
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS168_2-D2.T0338_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     144      -       -           -
LGA    H     145      E     144           #
LGA    -       -      H     145           -
LGA    P     146      P     146          2.431
LGA    -       -      H     147           -
LGA    H     147      T     148          2.449
LGA    T     148      D     149          2.646
LGA    D     149      V     150          4.147
LGA    V     150      V     151          2.324
LGA    V     151      K     152          1.786
LGA    K     152      C     153          3.178
LGA    C     153      T     154          1.585
LGA    T     154      Q     155          2.314
LGA    Q     155      L     156          4.651
LGA    -       -      V     157           -
LGA    L     156      R     158          2.632
LGA    V     157      A     159          5.009
LGA    R     158      -       -           -
LGA    A     159      S     160          6.316
LGA    S     160      K     161          1.672
LGA    K     161      D     162          1.631
LGA    D     162      L     163          1.406
LGA    L     163      A     164          1.546
LGA    A     164      Q     165          1.495
LGA    Q     165      T     166          1.403
LGA    T     166      S     167          1.539
LGA    S     167      Y     168          1.520
LGA    Y     168      F     169          1.501
LGA    F     169      M     170          1.841
LGA    M     170      A     171          1.986
LGA    A     171      T     172          1.932
LGA    T     172      N     173          1.696
LGA    N     173      S     174          1.900
LGA    S     174      L     175          2.587
LGA    L     175      H     176          2.303
LGA    H     176      L     177          2.751
LGA    L     177      T     178          3.139
LGA    T     178      T     179          2.665
LGA    -       -      F     180           -
LGA    -       -      C     181           -
LGA    T     179      L     182          4.386
LGA    F     180      Q     183          2.691
LGA    C     181      Y     184          4.231
LGA    L     182      K     185          1.818
LGA    -       -      P     186           -
LGA    -       -      T     187           -
LGA    Q     183      V     188          3.561
LGA    Y     184      I     189          3.056
LGA    K     185      A     190           #
LGA    P     186      C     191           #
LGA    T     187      V     192          3.900
LGA    V     188      C     193          3.227
LGA    I     189      I     194           #
LGA    A     190      H     195          4.302
LGA    C     191      L     196           -
LGA    V     192      A     197           -
LGA    -       -      C     198           -
LGA    -       -      K     199           -
LGA    -       -      W     200           -
LGA    -       -      S     201           -
LGA    -       -      N     202           -
LGA    -       -      W     203           -
LGA    -       -      E     204           -
LGA    -       -      I     205           -
LGA    -       -      P     206           -
LGA    -       -      V     207           -
LGA    -       -      S     208           -
LGA    -       -      T     209           -
LGA    -       -      D     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      H     213           -
LGA    C     193      W     214          5.504
LGA    I     194      W     215          4.095
LGA    H     195      E     216           #
LGA    L     196      -       -           -
LGA    A     197      Y     217          1.025
LGA    C     198      V     218           #
LGA    K     199      D     219           -
LGA    W     200      P     220           -
LGA    S     201      T     221           -
LGA    N     202      -       -           -
LGA    W     203      -       -           -
LGA    E     204      -       -           -
LGA    I     205      -       -           -
LGA    P     206      -       -           -
LGA    V     207      -       -           -
LGA    S     208      -       -           -
LGA    T     209      -       -           -
LGA    D     210      -       -           -
LGA    G     211      -       -           -
LGA    K     212      -       -           -
LGA    H     213      -       -           -
LGA    W     214      -       -           -
LGA    W     215      -       -           -
LGA    E     216      -       -           -
LGA    Y     217      -       -           -
LGA    V     218      -       -           -
LGA    D     219      -       -           -
LGA    P     220      -       -           -
LGA    T     221      -       -           -
LGA    V     222      -       -           -
LGA    T     223      -       -           -
LGA    L     224      -       -           -
LGA    E     225      V     222           #
LGA    L     226      T     223          1.394
LGA    L     227      L     224          1.633
LGA    D     228      E     225          1.834
LGA    E     229      L     226          1.329
LGA    L     230      L     227          1.615
LGA    T     231      D     228          1.658
LGA    H     232      E     229          1.345
LGA    E     233      L     230          1.369
LGA    F     234      T     231          1.981
LGA    L     235      H     232          1.654
LGA    Q     236      E     233          1.643
LGA    I     237      F     234          2.208
LGA    L     238      L     235          2.280
LGA    E     239      Q     236          2.086
LGA    K     240      I     237          2.422
LGA    T     241      L     238           #
LGA    P     242      E     239          3.012
LGA    N     243      K     240          4.378
LGA    R     244      T     241          2.543
LGA    L     245      P     242          4.357
LGA    -       -      N     243           -
LGA    -       -      R     244           -
LGA    K     246      L     245          3.287
LGA    K     247      K     246          2.348
LGA    I     248      K     247          2.612
LGA    R     249      I     248          4.121
LGA    N     250      R     249          4.295
LGA    W     251      N     250          2.541
LGA    R     252      W     251          3.160
LGA    A     253      -       -           -
LGA    N     254      -       -           -
LGA    Q     255      -       -           -
LGA    A     256      R     252          3.516
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     71    2.86     9.86     39.796     2.395

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.916646 * X  +   0.245536 * Y  +   0.315392 * Z  + -26.914862
  Y_new =  -0.399481 * X  +  -0.536680 * Y  +  -0.743229 * Z  +  22.271967
  Z_new =  -0.013225 * X  +  -0.807271 * Y  +   0.590033 * Z  +  66.054115 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.939633    2.201960  [ DEG:   -53.8370    126.1630 ]
  Theta =   0.013225    3.128368  [ DEG:     0.7577    179.2423 ]
  Phi   =  -2.730604    0.410989  [ DEG:  -156.4521     23.5479 ]
 
# 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_2-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS168_2-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   71   2.86    9.86  39.796
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS168_2-D2
PFRMAT TS
TARGET T0338
MODEL 2
PARENT N/A
ATOM    144  CA  GLU   144     -30.368  10.009  60.648  1.00 25.00           C
ATOM    145  CA  HIS   145     -29.430  12.371  63.523  1.00 25.00           C
ATOM    146  CA  PRO   146     -27.058  14.658  65.425  1.00 25.00           C
ATOM    147  CA  HIS   147     -30.135  16.675  66.496  1.00 25.00           C
ATOM    148  CA  THR   148     -33.195  14.380  66.695  1.00 25.00           C
ATOM    149  CA  ASP   149     -31.884  12.874  69.963  1.00 25.00           C
ATOM    150  CA  VAL   150     -31.345  16.386  71.393  1.00 25.00           C
ATOM    151  CA  VAL   151     -34.910  17.365  70.394  1.00 25.00           C
ATOM    152  CA  LYS   152     -36.276  14.207  72.075  1.00 25.00           C
ATOM    153  CA  CYS   153     -34.303  15.018  75.257  1.00 25.00           C
ATOM    154  CA  THR   154     -35.689  18.588  75.235  1.00 25.00           C
ATOM    155  CA  GLN   155     -39.246  17.232  74.827  1.00 25.00           C
ATOM    156  CA  LEU   156     -38.692  14.826  77.756  1.00 25.00           C
ATOM    157  CA  VAL   157     -37.776  17.770  79.994  1.00 25.00           C
ATOM    158  CA  ARG   158     -39.083  21.312  80.066  1.00 25.00           C
ATOM    159  CA  ALA   159     -35.646  22.244  78.594  1.00 25.00           C
ATOM    160  CA  SER   160     -33.409  20.898  81.352  1.00 25.00           C
ATOM    161  CA  LYS   161     -29.829  20.720  82.637  1.00 25.00           C
ATOM    162  CA  ASP   162     -28.903  17.220  81.389  1.00 25.00           C
ATOM    163  CA  LEU   163     -30.333  18.047  77.934  1.00 25.00           C
ATOM    164  CA  ALA   164     -28.316  21.301  77.850  1.00 25.00           C
ATOM    165  CA  GLN   165     -25.139  19.384  78.803  1.00 25.00           C
ATOM    166  CA  THR   166     -25.814  16.837  76.024  1.00 25.00           C
ATOM    167  CA  SER   167     -26.308  19.679  73.505  1.00 25.00           C
ATOM    168  CA  TYR   168     -23.015  21.280  74.628  1.00 25.00           C
ATOM    169  CA  PHE   169     -21.218  17.923  74.225  1.00 25.00           C
ATOM    170  CA  MET   170     -22.687  17.529  70.711  1.00 25.00           C
ATOM    171  CA  ALA   171     -21.528  21.064  69.802  1.00 25.00           C
ATOM    172  CA  THR   172     -18.014  20.272  71.101  1.00 25.00           C
ATOM    173  CA  ASN   173     -17.946  17.052  69.027  1.00 25.00           C
ATOM    174  CA  SER   174     -19.038  19.004  65.918  1.00 25.00           C
ATOM    175  CA  LEU   175     -16.279  21.586  66.540  1.00 25.00           C
ATOM    176  CA  HIS   176     -13.699  18.778  66.902  1.00 25.00           C
ATOM    177  CA  LEU   177     -14.734  16.138  64.291  1.00 25.00           C
ATOM    178  CA  THR   178     -14.724  15.812  60.494  1.00 25.00           C
ATOM    179  CA  THR   179     -13.136  12.398  60.900  1.00 25.00           C
ATOM    180  CA  PHE   180     -16.546  11.237  62.080  1.00 25.00           C
ATOM    181  CA  CYS   181     -19.058  14.013  62.677  1.00 25.00           C
ATOM    182  CA  LEU   182     -21.767  11.719  61.375  1.00 25.00           C
ATOM    183  CA  GLN   183     -20.363   9.285  63.953  1.00 25.00           C
ATOM    184  CA  TYR   184     -19.020  11.678  66.547  1.00 25.00           C
ATOM    185  CA  LYS   185     -18.421  11.737  70.352  1.00 25.00           C
ATOM    186  CA  PRO   186     -19.921  11.170  73.786  1.00 25.00           C
ATOM    187  CA  THR   187     -22.765  13.705  73.389  1.00 25.00           C
ATOM    188  CA  VAL   188     -22.780  13.130  69.602  1.00 25.00           C
ATOM    189  CA  ILE   189     -22.921   9.343  70.154  1.00 25.00           C
ATOM    190  CA  ALA   190     -25.846   9.781  72.586  1.00 25.00           C
ATOM    191  CA  CYS   191     -27.679  11.963  70.029  1.00 25.00           C
ATOM    192  CA  VAL   192     -27.106   9.315  67.322  1.00 25.00           C
ATOM    193  CA  CYS   193     -28.462   6.599  69.658  1.00 25.00           C
ATOM    194  CA  ILE   194     -31.553   8.738  70.391  1.00 25.00           C
ATOM    195  CA  HIS   195     -32.114   9.258  66.640  1.00 25.00           C
ATOM    196  CA  LEU   196     -31.818   5.487  66.047  1.00 25.00           C
ATOM    197  CA  ALA   197     -34.349   4.824  68.843  1.00 25.00           C
ATOM    198  CA  CYS   198     -36.756   7.373  67.302  1.00 25.00           C
ATOM    199  CA  LYS   199     -36.378   5.698  63.880  1.00 25.00           C
ATOM    200  CA  TRP   200     -37.092   2.278  65.448  1.00 25.00           C
ATOM    201  CA  SER   201     -40.211   3.688  67.164  1.00 25.00           C
ATOM    202  CA  ASN   202     -39.935   4.662  70.870  1.00 25.00           C
ATOM    203  CA  TRP   203     -37.878   4.273  74.095  1.00 25.00           C
ATOM    204  CA  GLU   204     -39.339   6.261  76.946  1.00 25.00           C
ATOM    205  CA  ILE   205     -35.897   7.401  78.183  1.00 25.00           C
ATOM    206  CA  PRO   206     -35.810   7.266  81.951  1.00 25.00           C
ATOM    207  CA  VAL   207     -38.009   4.219  82.413  1.00 25.00           C
ATOM    208  CA  SER   208     -40.839   5.868  84.380  1.00 25.00           C
ATOM    209  CA  THR   209     -39.277   5.994  87.881  1.00 25.00           C
ATOM    210  CA  ASP   210     -35.858   4.452  88.653  1.00 25.00           C
ATOM    211  CA  GLY   211     -32.862   4.935  86.354  1.00 25.00           C
ATOM    212  CA  LYS   212     -30.257   2.792  88.146  1.00 25.00           C
ATOM    213  CA  HIS   213     -27.648   3.524  85.394  1.00 25.00           C
ATOM    214  CA  TRP   214     -28.080   4.273  81.673  1.00 25.00           C
ATOM    215  CA  TRP   215     -31.318   2.504  80.645  1.00 25.00           C
ATOM    216  CA  GLU   216     -29.483   0.765  77.768  1.00 25.00           C
ATOM    217  CA  TYR   217     -26.724  -0.359  80.175  1.00 25.00           C
ATOM    218  CA  VAL   218     -23.068  -0.750  81.220  1.00 25.00           C
ATOM    219  CA  ASP   219     -23.313  -4.060  79.364  1.00 25.00           C
ATOM    220  CA  PRO   220     -23.883  -7.756  80.064  1.00 25.00           C
ATOM    221  CA  THR   221     -25.505  -7.943  76.661  1.00 25.00           C
ATOM    222  CA  VAL   222     -24.894  -6.586  73.209  1.00 25.00           C
ATOM    223  CA  THR   223     -21.592  -5.240  74.665  1.00 25.00           C
ATOM    224  CA  LEU   224     -22.920  -1.791  73.965  1.00 25.00           C
ATOM    225  CA  GLU   225     -20.545  -1.789  70.961  1.00 25.00           C
ATOM    226  CA  LEU   226     -21.904   1.618  69.858  1.00 25.00           C
ATOM    227  CA  LEU   227     -21.394   2.993  73.396  1.00 25.00           C
ATOM    228  CA  ASP   228     -17.800   1.669  73.420  1.00 25.00           C
ATOM    229  CA  GLU   229     -17.146   3.315  70.024  1.00 25.00           C
ATOM    230  CA  LEU   230     -18.555   6.627  71.330  1.00 25.00           C
ATOM    231  CA  THR   231     -16.308   6.393  74.423  1.00 25.00           C
ATOM    232  CA  HIS   232     -13.267   5.722  72.192  1.00 25.00           C
ATOM    233  CA  GLU   233     -14.158   8.750  70.025  1.00 25.00           C
ATOM    234  CA  PHE   234     -14.477  10.930  73.157  1.00 25.00           C
ATOM    235  CA  LEU   235     -11.063   9.704  74.387  1.00 25.00           C
ATOM    236  CA  GLN   236      -9.518  10.511  70.978  1.00 25.00           C
ATOM    237  CA  ILE   237     -11.056  14.016  71.082  1.00 25.00           C
ATOM    238  CA  LEU   238      -9.656  14.553  74.606  1.00 25.00           C
ATOM    239  CA  GLU   239      -6.192  13.422  73.427  1.00 25.00           C
ATOM    240  CA  LYS   240      -6.383  15.839  70.463  1.00 25.00           C
ATOM    241  CA  THR   241      -4.422  19.080  70.751  1.00 25.00           C
ATOM    242  CA  PRO   242      -5.046  18.999  74.519  1.00 25.00           C
ATOM    243  CA  ASN   243      -3.967  22.458  75.762  1.00 25.00           C
ATOM    244  CA  ARG   244      -7.179  23.994  74.349  1.00 25.00           C
ATOM    245  CA  LEU   245      -9.264  21.296  76.090  1.00 25.00           C
ATOM    246  CA  LYS   246      -7.452  21.988  79.392  1.00 25.00           C
ATOM    247  CA  LYS   247      -8.118  25.739  78.998  1.00 25.00           C
ATOM    248  CA  ILE   248     -11.822  25.036  78.328  1.00 25.00           C
ATOM    249  CA  ARG   249     -11.992  22.822  81.448  1.00 25.00           C
ATOM    250  CA  ASN   250     -10.352  25.587  83.529  1.00 25.00           C
ATOM    251  CA  TRP   251     -12.874  28.133  82.180  1.00 25.00           C
ATOM    252  CA  ARG   252     -15.762  25.776  83.061  1.00 25.00           C
ATOM    253  CA  ALA   253     -14.359  25.341  86.599  1.00 25.00           C
ATOM    254  CA  ASN   254     -14.659  21.628  86.311  1.00 25.00           C
ATOM    255  CA  GLN   255     -18.113  21.479  84.785  1.00 25.00           C
ATOM    256  CA  ALA   256     -19.412  21.457  81.175  1.00 25.00           C
TER
END
