     205          2.667
LGA    G     206      G     206          1.690
LGA    R     207      R     207          1.747
LGA    G     208      G     208          1.645
LGA    I     209      I     209          1.552
LGA    S     210      S     210          0.709
LGA    P     211      P     211          1.155
LGA    E     212      E     212          1.314
LGA    V     213      V     213          1.448
LGA    A     214      A     214          0.988
LGA    A     215      A     215          0.520
LGA    E     216      E     216          0.746
LGA    I     217      I     217          1.256
LGA    T     218      T     218          2.106
LGA    D     219      D     219          4.266
LGA    R     220      R     220          4.286
LGA    L     221      L     221           #
LGA    T     222      T     222          4.639
LGA    I     223      I     223          1.918
LGA    L     237      L     237          2.102
LGA    N     238      N     238          1.547
LGA    V     239      V     239          3.198
LGA    A     240      A     240          2.555
LGA    I     241      I     241          1.853
LGA    A     242      A     242          2.020
LGA    T     243      T     243          1.880
LGA    A     244      A     244          1.075
LGA    I     245      I     245          1.078
LGA    L     246      L     246          1.787
LGA    C     247      C     247          1.208
LGA    S     248      S     248          1.225
LGA    E     249      E     249          2.352
LGA    W     250      W     250          1.901
LGA    R     251      R     251          1.553
LGA    R     252      R     252          3.222
LGA    R     253      R     253          1.839
LGA    S     254      S     254          0.930

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    138    2.26    92.75     68.217     5.856

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.583702 * X  +  -0.728947 * Y  +   0.357671 * Z  +  20.738588
  Y_new =  -0.206805 * X  +  -0.292506 * Y  +  -0.933634 * Z  +   9.380757
  Z_new =   0.785190 * X  +  -0.618932 * Y  +   0.019986 * Z  +  45.881996 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.538516    1.603077  [ DEG:   -88.1505     91.8495 ]
  Theta =  -0.903003   -2.238590  [ DEG:   -51.7383   -128.2617 ]
  Phi   =  -2.801094    0.340499  [ DEG:  -160.4908     19.5092 ]
 
# 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: T0378TS393_5-D2                               
REMARK     2: T0378_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS393_5-D2.T0378_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  138   2.26   92.75  68.217
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS393_5-D2
PFRMAT TS
TARGET T0378
MODEL 5
PARENT N/A
ATOM    100  CA  GLY   100      19.030  -7.134  47.864  1.00 25.00           C
ATOM    101  CA  LEU   101      20.712  -4.588  45.513  1.00 25.00           C
ATOM    102  CA  THR   102      20.855  -1.035  44.288  1.00 25.00           C
ATOM    103  CA  LEU   103      21.307   2.627  43.380  1.00 25.00           C
ATOM    104  CA  LEU   104      24.939   3.686  43.906  1.00 25.00           C
ATOM    105  CA  LEU   105      26.983   6.444  42.434  1.00 25.00           C
ATOM    106  CA  ASP   106      30.631   6.459  43.423  1.00 25.00           C
ATOM    107  CA  GLY   107      31.883  10.020  43.208  1.00 25.00           C
ATOM    108  CA  VAL   108      28.800  10.942  41.122  1.00 25.00           C
ATOM    109  CA  GLN   109      28.140  13.763  38.675  1.00 25.00           C
ATOM    110  CA  ASP   110      25.106  15.214  36.898  1.00 25.00           C
ATOM    111  CA  PRO   111      22.731  14.285  39.647  1.00 25.00           C
ATOM    112  CA  GLY   112      20.307  13.310  36.847  1.00 25.00           C
ATOM    113  CA  ASN   113      21.958   9.864  36.585  1.00 25.00           C
ATOM    114  CA  VAL   114      21.652   9.402  40.374  1.00 25.00           C
ATOM    115  CA  GLY   115      17.951  10.374  40.219  1.00 25.00           C
ATOM    116  CA  THR   116      17.386   7.864  37.381  1.00 25.00           C
ATOM    117  CA  ILE   117      19.127   5.130  39.421  1.00 25.00           C
ATOM    118  CA  LEU   118      16.930   5.956  42.448  1.00 25.00           C
ATOM    119  CA  ARG   119      13.796   5.769  40.256  1.00 25.00           C
ATOM    120  CA  THR   120      14.924   2.374  38.889  1.00 25.00           C
ATOM    121  CA  ALA   121      15.510   1.105  42.455  1.00 25.00           C
ATOM    122  CA  ASP   122      12.021   2.306  43.482  1.00 25.00           C
ATOM    123  CA  TRP   123      10.490   0.524  40.458  1.00 25.00           C
ATOM    124  CA  PHE   124      12.848  -2.400  40.436  1.00 25.00           C
ATOM    125  CA  GLY   125      12.412  -4.500  43.576  1.00 25.00           C
ATOM    126  CA  ILE   126      15.543  -3.331  45.386  1.00 25.00           C
ATOM    127  CA  ARG   127      15.098  -0.936  48.322  1.00 25.00           C
ATOM    128  CA  HIS   128      18.553   0.421  48.833  1.00 25.00           C
ATOM    129  CA  VAL   129      21.438   2.754  48.039  1.00 25.00           C
ATOM    130  CA  TRP   130      24.294   4.989  49.305  1.00 25.00           C
ATOM    131  CA  LEU   131      24.584   7.994  46.919  1.00 25.00           C
ATOM    132  CA  GLY   132      28.308   8.584  47.410  1.00 25.00           C
ATOM    133  CA  THR   133      30.398  11.278  49.089  1.00 25.00           C
ATOM    134  CA  GLY   134      32.325  14.023  47.361  1.00 25.00           C
ATOM    135  CA  SER   135      31.122  15.176  43.951  1.00 25.00           C
ATOM    136  CA  ALA   136      27.366  14.823  43.478  1.00 25.00           C
ATOM    137  CA  ASP   137      24.207  16.700  44.408  1.00 25.00           C
ATOM    138  CA  VAL   138      22.244  14.083  46.330  1.00 25.00           C
ATOM    139  CA  PHE   139      19.520  16.676  47.146  1.00 25.00           C
ATOM    140  CA  SER   140      19.579  19.956  45.220  1.00 25.00           C
ATOM    141  CA  PRO   141      16.398  20.204  43.129  1.00 25.00           C
ATOM    142  CA  LYS   142      17.726  19.027  39.736  1.00 25.00           C
ATOM    143  CA  VAL   143      18.011  15.445  41.063  1.00 25.00           C
ATOM    144  CA  VAL   144      14.416  15.618  42.370  1.00 25.00           C
ATOM    145  CA  GLN   145      13.212  16.891  38.964  1.00 25.00           C
ATOM    146  CA  ALA   146      15.058  14.027  37.215  1.00 25.00           C
ATOM    147  CA  SER   147      13.452  11.501  39.604  1.00 25.00           C
ATOM    148  CA  MET   148       9.815  12.271  38.897  1.00 25.00           C
ATOM    149  CA  GLY   149       8.972  10.635  42.257  1.00 25.00           C
ATOM    150  CA  ALA   150      11.421   8.792  44.509  1.00 25.00           C
ATOM    151  CA  LEU   151      13.812   9.920  47.280  1.00 25.00           C
ATOM    152  CA  ALA   152      11.960   7.717  49.807  1.00 25.00           C
ATOM    153  CA  ARG   153      11.327   4.210  48.508  1.00 25.00           C
ATOM    154  CA  VAL   154      14.629   4.693  46.817  1.00 25.00           C
ATOM    155  CA  GLN   155      16.471   5.332  50.068  1.00 25.00           C
ATOM    156  CA  PRO   156      19.325   7.743  49.589  1.00 25.00           C
ATOM    157  CA  THR   157      22.188   8.829  51.949  1.00 25.00           C
ATOM    158  CA  PRO   158      25.525  10.356  51.075  1.00 25.00           C
ATOM    159  CA  LEU   159      27.656   8.643  53.638  1.00 25.00           C
ATOM    160  CA  LYS   160      29.907  11.264  55.334  1.00 25.00           C
ATOM    161  CA  ASN   161      32.785   8.806  54.830  1.00 25.00           C
ATOM    162  CA  THR   162      32.758   5.678  52.593  1.00 25.00           C
ATOM    163  CA  VAL   163      35.030   2.870  53.867  1.00 25.00           C
ATOM    164  CA  ASP   164      33.313   2.999  57.288  1.00 25.00           C
ATOM    165  CA  THR   165      29.881   2.811  55.600  1.00 25.00           C
ATOM    166  CA  LEU   166      31.032  -0.205  53.539  1.00 25.00           C
ATOM    167  CA  ALA   167      32.308  -1.921  56.717  1.00 25.00           C
ATOM    168  CA  TYR   168      28.956  -1.261  58.448  1.00 25.00           C
ATOM    169  CA  PHE   169      27.088  -2.726  55.443  1.00 25.00           C
ATOM    170  CA  ARG   170      29.331  -5.828  55.530  1.00 25.00           C
ATOM    171  CA  ARG   171      28.664  -6.237  59.278  1.00 25.00           C
ATOM    172  CA  GLN   172      26.938  -9.453  58.371  1.00 25.00           C
ATOM    173  CA  GLY   173      26.727 -10.399  54.741  1.00 25.00           C
ATOM    174  CA  ILE   174      26.269  -7.804  51.942  1.00 25.00           C
ATOM    175  CA  PRO   175      29.152  -5.979  50.242  1.00 25.00           C
ATOM    176  CA  VAL   176      31.004  -3.805  47.729  1.00 25.00           C
ATOM    177  CA  TYR   177      30.311  -3.462  44.021  1.00 25.00           C
ATOM    178  CA  GLY   178      30.798  -3.271  40.248  1.00 25.00           C
ATOM    179  CA  ALA   179      30.715  -2.345  36.602  1.00 25.00           C
ATOM    180  CA  PHE   180      33.777  -3.993  35.204  1.00 25.00           C
ATOM    181  CA  LEU   181      36.458  -3.594  32.544  1.00 25.00           C
ATOM    182  CA  ASP   182      39.034  -0.962  33.657  1.00 25.00           C
ATOM    183  CA  GLY   183      40.505  -3.906  35.533  1.00 25.00           C
ATOM    184  CA  GLN   184      38.767  -7.068  36.765  1.00 25.00           C
ATOM    185  CA  SER   185      37.038  -8.820  33.870  1.00 25.00           C
ATOM    186  CA  LEU   186      33.423  -9.885  33.349  1.00 25.00           C
ATOM    187  CA  TYR   187      30.377  -7.739  33.770  1.00 25.00           C
ATOM    188  CA  GLU   188      27.072  -9.124  32.478  1.00 25.00           C
ATOM    189  CA  ALA   189      25.931 -12.552  33.747  1.00 25.00           C
ATOM    190  CA  PRO   190      29.053 -12.801  35.953  1.00 25.00           C
ATOM    191  CA  LEU   191      31.344 -11.657  38.827  1.00 25.00           C
ATOM    192  CA  PRO   192      30.382 -14.823  40.615  1.00 25.00           C
ATOM    193  CA  ASN   193      26.829 -15.768  41.511  1.00 25.00           C
ATOM    194  CA  PHE   194      24.498 -12.819  42.072  1.00 25.00           C
ATOM    195  CA  THR   195      21.624 -12.439  44.498  1.00 25.00           C
ATOM    196  CA  GLU   196      23.842 -11.667  47.401  1.00 25.00           C
ATOM    197  CA  PRO   197      24.833  -8.516  45.576  1.00 25.00           C
ATOM    198  CA  ALA   198      25.403  -5.240  47.423  1.00 25.00           C
ATOM    199  CA  ILE   199      25.726  -1.616  46.235  1.00 25.00           C
ATOM    200  CA  LEU   200      25.890  -1.068  42.432  1.00 25.00           C
ATOM    201  CA  VAL   201      28.974   1.145  42.208  1.00 25.00           C
ATOM    202  CA  LEU   202      29.267   3.238  39.041  1.00 25.00           C
ATOM    203  CA  GLY   203      29.583   6.804  37.774  1.00 25.00           C
ATOM    204  CA  SER   204      32.208   9.582  37.626  1.00 25.00           C
ATOM    205  CA  GLU   205      32.277  11.205  34.220  1.00 25.00           C
ATOM    206  CA  GLY   206      35.870  10.393  33.315  1.00 25.00           C
ATOM    207  CA  ARG   207      38.242   9.082  35.991  1.00 25.00           C
ATOM    208  CA  GLY   208      35.789   6.130  36.112  1.00 25.00           C
ATOM    209  CA  ILE   209      36.111   6.010  39.863  1.00 25.00           C
ATOM    210  CA  SER   210      37.911   7.260  42.965  1.00 25.00           C
ATOM    211  CA  PRO   211      40.582   4.556  43.524  1.00 25.00           C
ATOM    212  CA  GLU   212      39.544   4.407  47.208  1.00 25.00           C
ATOM    213  CA  VAL   213      36.147   2.942  46.217  1.00 25.00           C
ATOM    214  CA  ALA   214      37.887   0.312  44.044  1.00 25.00           C
ATOM    215  CA  ALA   215      40.202  -0.597  46.956  1.00 25.00           C
ATOM    216  CA  GLU   216      37.180  -0.938  49.284  1.00 25.00           C
ATOM    217  CA  ILE   217      36.335  -3.945  47.113  1.00 25.00           C
ATOM    218  CA  THR   218      36.459  -6.605  44.362  1.00 25.00           C
ATOM    219  CA  ASP   219      36.649  -4.431  41.246  1.00 25.00           C
ATOM    220  CA  ARG   220      35.896  -1.456  38.977  1.00 25.00           C
ATOM    221  CA  LEU   221      34.887   0.679  36.049  1.00 25.00           C
ATOM    222  CA  THR   222      32.817   0.225  32.915  1.00 25.00           C
ATOM    223  CA  ILE   223      31.649  -2.468  30.450  1.00 25.00           C
ATOM    237  CA  LEU   237      28.090   5.567  28.324  1.00 25.00           C
ATOM    238  CA  ASN   238      28.842   8.461  30.714  1.00 25.00           C
ATOM    239  CA  VAL   239      25.570   8.399  32.729  1.00 25.00           C
ATOM    240  CA  ALA   240      21.847   7.507  32.811  1.00 25.00           C
ATOM    241  CA  ILE   241      22.397   4.858  30.100  1.00 25.00           C
ATOM    242  CA  ALA   242      25.322   3.392  32.090  1.00 25.00           C
ATOM    243  CA  THR   243      23.148   3.272  35.242  1.00 25.00           C
ATOM    244  CA  ALA   244      20.370   1.501  33.288  1.00 25.00           C
ATOM    245  CA  ILE   245      22.900  -1.041  31.947  1.00 25.00           C
ATOM    246  CA  LEU   246      24.192  -1.667  35.497  1.00 25.00           C
ATOM    247  CA  CYS   247      20.605  -2.185  36.737  1.00 25.00           C
ATOM    248  CA  SER   248      19.952  -4.658  33.887  1.00 25.00           C
ATOM    249  CA  GLU   249      23.157  -6.559  34.769  1.00 25.00           C
ATOM    250  CA  TRP   250      22.090  -6.704  38.443  1.00 25.00           C
ATOM    251  CA  ARG   251      18.647  -8.031  37.417  1.00 25.00           C
ATOM    252  CA  ARG   252      20.302 -10.704  35.230  1.00 25.00           C
ATOM    253  CA  ARG   253      20.451 -13.675  37.609  1.00 25.00           C
ATOM    254  CA  SER   254      17.035 -12.653  38.897  1.00 25.00           C
TER
END
