
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS168_3-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          5.357
LGA    H     145      H     145          1.040
LGA    P     146      P     146          1.873
LGA    H     147      H     147           #
LGA    T     148      T     148           -
LGA    D     149      D     149           #
LGA    V     150      V     150          3.657
LGA    V     151      V     151           #
LGA    K     152      K     152           #
LGA    C     153      C     153          3.045
LGA    T     154      T     154          3.608
LGA    Q     155      Q     155           #
LGA    L     156      L     156          4.725
LGA    V     157      V     157          1.209
LGA    R     158      R     158          0.777
LGA    A     159      A     159          0.473
LGA    S     160      S     160          0.957
LGA    K     161      K     161          1.052
LGA    D     162      D     162          1.525
LGA    L     163      L     163          1.882
LGA    A     164      A     164          1.619
LGA    Q     165      Q     165          1.240
LGA    T     166      T     166          1.595
LGA    S     167      S     167          2.060
LGA    Y     168      Y     168          1.967
LGA    F     169      F     169          1.392
LGA    M     170      M     170          1.814
LGA    A     171      A     171          2.309
LGA    T     172      T     172          1.717
LGA    N     173      N     173          1.508
LGA    S     174      S     174          2.749
LGA    L     175      L     175          2.785
LGA    H     176      H     176          1.599
LGA    L     177      L     177          1.768
LGA    T     178      T     178           #
LGA    T     179      -       -           -
LGA    F     180      -       -           -
LGA    C     181      -       -           -
LGA    L     182      T     179          4.580
LGA    Q     183      F     180          2.244
LGA    Y     184      C     181          5.642
LGA    K     185      L     182           #
LGA    -       -      Q     183           -
LGA    -       -      Y     184           -
LGA    -       -      K     185           -
LGA    P     186      P     186          5.043
LGA    T     187      T     187          4.227
LGA    V     188      V     188          2.995
LGA    I     189      I     189          3.516
LGA    A     190      A     190          3.536
LGA    C     191      C     191          2.388
LGA    V     192      V     192          2.493
LGA    C     193      C     193          2.669
LGA    I     194      I     194          2.032
LGA    H     195      H     195          2.680
LGA    L     196      L     196          3.175
LGA    A     197      A     197          2.716
LGA    C     198      C     198          3.129
LGA    K     199      K     199          3.990
LGA    W     200      W     200          4.133
LGA    S     201      S     201          3.970
LGA    N     202      N     202          4.241
LGA    W     203      W     203          3.756
LGA    E     204      E     204          2.089
LGA    I     205      I     205          2.041
LGA    P     206      P     206          1.790
LGA    V     207      V     207          2.462
LGA    S     208      S     208           -
LGA    T     209      -       -           -
LGA    D     210      T     209          3.549
LGA    G     211      D     210          3.206
LGA    K     212      G     211           #
LGA    H     213      K     212          3.753
LGA    W     214      H     213          4.110
LGA    W     215      W     214          4.995
LGA    E     216      W     215           #
LGA    -       -      E     216           -
LGA    -       -      Y     217           -
LGA    -       -      V     218           -
LGA    -       -      D     219           -
LGA    -       -      P     220           -
LGA    Y     217      T     221           #
LGA    -       -      V     222           -
LGA    V     218      T     223           #
LGA    D     219      -       -           -
LGA    P     220      -       -           -
LGA    T     221      -       -           -
LGA    V     222      -       -           -
LGA    T     223      -       -           -
LGA    L     224      L     224          1.791
LGA    E     225      E     225          2.246
LGA    L     226      L     226          1.990
LGA    L     227      L     227          1.270
LGA    D     228      D     228          2.031
LGA    E     229      E     229          2.503
LGA    L     230      L     230          1.983
LGA    T     231      T     231          1.270
LGA    H     232      H     232          2.406
LGA    E     233      E     233          2.454
LGA    F     234      F     234          1.366
LGA    L     235      L     235          1.835
LGA    Q     236      Q     236          2.445
LGA    I     237      I     237          1.979
LGA    L     238      L     238          1.406
LGA    E     239      E     239          2.264
LGA    K     240      K     240          2.427
LGA    T     241      T     241          3.160
LGA    P     242      -       -           -
LGA    N     243      -       -           -
LGA    R     244      -       -           -
LGA    L     245      -       -           -
LGA    K     246      P     242          2.597
LGA    K     247      N     243          1.453
LGA    I     248      R     244          1.654
LGA    R     249      L     245          0.905
LGA    N     250      K     246          2.058
LGA    W     251      K     247          2.802
LGA    R     252      I     248          3.264
LGA    A     253      R     249          3.879
LGA    N     254      -       -           -
LGA    Q     255      N     250          2.332
LGA    A     256      W     251          2.032
LGA    -       -      R     252           -
LGA    -       -      A     253           -
LGA    -       -      N     254           -
LGA    -       -      Q     255           -
LGA    -       -      A     256           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  113  113    5.0     86    2.78    80.23     48.420     2.991

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.074355 * X  +  -0.666911 * Y  +   0.741418 * Z  + -29.359123
  Y_new =  -0.380983 * X  +  -0.668083 * Y  +  -0.639153 * Z  +  22.444313
  Z_new =   0.921587 * X  +  -0.329992 * Y  +  -0.204407 * Z  +  69.776291 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.125380    1.016212  [ DEG:  -121.7753     58.2247 ]
  Theta =  -1.172150   -1.969443  [ DEG:   -67.1592   -112.8408 ]
  Phi   =  -1.763538    1.378054  [ DEG:  -101.0433     78.9567 ]
 
# 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_3-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS168_3-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   86   2.78   80.23  48.420
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS168_3-D2
PFRMAT TS
TARGET T0338
MODEL 3
PARENT N/A
ATOM    144  CA  GLU   144     -22.548  15.809  60.238  1.00 25.00           C
ATOM    145  CA  HIS   145     -24.874  18.071  62.158  1.00 25.00           C
ATOM    146  CA  PRO   146     -27.457  16.476  64.421  1.00 25.00           C
ATOM    147  CA  HIS   147     -28.595  13.102  63.036  1.00 25.00           C
ATOM    148  CA  THR   148     -30.210   9.715  63.802  1.00 25.00           C
ATOM    149  CA  ASP   149     -28.232   9.484  67.073  1.00 25.00           C
ATOM    150  CA  VAL   150     -29.356  13.016  68.032  1.00 25.00           C
ATOM    151  CA  VAL   151     -32.996  12.087  67.289  1.00 25.00           C
ATOM    152  CA  LYS   152     -32.660   8.942  69.448  1.00 25.00           C
ATOM    153  CA  CYS   153     -31.189  11.029  72.302  1.00 25.00           C
ATOM    154  CA  THR   154     -34.088  13.515  72.011  1.00 25.00           C
ATOM    155  CA  GLN   155     -36.604  10.629  72.119  1.00 25.00           C
ATOM    156  CA  LEU   156     -34.884   9.212  75.232  1.00 25.00           C
ATOM    157  CA  VAL   157     -36.057  12.503  76.817  1.00 25.00           C
ATOM    158  CA  ARG   158     -36.907  14.075  80.204  1.00 25.00           C
ATOM    159  CA  ALA   159     -33.570  15.828  79.669  1.00 25.00           C
ATOM    160  CA  SER   160     -33.501  18.712  82.173  1.00 25.00           C
ATOM    161  CA  LYS   161     -31.257  21.339  80.448  1.00 25.00           C
ATOM    162  CA  ASP   162     -27.727  20.152  81.339  1.00 25.00           C
ATOM    163  CA  LEU   163     -27.902  17.490  78.592  1.00 25.00           C
ATOM    164  CA  ALA   164     -29.044  20.133  76.067  1.00 25.00           C
ATOM    165  CA  GLN   165     -26.145  22.410  77.104  1.00 25.00           C
ATOM    166  CA  THR   166     -23.682  19.509  76.681  1.00 25.00           C
ATOM    167  CA  SER   167     -25.109  18.772  73.204  1.00 25.00           C
ATOM    168  CA  TYR   168     -24.749  22.462  72.247  1.00 25.00           C
ATOM    169  CA  PHE   169     -21.119  22.450  73.469  1.00 25.00           C
ATOM    170  CA  MET   170     -20.411  19.297  71.414  1.00 25.00           C
ATOM    171  CA  ALA   171     -21.959  20.937  68.318  1.00 25.00           C
ATOM    172  CA  THR   172     -19.801  24.054  68.861  1.00 25.00           C
ATOM    173  CA  ASN   173     -16.676  21.865  69.181  1.00 25.00           C
ATOM    174  CA  SER   174     -17.592  20.041  65.940  1.00 25.00           C
ATOM    175  CA  LEU   175     -18.071  23.396  64.158  1.00 25.00           C
ATOM    176  CA  HIS   176     -14.661  24.588  65.430  1.00 25.00           C
ATOM    177  CA  LEU   177     -12.849  21.312  66.194  1.00 25.00           C
ATOM    178  CA  THR   178     -12.267  21.140  62.419  1.00 25.00           C
ATOM    179  CA  THR   179     -11.993  24.608  60.880  1.00 25.00           C
ATOM    180  CA  PHE   180     -15.686  24.641  59.969  1.00 25.00           C
ATOM    181  CA  CYS   181     -16.760  21.034  59.697  1.00 25.00           C
ATOM    182  CA  LEU   182     -17.137  17.534  61.017  1.00 25.00           C
ATOM    183  CA  GLN   183     -15.419  14.088  61.138  1.00 25.00           C
ATOM    184  CA  TYR   184     -16.488  10.909  62.841  1.00 25.00           C
ATOM    185  CA  LYS   185     -20.113  12.043  62.750  1.00 25.00           C
ATOM    186  CA  PRO   186     -20.404  15.278  64.759  1.00 25.00           C
ATOM    187  CA  THR   187     -23.841  13.800  65.576  1.00 25.00           C
ATOM    188  CA  VAL   188     -22.178  10.914  67.466  1.00 25.00           C
ATOM    189  CA  ILE   189     -20.040  13.404  69.439  1.00 25.00           C
ATOM    190  CA  ALA   190     -23.168  15.436  70.310  1.00 25.00           C
ATOM    191  CA  CYS   191     -24.941  12.250  71.480  1.00 25.00           C
ATOM    192  CA  VAL   192     -21.920  11.335  73.648  1.00 25.00           C
ATOM    193  CA  CYS   193     -21.918  14.849  75.172  1.00 25.00           C
ATOM    194  CA  ILE   194     -25.661  14.554  75.921  1.00 25.00           C
ATOM    195  CA  HIS   195     -25.086  11.152  77.584  1.00 25.00           C
ATOM    196  CA  LEU   196     -22.264  12.639  79.703  1.00 25.00           C
ATOM    197  CA  ALA   197     -24.542  15.534  80.750  1.00 25.00           C
ATOM    198  CA  CYS   198     -27.295  13.052  81.714  1.00 25.00           C
ATOM    199  CA  LYS   199     -24.783  11.029  83.778  1.00 25.00           C
ATOM    200  CA  TRP   200     -23.624  14.224  85.544  1.00 25.00           C
ATOM    201  CA  SER   201     -27.261  15.148  86.312  1.00 25.00           C
ATOM    202  CA  ASN   202     -27.553  11.794  87.933  1.00 25.00           C
ATOM    203  CA  TRP   203     -30.337   9.832  86.294  1.00 25.00           C
ATOM    204  CA  GLU   204     -28.299   6.837  85.207  1.00 25.00           C
ATOM    205  CA  ILE   205     -29.613   7.287  81.633  1.00 25.00           C
ATOM    206  CA  PRO   206     -32.047   4.405  82.012  1.00 25.00           C
ATOM    207  CA  VAL   207     -34.091   1.394  80.904  1.00 25.00           C
ATOM    208  CA  SER   208     -33.459  -1.526  83.169  1.00 25.00           C
ATOM    209  CA  THR   209     -35.552  -3.551  80.796  1.00 25.00           C
ATOM    210  CA  ASP   210     -36.846  -3.513  77.222  1.00 25.00           C
ATOM    211  CA  GLY   211     -37.840  -0.594  74.999  1.00 25.00           C
ATOM    212  CA  LYS   212     -37.287  -2.302  71.634  1.00 25.00           C
ATOM    213  CA  HIS   213     -33.781  -3.277  70.742  1.00 25.00           C
ATOM    214  CA  TRP   214     -31.323  -0.424  71.205  1.00 25.00           C
ATOM    215  CA  TRP   215     -31.386   0.484  74.925  1.00 25.00           C
ATOM    216  CA  GLU   216     -28.748  -2.196  75.649  1.00 25.00           C
ATOM    217  CA  TYR   217     -26.552  -0.834  72.821  1.00 25.00           C
ATOM    218  CA  VAL   218     -26.198  -3.898  70.533  1.00 25.00           C
ATOM    219  CA  ASP   219     -23.871  -6.093  68.396  1.00 25.00           C
ATOM    220  CA  PRO   220     -20.333  -4.915  69.142  1.00 25.00           C
ATOM    221  CA  THR   221     -18.639  -5.112  72.539  1.00 25.00           C
ATOM    222  CA  VAL   222     -16.971  -3.053  75.227  1.00 25.00           C
ATOM    223  CA  THR   223     -19.484  -0.210  75.172  1.00 25.00           C
ATOM    224  CA  LEU   224     -21.980  -0.040  72.307  1.00 25.00           C
ATOM    225  CA  GLU   225     -18.814  -0.167  70.154  1.00 25.00           C
ATOM    226  CA  LEU   226     -19.912   3.006  68.311  1.00 25.00           C
ATOM    227  CA  LEU   227     -20.541   4.761  71.656  1.00 25.00           C
ATOM    228  CA  ASP   228     -17.072   3.709  72.890  1.00 25.00           C
ATOM    229  CA  GLU   229     -15.493   5.049  69.668  1.00 25.00           C
ATOM    230  CA  LEU   230     -17.356   8.366  70.106  1.00 25.00           C
ATOM    231  CA  THR   231     -16.134   8.603  73.728  1.00 25.00           C
ATOM    232  CA  HIS   232     -12.541   7.934  72.585  1.00 25.00           C
ATOM    233  CA  GLU   233     -12.857  10.658  69.913  1.00 25.00           C
ATOM    234  CA  PHE   234     -14.187  13.112  72.535  1.00 25.00           C
ATOM    235  CA  LEU   235     -11.255  12.265  74.849  1.00 25.00           C
ATOM    236  CA  GLN   236      -8.790  12.836  71.974  1.00 25.00           C
ATOM    237  CA  ILE   237     -10.424  16.215  71.212  1.00 25.00           C
ATOM    238  CA  LEU   238     -10.168  17.200  74.903  1.00 25.00           C
ATOM    239  CA  GLU   239      -6.469  16.209  74.936  1.00 25.00           C
ATOM    240  CA  LYS   240      -5.856  18.298  71.786  1.00 25.00           C
ATOM    241  CA  THR   241      -3.961  21.506  71.093  1.00 25.00           C
ATOM    242  CA  PRO   242      -5.524  23.626  68.363  1.00 25.00           C
ATOM    243  CA  ASN   243      -4.404  26.702  70.352  1.00 25.00           C
ATOM    244  CA  ARG   244      -8.035  27.895  70.599  1.00 25.00           C
ATOM    245  CA  LEU   245      -9.116  24.432  71.827  1.00 25.00           C
ATOM    246  CA  LYS   246      -6.331  24.468  74.455  1.00 25.00           C
ATOM    247  CA  LYS   247      -7.439  27.946  75.617  1.00 25.00           C
ATOM    248  CA  ILE   248     -11.060  26.729  75.887  1.00 25.00           C
ATOM    249  CA  ARG   249      -9.915  23.701  77.935  1.00 25.00           C
ATOM    250  CA  ASN   250      -7.912  25.996  80.255  1.00 25.00           C
ATOM    251  CA  TRP   251     -10.973  28.253  80.704  1.00 25.00           C
ATOM    252  CA  ARG   252     -13.134  25.201  81.530  1.00 25.00           C
ATOM    253  CA  ALA   253     -10.543  24.031  84.097  1.00 25.00           C
ATOM    254  CA  ASN   254     -12.731  25.250  87.018  1.00 25.00           C
ATOM    255  CA  GLN   255     -15.248  27.792  85.729  1.00 25.00           C
ATOM    256  CA  ALA   256     -18.084  26.579  83.527  1.00 25.00           C
TER
END
