
#######################################################
#                                                     #
#                        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 T0338TS393_5-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS393_5-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          3.868
LGA    P     146      H     145          2.786
LGA    H     147      P     146           #
LGA    T     148      H     147           -
LGA    -       -      T     148           -
LGA    D     149      D     149          4.520
LGA    V     150      V     150          3.377
LGA    V     151      V     151           #
LGA    K     152      K     152          4.529
LGA    C     153      C     153          0.173
LGA    T     154      T     154          4.452
LGA    Q     155      Q     155          4.584
LGA    L     156      L     156          0.636
LGA    V     157      V     157          4.942
LGA    R     158      R     158          1.667
LGA    A     159      A     159          2.793
LGA    S     160      S     160          2.094
LGA    -       -      K     161           -
LGA    K     161      D     162          0.354
LGA    D     162      L     163          2.905
LGA    L     163      A     164          3.870
LGA    A     164      Q     165          2.047
LGA    Q     165      T     166          1.258
LGA    T     166      S     167          3.323
LGA    S     167      Y     168          3.066
LGA    Y     168      F     169          1.051
LGA    F     169      M     170          1.952
LGA    M     170      A     171          3.334
LGA    A     171      T     172          2.381
LGA    T     172      N     173          0.592
LGA    N     173      S     174          2.252
LGA    S     174      L     175          2.724
LGA    L     175      H     176          2.112
LGA    H     176      L     177          1.592
LGA    L     177      T     178          2.014
LGA    T     178      T     179          2.036
LGA    T     179      F     180           #
LGA    F     180      C     181          4.088
LGA    C     181      L     182          5.721
LGA    L     182      Q     183          5.050
LGA    Q     183      Y     184          1.743
LGA    Y     184      K     185          4.405
LGA    K     185      -       -           -
LGA    P     186      P     186          3.634
LGA    T     187      T     187          3.314
LGA    V     188      V     188          2.386
LGA    -       -      I     189           -
LGA    -       -      A     190           -
LGA    -       -      C     191           -
LGA    I     189      V     192          2.721
LGA    A     190      C     193          2.861
LGA    C     191      I     194          3.459
LGA    V     192      H     195          2.552
LGA    C     193      L     196          2.911
LGA    I     194      -       -           -
LGA    H     195      -       -           -
LGA    L     196      -       -           -
LGA    A     197      A     197          3.564
LGA    C     198      C     198          3.345
LGA    K     199      K     199          4.167
LGA    -       -      W     200           -
LGA    W     200      S     201          3.728
LGA    S     201      N     202          2.685
LGA    N     202      W     203          3.860
LGA    W     203      E     204          4.542
LGA    E     204      I     205          2.965
LGA    I     205      -       -           -
LGA    P     206      P     206          1.477
LGA    V     207      V     207          1.991
LGA    S     208      S     208          3.268
LGA    T     209      T     209          3.487
LGA    D     210      D     210          3.416
LGA    -       -      G     211           -
LGA    G     211      K     212          5.217
LGA    K     212      H     213           -
LGA    H     213      W     214           -
LGA    -       -      W     215           -
LGA    W     214      E     216          2.341
LGA    W     215      Y     217           #
LGA    E     216      V     218           -
LGA    -       -      D     219           -
LGA    -       -      P     220           -
LGA    Y     217      T     221          3.568
LGA    V     218      V     222           #
LGA    D     219      -       -           -
LGA    P     220      -       -           -
LGA    T     221      -       -           -
LGA    V     222      -       -           -
LGA    T     223      T     223           #
LGA    L     224      L     224          2.504
LGA    E     225      E     225          2.558
LGA    L     226      L     226          1.796
LGA    L     227      L     227          1.648
LGA    D     228      D     228          2.081
LGA    E     229      E     229          1.957
LGA    L     230      L     230          1.000
LGA    T     231      T     231          1.648
LGA    H     232      H     232          2.010
LGA    E     233      E     233          1.566
LGA    F     234      F     234          1.187
LGA    L     235      L     235          1.582
LGA    Q     236      Q     236          1.752
LGA    I     237      I     237          1.379
LGA    L     238      L     238          1.107
LGA    E     239      E     239          1.489
LGA    K     240      K     240          1.607
LGA    T     241      T     241           #
LGA    P     242      P     242           -
LGA    N     243      N     243           -
LGA    R     244      R     244           -
LGA    L     245      L     245           -
LGA    K     246      K     246           -
LGA    K     247      K     247           -
LGA    I     248      I     248           -
LGA    R     249      R     249           -
LGA    N     250      N     250           -
LGA    W     251      W     251           -
LGA    R     252      R     252           -
LGA    A     253      A     253           -
LGA    N     254      N     254           -
LGA    Q     255      Q     255           -
LGA    A     256      A     256           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  113  113    5.0     77    2.95    51.95     40.690     2.525

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.145975 * X  +  -0.989197 * Y  +  -0.013453 * Z  + -22.562914
  Y_new =   0.032426 * X  +   0.008807 * Y  +  -0.999435 * Z  +  23.740995
  Z_new =   0.988757 * X  +  -0.146329 * Y  +   0.030790 * Z  +  66.494080 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.363404    1.778189  [ DEG:   -78.1173    101.8827 ]
  Theta =  -1.420700   -1.720892  [ DEG:   -81.4001    -98.5999 ]
  Phi   =   2.923007   -0.218586  [ DEG:   167.4760    -12.5240 ]
 
# 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: T0338TS393_5-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_5-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   77   2.95   51.95  40.690
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_5-D2
PFRMAT TS
TARGET T0338
MODEL 5
PARENT N/A
ATOM    144  CA  GLU   144     -25.179  12.899  57.533  1.00 25.00           C
ATOM    145  CA  HIS   145     -25.383  15.328  60.466  1.00 25.00           C
ATOM    146  CA  PRO   146     -27.890  17.328  62.584  1.00 25.00           C
ATOM    147  CA  HIS   147     -29.773  14.023  62.532  1.00 25.00           C
ATOM    148  CA  THR   148     -32.313  11.255  63.279  1.00 25.00           C
ATOM    149  CA  ASP   149     -30.602  10.558  66.635  1.00 25.00           C
ATOM    150  CA  VAL   150     -30.708  14.289  67.491  1.00 25.00           C
ATOM    151  CA  VAL   151     -34.432  14.412  66.607  1.00 25.00           C
ATOM    152  CA  LYS   152     -35.085  11.359  68.827  1.00 25.00           C
ATOM    153  CA  CYS   153     -33.185  13.018  71.709  1.00 25.00           C
ATOM    154  CA  THR   154     -35.243  16.216  71.258  1.00 25.00           C
ATOM    155  CA  GLN   155     -38.480  14.168  71.302  1.00 25.00           C
ATOM    156  CA  LEU   156     -37.348  12.403  74.507  1.00 25.00           C
ATOM    157  CA  VAL   157     -37.191  15.944  75.906  1.00 25.00           C
ATOM    158  CA  ARG   158     -35.862  15.693  79.431  1.00 25.00           C
ATOM    159  CA  ALA   159     -32.956  17.665  78.079  1.00 25.00           C
ATOM    160  CA  SER   160     -31.416  19.164  81.201  1.00 25.00           C
ATOM    161  CA  LYS   161     -28.211  20.891  82.181  1.00 25.00           C
ATOM    162  CA  ASP   162     -25.725  17.979  82.100  1.00 25.00           C
ATOM    163  CA  LEU   163     -27.185  16.793  78.764  1.00 25.00           C
ATOM    164  CA  ALA   164     -26.871  20.335  77.340  1.00 25.00           C
ATOM    165  CA  GLN   165     -23.227  20.507  78.507  1.00 25.00           C
ATOM    166  CA  THR   166     -22.516  17.123  76.861  1.00 25.00           C
ATOM    167  CA  SER   167     -24.114  18.343  73.603  1.00 25.00           C
ATOM    168  CA  TYR   168     -21.979  21.520  73.716  1.00 25.00           C
ATOM    169  CA  PHE   169     -18.830  19.414  74.272  1.00 25.00           C
ATOM    170  CA  MET   170     -19.766  17.185  71.301  1.00 25.00           C
ATOM    171  CA  ALA   171     -20.298  20.282  69.113  1.00 25.00           C
ATOM    172  CA  THR   172     -16.884  21.652  70.179  1.00 25.00           C
ATOM    173  CA  ASN   173     -15.246  18.295  69.334  1.00 25.00           C
ATOM    174  CA  SER   174     -16.937  18.308  65.897  1.00 25.00           C
ATOM    175  CA  LEU   175     -15.695  21.877  65.272  1.00 25.00           C
ATOM    176  CA  HIS   176     -12.144  20.842  66.262  1.00 25.00           C
ATOM    177  CA  LEU   177     -12.305  17.799  63.918  1.00 25.00           C
ATOM    178  CA  THR   178     -14.636  16.251  61.291  1.00 25.00           C
ATOM    179  CA  THR   179     -15.482  19.421  59.365  1.00 25.00           C
ATOM    180  CA  PHE   180     -18.790  19.896  61.239  1.00 25.00           C
ATOM    181  CA  CYS   181     -20.466  16.563  60.460  1.00 25.00           C
ATOM    182  CA  LEU   182     -19.578  13.865  57.972  1.00 25.00           C
ATOM    183  CA  GLN   183     -20.125  10.425  59.620  1.00 25.00           C
ATOM    184  CA  TYR   184     -19.672  11.466  63.245  1.00 25.00           C
ATOM    185  CA  LYS   185     -19.059  14.555  65.386  1.00 25.00           C
ATOM    186  CA  PRO   186     -22.854  15.202  65.194  1.00 25.00           C
ATOM    187  CA  THR   187     -26.099  13.496  66.302  1.00 25.00           C
ATOM    188  CA  VAL   188     -24.123  10.417  67.435  1.00 25.00           C
ATOM    189  CA  ILE   189     -21.722  12.654  69.409  1.00 25.00           C
ATOM    190  CA  ALA   190     -24.690  14.418  71.067  1.00 25.00           C
ATOM    191  CA  CYS   191     -26.218  11.030  71.993  1.00 25.00           C
ATOM    192  CA  VAL   192     -22.878   9.905  73.489  1.00 25.00           C
ATOM    193  CA  CYS   193     -22.667  13.145  75.520  1.00 25.00           C
ATOM    194  CA  ILE   194     -26.239  12.607  76.794  1.00 25.00           C
ATOM    195  CA  HIS   195     -25.367   9.015  77.796  1.00 25.00           C
ATOM    196  CA  LEU   196     -22.256  10.263  79.651  1.00 25.00           C
ATOM    197  CA  ALA   197     -24.367  12.884  81.480  1.00 25.00           C
ATOM    198  CA  CYS   198     -26.902  10.188  82.467  1.00 25.00           C
ATOM    199  CA  LYS   199     -24.068   7.965  83.771  1.00 25.00           C
ATOM    200  CA  TRP   200     -22.675  10.895  85.807  1.00 25.00           C
ATOM    201  CA  SER   201     -26.150  11.561  87.272  1.00 25.00           C
ATOM    202  CA  ASN   202     -29.831  12.370  86.703  1.00 25.00           C
ATOM    203  CA  TRP   203     -31.726  10.633  83.924  1.00 25.00           C
ATOM    204  CA  GLU   204     -33.289   9.393  80.701  1.00 25.00           C
ATOM    205  CA  ILE   205     -32.054   6.363  78.784  1.00 25.00           C
ATOM    206  CA  PRO   206     -33.399   3.059  80.038  1.00 25.00           C
ATOM    207  CA  VAL   207     -34.361  -0.468  78.954  1.00 25.00           C
ATOM    208  CA  SER   208     -37.895   0.379  79.981  1.00 25.00           C
ATOM    209  CA  THR   209     -39.950   1.752  77.025  1.00 25.00           C
ATOM    210  CA  ASP   210     -37.941  -0.344  74.589  1.00 25.00           C
ATOM    211  CA  GLY   211     -37.783   0.786  70.920  1.00 25.00           C
ATOM    212  CA  LYS   212     -36.923  -0.342  67.347  1.00 25.00           C
ATOM    213  CA  HIS   213     -34.090   0.614  65.049  1.00 25.00           C
ATOM    214  CA  TRP   214     -31.156   1.822  67.197  1.00 25.00           C
ATOM    215  CA  TRP   215     -29.925   0.631  70.622  1.00 25.00           C
ATOM    216  CA  GLU   216     -28.764  -2.678  69.083  1.00 25.00           C
ATOM    217  CA  TYR   217     -26.907  -0.773  66.327  1.00 25.00           C
ATOM    218  CA  VAL   218     -23.713  -2.425  67.462  1.00 25.00           C
ATOM    219  CA  ASP   219     -22.560  -5.570  65.696  1.00 25.00           C
ATOM    220  CA  PRO   220     -19.189  -3.799  65.385  1.00 25.00           C
ATOM    221  CA  THR   221     -17.947  -4.851  68.859  1.00 25.00           C
ATOM    222  CA  VAL   222     -20.873  -4.122  71.218  1.00 25.00           C
ATOM    223  CA  THR   223     -19.711  -2.713  74.559  1.00 25.00           C
ATOM    224  CA  LEU   224     -19.508   0.794  73.057  1.00 25.00           C
ATOM    225  CA  GLU   225     -15.907   0.518  71.784  1.00 25.00           C
ATOM    226  CA  LEU   226     -16.605   3.209  69.150  1.00 25.00           C
ATOM    227  CA  LEU   227     -18.095   5.491  71.841  1.00 25.00           C
ATOM    228  CA  ASP   228     -15.010   4.948  74.045  1.00 25.00           C
ATOM    229  CA  GLU   229     -12.721   5.795  71.092  1.00 25.00           C
ATOM    230  CA  LEU   230     -14.732   8.985  70.419  1.00 25.00           C
ATOM    231  CA  THR   231     -14.452   9.971  74.108  1.00 25.00           C
ATOM    232  CA  HIS   232     -10.669   9.379  74.004  1.00 25.00           C
ATOM    233  CA  GLU   233     -10.393  11.540  70.854  1.00 25.00           C
ATOM    234  CA  PHE   234     -12.401  14.322  72.556  1.00 25.00           C
ATOM    235  CA  LEU   235     -10.110  14.135  75.620  1.00 25.00           C
ATOM    236  CA  GLN   236      -7.028  14.359  73.357  1.00 25.00           C
ATOM    237  CA  ILE   237      -8.520  17.408  71.584  1.00 25.00           C
ATOM    238  CA  LEU   238      -9.214  19.066  74.965  1.00 25.00           C
ATOM    239  CA  GLU   239      -5.611  18.382  76.069  1.00 25.00           C
ATOM    240  CA  LYS   240      -4.298  19.902  72.808  1.00 25.00           C
ATOM    241  CA  THR   241      -0.831  19.246  71.240  1.00 25.00           C
ATOM    242  CA  PRO   242       0.384  21.288  68.250  1.00 25.00           C
ATOM    243  CA  ASN   243       0.527  18.233  65.944  1.00 25.00           C
ATOM    244  CA  ARG   244      -3.256  17.756  66.302  1.00 25.00           C
ATOM    245  CA  LEU   245      -3.826  21.449  65.460  1.00 25.00           C
ATOM    246  CA  LYS   246      -1.587  21.115  62.371  1.00 25.00           C
ATOM    247  CA  LYS   247      -3.536  18.011  61.262  1.00 25.00           C
ATOM    248  CA  ILE   248      -6.840  19.894  61.712  1.00 25.00           C
ATOM    249  CA  ARG   249      -5.485  22.817  59.641  1.00 25.00           C
ATOM    250  CA  ASN   250      -4.393  20.390  56.887  1.00 25.00           C
ATOM    251  CA  TRP   251      -7.869  18.782  56.891  1.00 25.00           C
ATOM    252  CA  ARG   252      -9.495  22.238  56.620  1.00 25.00           C
ATOM    253  CA  ALA   253      -7.196  23.118  53.686  1.00 25.00           C
ATOM    254  CA  ASN   254      -7.978  21.336  50.397  1.00 25.00           C
ATOM    255  CA  GLN   255     -11.515  21.420  51.794  1.00 25.00           C
ATOM    256  CA  ALA   256     -14.565  23.134  53.287  1.00 25.00           C
TER
END
