
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS393_1-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           #
LGA    -       -      H     145           -
LGA    H     145      P     146          4.852
LGA    -       -      H     147           -
LGA    P     146      T     148          4.833
LGA    H     147      D     149          3.582
LGA    T     148      -       -           -
LGA    D     149      V     150          4.795
LGA    V     150      V     151          3.607
LGA    V     151      K     152          2.632
LGA    K     152      C     153          2.232
LGA    C     153      T     154          1.355
LGA    T     154      Q     155          1.146
LGA    Q     155      L     156          2.326
LGA    L     156      V     157          2.989
LGA    -       -      R     158           -
LGA    V     157      A     159          1.239
LGA    R     158      S     160          1.129
LGA    A     159      K     161          3.179
LGA    S     160      D     162          2.311
LGA    K     161      L     163           -
LGA    D     162      A     164           -
LGA    L     163      Q     165           #
LGA    A     164      T     166          2.932
LGA    Q     165      -       -           -
LGA    T     166      S     167           #
LGA    S     167      Y     168          4.268
LGA    Y     168      F     169          2.298
LGA    F     169      M     170          3.977
LGA    M     170      A     171          3.743
LGA    A     171      T     172          1.286
LGA    T     172      N     173          1.855
LGA    N     173      S     174          2.168
LGA    S     174      L     175          1.760
LGA    L     175      H     176          3.091
LGA    H     176      -       -           -
LGA    L     177      L     177          2.566
LGA    T     178      T     178          1.867
LGA    T     179      T     179          2.153
LGA    F     180      F     180          3.161
LGA    C     181      C     181          2.920
LGA    L     182      L     182           #
LGA    -       -      Q     183           -
LGA    -       -      Y     184           -
LGA    -       -      K     185           -
LGA    -       -      P     186           -
LGA    -       -      T     187           -
LGA    Q     183      V     188           #
LGA    Y     184      I     189          1.839
LGA    K     185      -       -           -
LGA    P     186      A     190          3.130
LGA    T     187      C     191          3.298
LGA    V     188      V     192          2.784
LGA    I     189      C     193          2.316
LGA    A     190      I     194          2.316
LGA    C     191      H     195          2.396
LGA    V     192      L     196          2.284
LGA    C     193      A     197          1.912
LGA    I     194      C     198          1.768
LGA    H     195      K     199          2.022
LGA    L     196      W     200          1.758
LGA    A     197      S     201          1.394
LGA    C     198      N     202          1.315
LGA    K     199      -       -           -
LGA    W     200      -       -           -
LGA    S     201      -       -           -
LGA    N     202      -       -           -
LGA    W     203      -       -           -
LGA    E     204      W     203          4.557
LGA    I     205      E     204          2.311
LGA    P     206      I     205          4.756
LGA    V     207      -       -           -
LGA    S     208      P     206          4.591
LGA    T     209      V     207           #
LGA    D     210      S     208          3.598
LGA    G     211      T     209          3.145
LGA    -       -      D     210           -
LGA    K     212      G     211          3.612
LGA    H     213      K     212          1.978
LGA    W     214      H     213          2.655
LGA    W     215      W     214          3.721
LGA    E     216      W     215           -
LGA    Y     217      E     216           -
LGA    V     218      Y     217           -
LGA    D     219      V     218           -
LGA    P     220      D     219           -
LGA    T     221      P     220           -
LGA    V     222      T     221           -
LGA    -       -      V     222           -
LGA    T     223      T     223          3.400
LGA    L     224      L     224          2.183
LGA    E     225      E     225          2.610
LGA    L     226      L     226          1.982
LGA    L     227      L     227          0.975
LGA    D     228      D     228          1.704
LGA    E     229      E     229          2.092
LGA    L     230      L     230          1.929
LGA    T     231      T     231          1.162
LGA    H     232      H     232          1.167
LGA    E     233      E     233          1.997
LGA    F     234      F     234          2.407
LGA    L     235      L     235          1.726
LGA    Q     236      Q     236          0.938
LGA    I     237      I     237          2.873
LGA    L     238      L     238          3.188
LGA    E     239      E     239          1.658
LGA    K     240      K     240          2.092
LGA    T     241      T     241          1.531
LGA    P     242      P     242          1.161
LGA    N     243      N     243          2.957
LGA    R     244      -       -           -
LGA    L     245      -       -           -
LGA    K     246      R     244          4.986
LGA    K     247      L     245           -
LGA    I     248      K     246           -
LGA    R     249      K     247           #
LGA    N     250      I     248           -
LGA    W     251      R     249           -
LGA    R     252      N     250           -
LGA    A     253      -       -           -
LGA    N     254      -       -           -
LGA    Q     255      -       -           -
LGA    A     256      W     251           #
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     76    2.76    38.16     42.138     2.653

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.875985 * X  +   0.110764 * Y  +   0.469449 * Z  + -25.509388
  Y_new =   0.435628 * X  +   0.236157 * Y  +  -0.868596 * Z  +  24.088018
  Z_new =  -0.207073 * X  +   0.965381 * Y  +   0.158618 * Z  +  71.022919 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.407945   -1.733647  [ DEG:    80.6693    -99.3307 ]
  Theta =   0.208582    2.933011  [ DEG:    11.9509    168.0491 ]
  Phi   =   0.461486   -2.680107  [ DEG:    26.4412   -153.5588 ]
 
# 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_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_1-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   76   2.76   38.16  42.138
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_1-D2
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM    144  CA  GLU   144     -25.897  12.573  58.888  1.00 25.00           C
ATOM    145  CA  HIS   145     -26.582  12.522  62.688  1.00 25.00           C
ATOM    146  CA  PRO   146     -29.535  14.277  64.340  1.00 25.00           C
ATOM    147  CA  HIS   147     -33.277  13.623  64.581  1.00 25.00           C
ATOM    148  CA  THR   148     -33.603  10.489  66.758  1.00 25.00           C
ATOM    149  CA  ASP   149     -30.648  11.643  68.904  1.00 25.00           C
ATOM    150  CA  VAL   150     -32.255  15.096  69.306  1.00 25.00           C
ATOM    151  CA  VAL   151     -35.560  13.463  70.346  1.00 25.00           C
ATOM    152  CA  LYS   152     -33.712  11.297  72.907  1.00 25.00           C
ATOM    153  CA  CYS   153     -31.958  14.402  74.303  1.00 25.00           C
ATOM    154  CA  THR   154     -35.322  16.210  74.582  1.00 25.00           C
ATOM    155  CA  GLN   155     -36.817  13.197  76.414  1.00 25.00           C
ATOM    156  CA  LEU   156     -33.840  13.156  78.824  1.00 25.00           C
ATOM    157  CA  VAL   157     -33.516  16.808  79.756  1.00 25.00           C
ATOM    158  CA  ARG   158     -33.085  17.676  83.450  1.00 25.00           C
ATOM    159  CA  ALA   159     -30.064  19.901  82.928  1.00 25.00           C
ATOM    160  CA  SER   160     -27.197  22.178  84.023  1.00 25.00           C
ATOM    161  CA  LYS   161     -23.690  23.710  84.458  1.00 25.00           C
ATOM    162  CA  ASP   162     -21.274  20.792  83.898  1.00 25.00           C
ATOM    163  CA  LEU   163     -23.672  19.268  81.331  1.00 25.00           C
ATOM    164  CA  ALA   164     -23.920  22.636  79.525  1.00 25.00           C
ATOM    165  CA  GLN   165     -20.100  22.911  79.463  1.00 25.00           C
ATOM    166  CA  THR   166     -19.844  19.368  78.034  1.00 25.00           C
ATOM    167  CA  SER   167     -22.416  20.244  75.335  1.00 25.00           C
ATOM    168  CA  TYR   168     -20.444  23.404  74.445  1.00 25.00           C
ATOM    169  CA  PHE   169     -17.220  21.351  74.196  1.00 25.00           C
ATOM    170  CA  MET   170     -18.977  18.825  71.915  1.00 25.00           C
ATOM    171  CA  ALA   171     -20.254  21.675  69.700  1.00 25.00           C
ATOM    172  CA  THR   172     -16.719  23.133  69.493  1.00 25.00           C
ATOM    173  CA  ASN   173     -15.333  19.695  68.524  1.00 25.00           C
ATOM    174  CA  SER   174     -18.015  19.353  65.810  1.00 25.00           C
ATOM    175  CA  LEU   175     -17.133  22.829  64.465  1.00 25.00           C
ATOM    176  CA  HIS   176     -13.423  21.885  64.389  1.00 25.00           C
ATOM    177  CA  LEU   177     -11.309  19.250  66.213  1.00 25.00           C
ATOM    178  CA  THR   178     -13.121  15.897  66.062  1.00 25.00           C
ATOM    179  CA  THR   179     -11.324  15.006  62.784  1.00 25.00           C
ATOM    180  CA  PHE   180     -14.413  14.729  60.582  1.00 25.00           C
ATOM    181  CA  CYS   181     -16.140  18.071  61.194  1.00 25.00           C
ATOM    182  CA  LEU   182     -19.837  17.773  61.900  1.00 25.00           C
ATOM    183  CA  GLN   183     -19.082  14.150  62.582  1.00 25.00           C
ATOM    184  CA  TYR   184     -21.533  12.457  64.925  1.00 25.00           C
ATOM    185  CA  LYS   185     -22.951  15.904  65.498  1.00 25.00           C
ATOM    186  CA  PRO   186     -26.179  16.249  67.554  1.00 25.00           C
ATOM    187  CA  THR   187     -26.570  12.713  68.971  1.00 25.00           C
ATOM    188  CA  VAL   188     -22.858  12.653  69.912  1.00 25.00           C
ATOM    189  CA  ILE   189     -23.218  16.049  71.645  1.00 25.00           C
ATOM    190  CA  ALA   190     -26.266  14.768  73.577  1.00 25.00           C
ATOM    191  CA  CYS   191     -24.309  11.655  74.650  1.00 25.00           C
ATOM    192  CA  VAL   192     -21.403  13.856  75.820  1.00 25.00           C
ATOM    193  CA  CYS   193     -23.831  16.043  77.817  1.00 25.00           C
ATOM    194  CA  ILE   194     -25.355  12.921  79.429  1.00 25.00           C
ATOM    195  CA  HIS   195     -21.859  11.658  80.348  1.00 25.00           C
ATOM    196  CA  LEU   196     -21.009  15.057  81.893  1.00 25.00           C
ATOM    197  CA  ALA   197     -24.262  14.979  83.913  1.00 25.00           C
ATOM    198  CA  CYS   198     -23.444  11.446  85.142  1.00 25.00           C
ATOM    199  CA  LYS   199     -19.937  12.590  86.170  1.00 25.00           C
ATOM    200  CA  TRP   200     -21.435  15.564  88.060  1.00 25.00           C
ATOM    201  CA  SER   201     -23.883  13.226  89.851  1.00 25.00           C
ATOM    202  CA  ASN   202     -26.795  15.430  88.670  1.00 25.00           C
ATOM    203  CA  TRP   203     -28.313  12.739  86.451  1.00 25.00           C
ATOM    204  CA  GLU   204     -31.138  10.157  86.648  1.00 25.00           C
ATOM    205  CA  ILE   205     -30.347   8.931  83.128  1.00 25.00           C
ATOM    206  CA  PRO   206     -29.031   5.590  84.293  1.00 25.00           C
ATOM    207  CA  VAL   207     -31.193   2.633  85.488  1.00 25.00           C
ATOM    208  CA  SER   208     -34.860   3.608  85.332  1.00 25.00           C
ATOM    209  CA  THR   209     -37.955   3.476  83.118  1.00 25.00           C
ATOM    210  CA  ASP   210     -37.909   0.773  80.370  1.00 25.00           C
ATOM    211  CA  GLY   211     -38.095   0.723  76.565  1.00 25.00           C
ATOM    212  CA  LYS   212     -35.413  -0.271  74.083  1.00 25.00           C
ATOM    213  CA  HIS   213     -32.437  -2.284  72.878  1.00 25.00           C
ATOM    214  CA  TRP   214     -30.158   0.694  72.323  1.00 25.00           C
ATOM    215  CA  TRP   215     -29.964   2.479  75.706  1.00 25.00           C
ATOM    216  CA  GLU   216     -28.621  -0.713  77.341  1.00 25.00           C
ATOM    217  CA  TYR   217     -25.986  -1.047  74.582  1.00 25.00           C
ATOM    218  CA  VAL   218     -23.198  -2.614  76.600  1.00 25.00           C
ATOM    219  CA  ASP   219     -20.320  -4.075  78.630  1.00 25.00           C
ATOM    220  CA  PRO   220     -16.747  -3.217  77.759  1.00 25.00           C
ATOM    221  CA  THR   221     -17.877  -2.554  74.136  1.00 25.00           C
ATOM    222  CA  VAL   222     -19.796  -4.197  71.311  1.00 25.00           C
ATOM    223  CA  THR   223     -22.585  -2.622  69.189  1.00 25.00           C
ATOM    224  CA  LEU   224     -21.813   0.456  71.361  1.00 25.00           C
ATOM    225  CA  GLU   225     -18.364   0.551  69.700  1.00 25.00           C
ATOM    226  CA  LEU   226     -19.249   3.865  67.996  1.00 25.00           C
ATOM    227  CA  LEU   227     -20.405   5.309  71.351  1.00 25.00           C
ATOM    228  CA  ASP   228     -17.132   4.183  72.991  1.00 25.00           C
ATOM    229  CA  GLU   229     -15.126   5.821  70.168  1.00 25.00           C
ATOM    230  CA  LEU   230     -17.109   9.068  70.610  1.00 25.00           C
ATOM    231  CA  THR   231     -16.439   8.993  74.380  1.00 25.00           C
ATOM    232  CA  HIS   232     -12.702   8.463  73.731  1.00 25.00           C
ATOM    233  CA  GLU   233     -12.683  11.412  71.288  1.00 25.00           C
ATOM    234  CA  PHE   234     -14.440  13.608  73.887  1.00 25.00           C
ATOM    235  CA  LEU   235     -11.862  12.586  76.529  1.00 25.00           C
ATOM    236  CA  GLN   236      -9.014  13.435  74.114  1.00 25.00           C
ATOM    237  CA  ILE   237     -10.594  16.852  73.412  1.00 25.00           C
ATOM    238  CA  LEU   238     -10.907  17.507  77.173  1.00 25.00           C
ATOM    239  CA  GLU   239      -7.232  16.552  77.669  1.00 25.00           C
ATOM    240  CA  LYS   240      -6.208  18.919  74.838  1.00 25.00           C
ATOM    241  CA  THR   241      -5.122  22.429  73.987  1.00 25.00           C
ATOM    242  CA  PRO   242      -6.098  23.945  77.367  1.00 25.00           C
ATOM    243  CA  ASN   243      -4.095  27.155  76.773  1.00 25.00           C
ATOM    244  CA  ARG   244      -5.433  27.356  73.191  1.00 25.00           C
ATOM    245  CA  LEU   245      -9.012  26.893  74.475  1.00 25.00           C
ATOM    246  CA  LYS   246      -8.471  29.668  77.058  1.00 25.00           C
ATOM    247  CA  LYS   247      -7.120  31.984  74.322  1.00 25.00           C
ATOM    248  CA  ILE   248     -10.170  31.219  72.135  1.00 25.00           C
ATOM    249  CA  ARG   249     -12.501  31.985  75.076  1.00 25.00           C
ATOM    250  CA  ASN   250     -10.681  35.299  75.687  1.00 25.00           C
ATOM    251  CA  TRP   251     -11.023  36.199  71.980  1.00 25.00           C
ATOM    252  CA  ARG   252     -14.764  35.388  72.103  1.00 25.00           C
ATOM    253  CA  ALA   253     -15.163  37.587  75.213  1.00 25.00           C
ATOM    254  CA  ASN   254     -18.161  38.151  77.431  1.00 25.00           C
ATOM    255  CA  GLN   255     -19.710  34.705  77.679  1.00 25.00           C
ATOM    256  CA  ALA   256     -20.744  31.087  77.055  1.00 25.00           C
TER
END
