
#######################################################
#                                                     #
#                        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  113 (  113),  selected  113 , name T0338TS168_4-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS168_4-D2.T0338_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     144      E     144          3.621
LGA    H     145      H     145          1.054
LGA    P     146      P     146          3.024
LGA    H     147      H     147          1.331
LGA    T     148      T     148          2.248
LGA    D     149      D     149          2.025
LGA    V     150      V     150          0.887
LGA    V     151      V     151          0.999
LGA    K     152      K     152          2.336
LGA    C     153      C     153          2.438
LGA    T     154      T     154          1.187
LGA    Q     155      Q     155          1.085
LGA    L     156      L     156          2.783
LGA    V     157      V     157          3.200
LGA    -       -      R     158           -
LGA    R     158      A     159          2.503
LGA    A     159      S     160          1.631
LGA    S     160      K     161          4.287
LGA    K     161      D     162          1.852
LGA    D     162      L     163          1.423
LGA    L     163      A     164          1.243
LGA    A     164      Q     165          1.694
LGA    Q     165      T     166          1.671
LGA    T     166      S     167          0.909
LGA    S     167      Y     168          1.028
LGA    Y     168      F     169          1.545
LGA    F     169      M     170          1.579
LGA    M     170      A     171          0.992
LGA    A     171      T     172          0.531
LGA    T     172      N     173          1.860
LGA    N     173      S     174          2.312
LGA    S     174      L     175          2.131
LGA    L     175      H     176          2.102
LGA    H     176      L     177          4.577
LGA    L     177      T     178          1.724
LGA    T     178      T     179           #
LGA    T     179      F     180          3.620
LGA    F     180      C     181          3.632
LGA    C     181      L     182          3.106
LGA    L     182      Q     183           #
LGA    Q     183      Y     184          4.138
LGA    Y     184      K     185          2.401
LGA    -       -      P     186           -
LGA    -       -      T     187           -
LGA    K     185      V     188           #
LGA    P     186      I     189          2.939
LGA    T     187      A     190          1.608
LGA    V     188      C     191          2.548
LGA    I     189      V     192          2.241
LGA    A     190      C     193          2.217
LGA    C     191      I     194          2.535
LGA    V     192      H     195          1.590
LGA    C     193      L     196          2.807
LGA    I     194      A     197          3.956
LGA    H     195      C     198          3.088
LGA    L     196      K     199          2.188
LGA    A     197      W     200          4.744
LGA    C     198      S     201          5.526
LGA    K     199      N     202          2.787
LGA    W     200      W     203          4.189
LGA    S     201      -       -           -
LGA    N     202      -       -           -
LGA    W     203      -       -           -
LGA    E     204      E     204          2.567
LGA    I     205      I     205          2.366
LGA    P     206      P     206          4.051
LGA    V     207      V     207          1.594
LGA    S     208      S     208          1.881
LGA    T     209      T     209          4.887
LGA    D     210      D     210          4.955
LGA    G     211      G     211           #
LGA    K     212      K     212          5.611
LGA    H     213      H     213           #
LGA    W     214      W     214          5.530
LGA    -       -      W     215           -
LGA    -       -      E     216           -
LGA    W     215      Y     217          3.353
LGA    -       -      V     218           -
LGA    -       -      D     219           -
LGA    E     216      P     220          1.299
LGA    Y     217      T     221          5.296
LGA    V     218      V     222          5.309
LGA    D     219      T     223           #
LGA    P     220      -       -           -
LGA    T     221      -       -           -
LGA    V     222      L     224          4.759
LGA    T     223      E     225          3.318
LGA    L     224      L     226          2.587
LGA    E     225      -       -           -
LGA    L     226      -       -           -
LGA    L     227      L     227          1.586
LGA    D     228      D     228          2.096
LGA    E     229      E     229          2.913
LGA    L     230      L     230          2.333
LGA    T     231      T     231          1.582
LGA    H     232      H     232          1.513
LGA    E     233      E     233          3.837
LGA    F     234      F     234          4.415
LGA    L     235      L     235          3.439
LGA    Q     236      Q     236          4.201
LGA    I     237      I     237           #
LGA    L     238      L     238           #
LGA    E     239      -       -           -
LGA    K     240      -       -           -
LGA    T     241      E     239           #
LGA    -       -      K     240           -
LGA    -       -      T     241           -
LGA    -       -      P     242           -
LGA    -       -      N     243           -
LGA    -       -      R     244           -
LGA    P     242      L     245           #
LGA    N     243      K     246          3.524
LGA    R     244      K     247          2.051
LGA    L     245      I     248          4.607
LGA    K     246      R     249           #
LGA    K     247      N     250          3.949
LGA    I     248      -       -           -
LGA    R     249      W     251           #
LGA    N     250      R     252           -
LGA    W     251      A     253           #
LGA    R     252      N     254          1.278
LGA    A     253      Q     255           #
LGA    N     254      A     256           -
LGA    Q     255      -       -           -
LGA    A     256      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  113  113    5.0     85    3.01    42.35     46.319     2.736

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.712556 * X  +  -0.633421 * Y  +   0.301732 * Z  + -27.522354
  Y_new =   0.275174 * X  +  -0.647899 * Y  +  -0.710286 * Z  +  24.824516
  Z_new =   0.645402 * X  +  -0.423090 * Y  +   0.635965 * Z  +  68.081161 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.587036    2.554556  [ DEG:   -33.6347    146.3653 ]
  Theta =  -0.701549   -2.440043  [ DEG:   -40.1958   -139.8042 ]
  Phi   =   2.773057   -0.368535  [ DEG:   158.8845    -21.1155 ]
 
# 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: T0338TS168_4-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS168_4-D2.T0338_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  113  113   5.0   85   3.01   42.35  46.319
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS168_4-D2
PFRMAT TS
TARGET T0338
MODEL 4
PARENT N/A
ATOM    144  CA  GLU   144     -23.428  18.626  57.870  1.00 25.00           C
ATOM    145  CA  HIS   145     -25.302  18.055  61.161  1.00 25.00           C
ATOM    146  CA  PRO   146     -25.137  19.589  64.642  1.00 25.00           C
ATOM    147  CA  HIS   147     -28.238  18.441  66.553  1.00 25.00           C
ATOM    148  CA  THR   148     -31.587  16.670  65.987  1.00 25.00           C
ATOM    149  CA  ASP   149     -30.299  13.584  67.855  1.00 25.00           C
ATOM    150  CA  VAL   150     -29.146  15.796  70.762  1.00 25.00           C
ATOM    151  CA  VAL   151     -32.583  17.482  70.874  1.00 25.00           C
ATOM    152  CA  LYS   152     -34.290  14.053  70.919  1.00 25.00           C
ATOM    153  CA  CYS   153     -32.010  12.926  73.781  1.00 25.00           C
ATOM    154  CA  THR   154     -32.843  16.114  75.733  1.00 25.00           C
ATOM    155  CA  GLN   155     -36.584  15.502  75.183  1.00 25.00           C
ATOM    156  CA  LEU   156     -36.199  11.896  76.412  1.00 25.00           C
ATOM    157  CA  VAL   157     -34.285  13.091  79.544  1.00 25.00           C
ATOM    158  CA  ARG   158     -34.621  15.986  82.014  1.00 25.00           C
ATOM    159  CA  ALA   159     -31.995  18.627  81.153  1.00 25.00           C
ATOM    160  CA  SER   160     -29.889  19.533  84.188  1.00 25.00           C
ATOM    161  CA  LYS   161     -26.684  20.363  82.315  1.00 25.00           C
ATOM    162  CA  ASP   162     -26.854  17.261  80.076  1.00 25.00           C
ATOM    163  CA  LEU   163     -28.481  19.330  77.293  1.00 25.00           C
ATOM    164  CA  ALA   164     -25.734  21.978  77.622  1.00 25.00           C
ATOM    165  CA  GLN   165     -23.048  19.254  77.413  1.00 25.00           C
ATOM    166  CA  THR   166     -24.716  17.817  74.279  1.00 25.00           C
ATOM    167  CA  SER   167     -24.810  21.304  72.699  1.00 25.00           C
ATOM    168  CA  TYR   168     -21.098  21.795  73.504  1.00 25.00           C
ATOM    169  CA  PHE   169     -20.282  18.403  71.927  1.00 25.00           C
ATOM    170  CA  MET   170     -22.265  19.355  68.793  1.00 25.00           C
ATOM    171  CA  ALA   171     -20.380  22.682  68.581  1.00 25.00           C
ATOM    172  CA  THR   172     -17.040  20.839  68.912  1.00 25.00           C
ATOM    173  CA  ASN   173     -18.073  18.416  66.132  1.00 25.00           C
ATOM    174  CA  SER   174     -19.043  21.365  63.888  1.00 25.00           C
ATOM    175  CA  LEU   175     -15.660  23.029  64.571  1.00 25.00           C
ATOM    176  CA  HIS   176     -13.853  19.767  63.699  1.00 25.00           C
ATOM    177  CA  LEU   177     -12.743  18.812  67.177  1.00 25.00           C
ATOM    178  CA  THR   178     -14.196  15.350  67.384  1.00 25.00           C
ATOM    179  CA  THR   179     -12.327  14.705  64.078  1.00 25.00           C
ATOM    180  CA  PHE   180     -15.367  13.833  62.042  1.00 25.00           C
ATOM    181  CA  CYS   181     -15.241  16.888  59.785  1.00 25.00           C
ATOM    182  CA  LEU   182     -19.030  16.427  59.683  1.00 25.00           C
ATOM    183  CA  GLN   183     -20.772  13.227  58.855  1.00 25.00           C
ATOM    184  CA  TYR   184     -23.356  12.770  61.574  1.00 25.00           C
ATOM    185  CA  LYS   185     -20.462  12.236  63.950  1.00 25.00           C
ATOM    186  CA  PRO   186     -21.715  15.214  66.017  1.00 25.00           C
ATOM    187  CA  THR   187     -25.229  13.956  66.873  1.00 25.00           C
ATOM    188  CA  VAL   188     -23.750  10.731  68.314  1.00 25.00           C
ATOM    189  CA  ILE   189     -21.288  12.773  70.422  1.00 25.00           C
ATOM    190  CA  ALA   190     -24.161  14.952  71.711  1.00 25.00           C
ATOM    191  CA  CYS   191     -26.165  11.817  72.619  1.00 25.00           C
ATOM    192  CA  VAL   192     -23.135  10.390  74.477  1.00 25.00           C
ATOM    193  CA  CYS   193     -22.723  13.684  76.387  1.00 25.00           C
ATOM    194  CA  ILE   194     -26.435  13.630  77.328  1.00 25.00           C
ATOM    195  CA  HIS   195     -26.097  10.018  78.555  1.00 25.00           C
ATOM    196  CA  LEU   196     -23.042  10.990  80.650  1.00 25.00           C
ATOM    197  CA  ALA   197     -24.981  13.928  82.160  1.00 25.00           C
ATOM    198  CA  CYS   198     -27.902  11.599  83.003  1.00 25.00           C
ATOM    199  CA  LYS   199     -25.489   9.133  84.664  1.00 25.00           C
ATOM    200  CA  TRP   200     -23.945  11.983  86.707  1.00 25.00           C
ATOM    201  CA  SER   201     -27.434  13.122  87.799  1.00 25.00           C
ATOM    202  CA  ASN   202     -30.046  10.386  87.540  1.00 25.00           C
ATOM    203  CA  TRP   203     -32.323   9.135  84.761  1.00 25.00           C
ATOM    204  CA  GLU   204     -30.412   5.931  84.390  1.00 25.00           C
ATOM    205  CA  ILE   205     -29.539   5.655  80.748  1.00 25.00           C
ATOM    206  CA  PRO   206     -30.141   1.936  81.254  1.00 25.00           C
ATOM    207  CA  VAL   207     -33.666   1.223  80.025  1.00 25.00           C
ATOM    208  CA  SER   208     -37.178   1.659  78.602  1.00 25.00           C
ATOM    209  CA  THR   209     -40.281   3.149  77.119  1.00 25.00           C
ATOM    210  CA  ASP   210     -39.986   0.858  74.110  1.00 25.00           C
ATOM    211  CA  GLY   211     -37.082   2.119  71.934  1.00 25.00           C
ATOM    212  CA  LYS   212     -37.405  -0.805  69.456  1.00 25.00           C
ATOM    213  CA  HIS   213     -33.738  -1.794  69.274  1.00 25.00           C
ATOM    214  CA  TRP   214     -31.966   1.435  70.205  1.00 25.00           C
ATOM    215  CA  TRP   215     -33.554   2.623  66.929  1.00 25.00           C
ATOM    216  CA  GLU   216     -30.132   2.544  65.213  1.00 25.00           C
ATOM    217  CA  TYR   217     -29.535  -1.010  66.510  1.00 25.00           C
ATOM    218  CA  VAL   218     -26.729  -1.266  69.021  1.00 25.00           C
ATOM    219  CA  ASP   219     -26.594  -5.058  68.958  1.00 25.00           C
ATOM    220  CA  PRO   220     -23.585  -4.990  66.634  1.00 25.00           C
ATOM    221  CA  THR   221     -21.095  -4.680  69.475  1.00 25.00           C
ATOM    222  CA  VAL   222     -20.716  -3.143  72.923  1.00 25.00           C
ATOM    223  CA  THR   223     -17.043  -2.648  71.886  1.00 25.00           C
ATOM    224  CA  LEU   224     -18.412   0.679  70.655  1.00 25.00           C
ATOM    225  CA  GLU   225     -14.840   1.763  69.796  1.00 25.00           C
ATOM    226  CA  LEU   226     -16.176   4.953  68.154  1.00 25.00           C
ATOM    227  CA  LEU   227     -18.292   5.695  71.259  1.00 25.00           C
ATOM    228  CA  ASP   228     -15.230   5.180  73.499  1.00 25.00           C
ATOM    229  CA  GLU   229     -13.186   7.551  71.292  1.00 25.00           C
ATOM    230  CA  LEU   230     -15.968  10.176  71.493  1.00 25.00           C
ATOM    231  CA  THR   231     -16.054   9.828  75.307  1.00 25.00           C
ATOM    232  CA  HIS   232     -12.251  10.256  75.457  1.00 25.00           C
ATOM    233  CA  GLU   233     -12.494  13.390  73.267  1.00 25.00           C
ATOM    234  CA  PHE   234     -15.221  14.806  75.553  1.00 25.00           C
ATOM    235  CA  LEU   235     -13.040  14.114  78.624  1.00 25.00           C
ATOM    236  CA  GLN   236     -10.079  15.872  76.948  1.00 25.00           C
ATOM    237  CA  ILE   237     -12.297  18.887  76.134  1.00 25.00           C
ATOM    238  CA  LEU   238     -13.496  19.015  79.770  1.00 25.00           C
ATOM    239  CA  GLU   239      -9.870  18.890  80.996  1.00 25.00           C
ATOM    240  CA  LYS   240      -8.939  21.738  78.611  1.00 25.00           C
ATOM    241  CA  THR   241      -5.579  23.535  78.794  1.00 25.00           C
ATOM    242  CA  PRO   242      -6.947  24.808  82.085  1.00 25.00           C
ATOM    243  CA  ASN   243      -7.680  28.313  80.729  1.00 25.00           C
ATOM    244  CA  ARG   244     -10.858  27.017  79.028  1.00 25.00           C
ATOM    245  CA  LEU   245     -11.965  25.365  82.302  1.00 25.00           C
ATOM    246  CA  LYS   246     -11.347  28.639  84.191  1.00 25.00           C
ATOM    247  CA  LYS   247     -13.399  30.558  81.588  1.00 25.00           C
ATOM    248  CA  ILE   248     -16.247  28.021  81.929  1.00 25.00           C
ATOM    249  CA  ARG   249     -16.150  28.387  85.740  1.00 25.00           C
ATOM    250  CA  ASN   250     -16.279  32.200  85.402  1.00 25.00           C
ATOM    251  CA  TRP   251     -19.276  31.914  83.034  1.00 25.00           C
ATOM    252  CA  ARG   252     -21.051  29.605  85.521  1.00 25.00           C
ATOM    253  CA  ALA   253     -20.381  32.097  88.351  1.00 25.00           C
ATOM    254  CA  ASN   254     -21.304  35.784  87.875  1.00 25.00           C
ATOM    255  CA  GLN   255     -22.645  35.441  84.332  1.00 25.00           C
ATOM    256  CA  ALA   256     -24.241  32.393  82.607  1.00 25.00           C
TER
END
