
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0295TS168_4-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295TS168_4-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     181      -       -           -
LGA    N     182      -       -           -
LGA    F     183      -       -           -
LGA    D     184      -       -           -
LGA    E     185      -       -           -
LGA    W     186      T     181           #
LGA    D     187      N     182           -
LGA    N     188      F     183           #
LGA    L     189      D     184          3.099
LGA    L     190      E     185           #
LGA    R     191      W     186           #
LGA    I     192      D     187          4.392
LGA    C     193      N     188          1.639
LGA    F     194      L     189           #
LGA    S     195      L     190           #
LGA    R     196      R     191          4.395
LGA    K     197      I     192          1.367
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    R     198      S     195          3.325
LGA    K     199      R     196           -
LGA    T     200      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    -       -      T     200           -
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    L     201      I     204           #
LGA    H     202      F     205           -
LGA    A     203      K     206           -
LGA    I     204      R     207          3.894
LGA    F     205      -       -           -
LGA    K     206      -       -           -
LGA    R     207      -       -           -
LGA    N     208      N     208          3.403
LGA    A     209      A     209          2.813
LGA    V     210      V     210          2.581
LGA    L     211      L     211          0.634
LGA    N     212      N     212          1.866
LGA    M     213      M     213          2.417
LGA    L     214      L     214          1.305
LGA    E     215      E     215          0.762
LGA    H     216      H     216          1.863
LGA    N     217      N     217          1.581
LGA    Y     218      Y     218          0.314
LGA    K     219      K     219          0.970
LGA    N     220      N     220          1.355
LGA    W     221      W     221          0.926
LGA    C     222      C     222          0.331
LGA    T     223      T     223          0.788
LGA    L     224      L     224          0.955
LGA    N     225      N     225          2.906
LGA    K     226      K     226          1.037
LGA    Q     227      Q     227          4.239
LGA    V     228      V     228          3.402
LGA    P     229      P     229           #
LGA    V     230      -       -           -
LGA    N     231      -       -           -
LGA    F     232      -       -           -
LGA    P     233      -       -           -
LGA    F     234      V     230           #
LGA    K     235      N     231           #
LGA    K     236      F     232           #
LGA    Y     237      P     233           -
LGA    -       -      F     234           -
LGA    -       -      K     235           -
LGA    C     238      K     236           #
LGA    L     239      Y     237          3.031
LGA    D     240      C     238           #
LGA    V     241      L     239          2.228
LGA    L     242      -       -           -
LGA    E     243      -       -           -
LGA    H     244      -       -           -
LGA    L     245      D     240          5.246
LGA    -       -      V     241           -
LGA    -       -      L     242           -
LGA    D     246      E     243          3.348
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    -       -      D     246           -
LGA    M     247      M     247          3.607
LGA    C     248      C     248          3.860
LGA    E     249      E     249          3.142
LGA    K     250      -       -           -
LGA    R     251      K     250          4.267
LGA    S     252      R     251          4.583
LGA    I     253      S     252           -
LGA    -       -      I     253           -
LGA    N     254      N     254          3.962
LGA    L     255      L     255          2.959
LGA    D     256      D     256          4.719
LGA    E     257      E     257          4.290
LGA    N     258      N     258          2.942
LGA    D     259      D     259          3.251
LGA    F     260      F     260          2.010
LGA    L     261      L     261          0.990
LGA    K     262      K     262          1.177
LGA    L     263      L     263          1.494
LGA    L     264      L     264          0.951
LGA    L     265      L     265          1.818
LGA    E     266      E     266          2.898
LGA    F     267      F     267          3.551
LGA    N     268      N     268          3.992
LGA    K     269      K     269          4.424
LGA    K     270      K     270          4.442
LGA    G     271      G     271          2.681
LGA    I     272      I     272          1.429
LGA    H     273      H     273          1.233
LGA    F     274      F     274          3.268
LGA    F     275      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     58    2.91    79.31     39.711     1.925

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.270882 * X  +  -0.671366 * Y  +   0.689849 * Z  +   8.971676
  Y_new =  -0.129585 * X  +   0.735551 * Y  +   0.664960 * Z  +   0.815491
  Z_new =  -0.953851 * X  +   0.090732 * Y  +  -0.286246 * Z  +   6.219584 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.834639   -0.306953  [ DEG:   162.4129    -17.5871 ]
  Theta =   1.265808    1.875784  [ DEG:    72.5255    107.4745 ]
  Phi   =  -2.695390    0.446203  [ DEG:  -154.4344     25.5655 ]
 
# 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: T0295TS168_4-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS168_4-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   58   2.91   79.31  39.711
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS168_4-D2
PFRMAT TS
TARGET T0295
MODEL 4
PARENT N/A
ATOM    181  CA  THR   181      19.961   7.634  15.266  1.00 25.00           C
ATOM    182  CA  ASN   182      16.724   9.219  16.437  1.00 25.00           C
ATOM    183  CA  PHE   183      13.176   9.148  15.093  1.00 25.00           C
ATOM    184  CA  ASP   184      10.061  11.346  14.740  1.00 25.00           C
ATOM    185  CA  GLU   185      12.262  14.475  14.539  1.00 25.00           C
ATOM    186  CA  TRP   186      14.418  12.813  11.845  1.00 25.00           C
ATOM    187  CA  ASP   187      11.273  11.888   9.865  1.00 25.00           C
ATOM    188  CA  ASN   188      10.015  15.495  10.129  1.00 25.00           C
ATOM    189  CA  LEU   189      13.401  16.793   8.901  1.00 25.00           C
ATOM    190  CA  LEU   190      13.290  14.360   5.945  1.00 25.00           C
ATOM    191  CA  ARG   191       9.747  15.532   5.083  1.00 25.00           C
ATOM    192  CA  ILE   192      10.895  19.184   5.220  1.00 25.00           C
ATOM    193  CA  CYS   193      13.844  18.369   2.918  1.00 25.00           C
ATOM    194  CA  PHE   194      11.477  16.626   0.462  1.00 25.00           C
ATOM    195  CA  SER   195       9.155  19.671   0.500  1.00 25.00           C
ATOM    196  CA  ARG   196      12.134  21.982  -0.175  1.00 25.00           C
ATOM    197  CA  LYS   197      13.227  19.759  -3.096  1.00 25.00           C
ATOM    198  CA  ARG   198       9.674  19.845  -4.524  1.00 25.00           C
ATOM    199  CA  LYS   199       9.620  23.664  -4.224  1.00 25.00           C
ATOM    200  CA  THR   200      12.997  23.876  -6.018  1.00 25.00           C
ATOM    201  CA  LEU   201      11.684  21.610  -8.811  1.00 25.00           C
ATOM    202  CA  HIS   202       8.568  23.809  -9.165  1.00 25.00           C
ATOM    203  CA  ALA   203      10.769  26.937  -9.366  1.00 25.00           C
ATOM    204  CA  ILE   204      12.926  25.277 -12.060  1.00 25.00           C
ATOM    205  CA  PHE   205       9.781  24.351 -14.041  1.00 25.00           C
ATOM    206  CA  LYS   206       8.522  27.958 -13.776  1.00 25.00           C
ATOM    207  CA  ARG   207      11.910  29.256 -15.005  1.00 25.00           C
ATOM    208  CA  ASN   208      14.113  30.995 -12.373  1.00 25.00           C
ATOM    209  CA  ALA   209      15.298  32.325  -9.013  1.00 25.00           C
ATOM    210  CA  VAL   210      15.648  29.125  -6.968  1.00 25.00           C
ATOM    211  CA  LEU   211      19.385  28.716  -7.698  1.00 25.00           C
ATOM    212  CA  ASN   212      19.951  32.441  -7.014  1.00 25.00           C
ATOM    213  CA  MET   213      18.046  32.150  -3.706  1.00 25.00           C
ATOM    214  CA  LEU   214      20.169  29.118  -2.722  1.00 25.00           C
ATOM    215  CA  GLU   215      23.365  31.056  -3.556  1.00 25.00           C
ATOM    216  CA  HIS   216      22.160  34.008  -1.434  1.00 25.00           C
ATOM    217  CA  ASN   217      21.411  31.637   1.480  1.00 25.00           C
ATOM    218  CA  TYR   218      24.904  30.102   1.162  1.00 25.00           C
ATOM    219  CA  LYS   219      26.468  33.598   1.175  1.00 25.00           C
ATOM    220  CA  ASN   220      24.460  34.513   4.304  1.00 25.00           C
ATOM    221  CA  TRP   221      25.621  31.292   6.021  1.00 25.00           C
ATOM    222  CA  CYS   222      29.255  32.089   5.113  1.00 25.00           C
ATOM    223  CA  THR   223      28.859  35.626   6.528  1.00 25.00           C
ATOM    224  CA  LEU   224      27.762  34.016   9.772  1.00 25.00           C
ATOM    225  CA  ASN   225      31.276  33.909  11.292  1.00 25.00           C
ATOM    226  CA  LYS   226      33.332  33.888   8.092  1.00 25.00           C
ATOM    227  CA  GLN   227      37.112  33.640   8.287  1.00 25.00           C
ATOM    228  CA  VAL   228      37.269  32.544   4.714  1.00 25.00           C
ATOM    229  CA  PRO   229      40.480  31.822   2.832  1.00 25.00           C
ATOM    230  CA  VAL   230      43.335  29.906   1.295  1.00 25.00           C
ATOM    231  CA  ASN   231      43.035  28.097  -2.107  1.00 25.00           C
ATOM    232  CA  PHE   232      39.612  27.173  -0.819  1.00 25.00           C
ATOM    233  CA  PRO   233      39.345  23.435  -0.885  1.00 25.00           C
ATOM    234  CA  PHE   234      35.666  23.996  -1.867  1.00 25.00           C
ATOM    235  CA  LYS   235      35.461  26.722  -4.549  1.00 25.00           C
ATOM    236  CA  LYS   236      36.322  24.154  -7.258  1.00 25.00           C
ATOM    237  CA  TYR   237      33.607  21.804  -5.927  1.00 25.00           C
ATOM    238  CA  CYS   238      31.067  24.671  -5.975  1.00 25.00           C
ATOM    239  CA  LEU   239      32.043  25.509  -9.581  1.00 25.00           C
ATOM    240  CA  ASP   240      31.623  21.834 -10.575  1.00 25.00           C
ATOM    241  CA  VAL   241      28.172  21.756  -8.916  1.00 25.00           C
ATOM    242  CA  LEU   242      27.170  24.941 -10.792  1.00 25.00           C
ATOM    243  CA  GLU   243      28.347  23.396 -14.093  1.00 25.00           C
ATOM    244  CA  HIS   244      26.319  20.230 -13.364  1.00 25.00           C
ATOM    245  CA  LEU   245      29.428  18.063 -13.830  1.00 25.00           C
ATOM    246  CA  ASP   246      27.663  14.673 -13.408  1.00 25.00           C
ATOM    247  CA  MET   247      23.909  14.881 -13.483  1.00 25.00           C
ATOM    248  CA  CYS   248      24.034  13.604 -17.014  1.00 25.00           C
ATOM    249  CA  GLU   249      21.418  10.990 -18.065  1.00 25.00           C
ATOM    250  CA  LYS   250      22.161   8.636 -15.158  1.00 25.00           C
ATOM    251  CA  ARG   251      18.400   8.065 -15.130  1.00 25.00           C
ATOM    252  CA  SER   252      16.636   6.526 -12.151  1.00 25.00           C
ATOM    253  CA  ILE   253      17.832   3.008 -12.990  1.00 25.00           C
ATOM    254  CA  ASN   254      18.775   2.848  -9.353  1.00 25.00           C
ATOM    255  CA  LEU   255      20.813   5.875  -8.500  1.00 25.00           C
ATOM    256  CA  ASP   256      22.150   3.684  -5.702  1.00 25.00           C
ATOM    257  CA  GLU   257      21.460   6.805  -3.561  1.00 25.00           C
ATOM    258  CA  ASN   258      25.095   6.874  -2.356  1.00 25.00           C
ATOM    259  CA  ASP   259      25.738  10.051  -4.395  1.00 25.00           C
ATOM    260  CA  PHE   260      22.616  11.679  -2.888  1.00 25.00           C
ATOM    261  CA  LEU   261      23.794  10.736   0.632  1.00 25.00           C
ATOM    262  CA  LYS   262      27.242  12.234  -0.094  1.00 25.00           C
ATOM    263  CA  LEU   263      25.603  15.457  -1.358  1.00 25.00           C
ATOM    264  CA  LEU   264      23.460  15.638   1.811  1.00 25.00           C
ATOM    265  CA  LEU   265      26.579  15.153   3.979  1.00 25.00           C
ATOM    266  CA  GLU   266      28.375  17.940   2.062  1.00 25.00           C
ATOM    267  CA  PHE   267      25.368  20.257   2.564  1.00 25.00           C
ATOM    268  CA  ASN   268      25.353  19.466   6.311  1.00 25.00           C
ATOM    269  CA  LYS   269      29.101  20.223   6.511  1.00 25.00           C
ATOM    270  CA  LYS   270      29.875  23.421   4.635  1.00 25.00           C
ATOM    271  CA  GLY   271      26.399  24.946   4.274  1.00 25.00           C
ATOM    272  CA  ILE   272      24.138  24.962   1.220  1.00 25.00           C
ATOM    273  CA  HIS   273      21.560  23.617   3.672  1.00 25.00           C
ATOM    274  CA  PHE   274      20.188  20.134   3.434  1.00 25.00           C
ATOM    275  CA  PHE   275      20.011  18.302   6.773  1.00 25.00           C
TER
END
