
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0298TS102_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS102_1-D2.T0298_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      C     130           -
LGA    -       -      A     131           -
LGA    R     187      V     132          4.757
LGA    V     204      A     133           -
LGA    -       -      A     134           -
LGA    -       -      E     135           -
LGA    -       -      L     136           -
LGA    -       -      C     137           -
LGA    -       -      E     138           -
LGA    -       -      V     139           -
LGA    -       -      L     140           -
LGA    -       -      A     141           -
LGA    -       -      P     142           -
LGA    -       -      L     143           -
LGA    -       -      L     144           -
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    -       -      L     147           -
LGA    -       -      D     148           -
LGA    -       -      C     149           -
LGA    -       -      R     150           -
LGA    -       -      Q     151           -
LGA    -       -      L     152           -
LGA    -       -      N     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      A     156           -
LGA    D     205      C     157          3.082
LGA    A     206      L     158          2.769
LGA    E     207      S     159          0.972
LGA    -       -      V     160           -
LGA    -       -      S     161           -
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    -       -      G     167           -
LGA    -       -      V     168           -
LGA    -       -      K     169           -
LGA    -       -      E     170           -
LGA    -       -      L     171           -
LGA    -       -      A     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      T     175           -
LGA    -       -      A     176           -
LGA    -       -      E     177           -
LGA    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      N     180           -
LGA    -       -      A     181           -
LGA    -       -      R     182           -
LGA    -       -      P     183           -
LGA    -       -      L     184           -
LGA    -       -      E     185           -
LGA    -       -      P     186           -
LGA    -       -      R     187           -
LGA    -       -      L     188           -
LGA    -       -      F     189           -
LGA    -       -      D     190           -
LGA    -       -      R     191           -
LGA    -       -      Q     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      F     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      L     198           -
LGA    -       -      A     199           -
LGA    -       -      Q     200           -
LGA    -       -      V     201           -
LGA    -       -      G     202           -
LGA    -       -      A     203           -
LGA    -       -      V     204           -
LGA    -       -      D     205           -
LGA    -       -      A     206           -
LGA    -       -      E     207           -
LGA    -       -      G     208           -
LGA    -       -      H     209           -
LGA    -       -      S     210           -
LGA    -       -      A     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      R     215           -
LGA    -       -      I     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    -       -      A     222           -
LGA    -       -      L     223           -
LGA    -       -      L     224           -
LGA    -       -      G     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      P     230           -
LGA    -       -      L     231           -
LGA    -       -      N     232           -
LGA    -       -      V     233           -
LGA    -       -      T     234           -
LGA    -       -      C     235           -
LGA    -       -      I     236           -
LGA    -       -      Q     237           -
LGA    -       -      A     238           -
LGA    -       -      P     239           -
LGA    -       -      V     240           -
LGA    -       -      F     241           -
LGA    -       -      F     242           -
LGA    G     208      G     243          2.712
LGA    H     209      D     244          2.947
LGA    V     248      S     245          2.151
LGA    T     249      L     246          1.139
LGA    L     250      S     247          5.306
LGA    Q     251      V     248          2.724
LGA    C     252      T     249          5.235
LGA    A     253      L     250          3.614
LGA    V     256      Q     251           -
LGA    -       -      C     252           -
LGA    -       -      A     253           -
LGA    -       -      E     254           -
LGA    -       -      P     255           -
LGA    D     257      V     256          2.374
LGA    L     258      D     257          2.093
LGA    -       -      L     258           -
LGA    -       -      A     259           -
LGA    A     259      A     260          2.683
LGA    A     260      V     261          2.032
LGA    V     261      T     262          2.740
LGA    T     262      R     263          2.175
LGA    R     263      V     264          1.566
LGA    V     264      L     265          2.195
LGA    L     265      D     266          2.774
LGA    -       -      A     267           -
LGA    -       -      T     268           -
LGA    -       -      K     269           -
LGA    -       -      G     270           -
LGA    -       -      I     271           -
LGA    -       -      E     272           -
LGA    -       -      W     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      E     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      Y     279           -
LGA    -       -      P     280           -
LGA    -       -      T     281           -
LGA    -       -      V     282           -
LGA    -       -      V     283           -
LGA    -       -      G     284           -
LGA    -       -      D     285           -
LGA    -       -      A     286           -
LGA    -       -      L     287           -
LGA    -       -      G     288           -
LGA    -       -      Q     289           -
LGA    -       -      D     290           -
LGA    -       -      E     291           -
LGA    -       -      T     292           -
LGA    -       -      Y     293           -
LGA    -       -      V     294           -
LGA    -       -      G     295           -
LGA    -       -      R     296           -
LGA    -       -      V     297           -
LGA    -       -      R     298           -
LGA    -       -      A     299           -
LGA    -       -      G     300           -
LGA    -       -      Q     301           -
LGA    -       -      A     302           -
LGA    -       -      D     303           -
LGA    -       -      P     304           -
LGA    -       -      C     305           -
LGA    -       -      Q     306           -
LGA    -       -      V     307           -
LGA    -       -      N     308           -
LGA    -       -      L     309           -
LGA    -       -      W     310           -
LGA    -       -      I     311           -
LGA    -       -      V     312           -
LGA    -       -      S     313           -
LGA    -       -      D     314           -
LGA    -       -      N     315           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  186    5.0     21    2.99     9.52      7.588     0.680

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.992504 * X  +   0.064715 * Y  +  -0.103671 * Z  + -18.461292
  Y_new =   0.071368 * X  +   0.381705 * Y  +   0.921525 * Z  +  56.708828
  Z_new =   0.099209 * X  +  -0.922016 * Y  +   0.374225 * Z  +  21.117249 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.185233    1.956359  [ DEG:   -67.9089    112.0911 ]
  Theta =  -0.099372   -3.042221  [ DEG:    -5.6936   -174.3064 ]
  Phi   =   0.071784   -3.069809  [ DEG:     4.1129   -175.8871 ]
 
# 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: T0298TS102_1-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS102_1-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  186   5.0   21   2.99    9.52   7.588
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS102_1-D2
PFRMAT TS
TARGET T0298
MODEL 1
PARENT 1kaf_A
ATOM    389  N   ARG   187      -7.456  76.092   9.088  1.00  1.00
ATOM    390  CA  ARG   187      -6.357  75.350   8.493  1.00  1.00
ATOM    391  C   ARG   187      -6.718  73.879   8.582  1.00  1.00
ATOM    392  O   ARG   187      -7.026  73.377   9.660  1.00  1.00
ATOM    393  CB  ARG   187      -5.041  75.596   9.238  1.00  1.00
ATOM    394  N   VAL   204      -6.708  73.194   7.443  1.00  1.00
ATOM    395  CA  VAL   204      -7.015  71.771   7.424  1.00  1.00
ATOM    396  C   VAL   204      -5.699  71.042   7.208  1.00  1.00
ATOM    397  O   VAL   204      -5.018  71.260   6.203  1.00  1.00
ATOM    398  CB  VAL   204      -7.997  71.412   6.293  1.00  1.00
ATOM    399  N   ASP   205      -5.334  70.194   8.162  1.00  1.00
ATOM    400  CA  ASP   205      -4.085  69.442   8.091  1.00  1.00
ATOM    401  C   ASP   205      -4.193  68.219   7.191  1.00  1.00
ATOM    402  O   ASP   205      -5.290  67.796   6.825  1.00  1.00
ATOM    403  CB  ASP   205      -3.654  69.021   9.486  1.00  1.00
ATOM    404  N   ALA   206      -3.041  67.656   6.838  1.00  1.00
ATOM    405  CA  ALA   206      -2.998  66.480   5.982  1.00  1.00
ATOM    406  C   ALA   206      -3.736  65.296   6.602  1.00  1.00
ATOM    407  O   ALA   206      -4.352  64.499   5.893  1.00  1.00
ATOM    408  CB  ALA   206      -1.544  66.094   5.695  1.00  1.00
ATOM    409  N   GLU   207      -3.688  65.190   7.926  1.00  1.00
ATOM    410  CA  GLU   207      -4.355  64.086   8.612  1.00  1.00
ATOM    411  C   GLU   207      -5.858  64.295   8.784  1.00  1.00
ATOM    412  O   GLU   207      -6.548  63.441   9.343  1.00  1.00
ATOM    413  CB  GLU   207      -3.711  63.840   9.979  1.00  1.00
ATOM    414  N   GLY   208      -6.366  65.429   8.313  1.00  1.00
ATOM    415  CA  GLY   208      -7.790  65.690   8.431  1.00  1.00
ATOM    416  C   GLY   208      -8.185  66.542   9.623  1.00  1.00
ATOM    417  O   GLY   208      -9.348  66.926   9.751  1.00  1.00
ATOM    418  N   HIS   209      -7.236  66.826  10.507  1.00  1.00
ATOM    419  CA  HIS   209      -7.520  67.662  11.671  1.00  1.00
ATOM    420  C   HIS   209      -7.821  69.065  11.185  1.00  1.00
ATOM    421  O   HIS   209      -7.211  69.541  10.228  1.00  1.00
ATOM    422  CB  HIS   209      -6.321  67.697  12.623  1.00  1.00
ATOM    423  N   VAL   248      -8.761  69.728  11.846  1.00  1.00
ATOM    424  CA  VAL   248      -9.139  71.077  11.449  1.00  1.00
ATOM    425  C   VAL   248      -8.879  72.032  12.599  1.00  1.00
ATOM    426  O   VAL   248      -9.208  71.735  13.741  1.00  1.00
ATOM    427  CB  VAL   248     -10.631  71.143  11.072  1.00  1.00
ATOM    428  N   THR   249      -8.266  73.172  12.294  1.00  1.00
ATOM    429  CA  THR   249      -7.988  74.174  13.310  1.00  1.00
ATOM    430  C   THR   249      -8.656  75.478  12.908  1.00  1.00
ATOM    431  O   THR   249      -8.318  76.070  11.884  1.00  1.00
ATOM    432  CB  THR   249      -6.479  74.385  13.465  1.00  1.00
ATOM    433  N   LEU   250      -9.623  75.905  13.711  1.00  1.00
ATOM    434  CA  LEU   250     -10.349  77.149  13.462  1.00  1.00
ATOM    435  C   LEU   250      -9.923  78.137  14.540  1.00  1.00
ATOM    436  O   LEU   250      -9.959  77.813  15.728  1.00  1.00
ATOM    437  CB  LEU   250     -11.855  76.894  13.538  1.00  1.00
ATOM    438  N   GLN   251      -9.502  79.329  14.122  1.00  1.00
ATOM    439  CA  GLN   251      -9.043  80.364  15.048  1.00  1.00
ATOM    440  C   GLN   251      -9.721  81.708  14.823  1.00  1.00
ATOM    441  O   GLN   251     -10.106  82.041  13.708  1.00  1.00
ATOM    442  CB  GLN   251      -7.537  80.595  14.885  1.00  1.00
ATOM    443  N   CYS   252      -9.847  82.482  15.896  1.00  1.00
ATOM    444  CA  CYS   252     -10.419  83.824  15.833  1.00  1.00
ATOM    445  C   CYS   252      -9.946  84.570  17.079  1.00  1.00
ATOM    446  O   CYS   252      -9.686  83.962  18.111  1.00  1.00
ATOM    447  CB  CYS   252     -11.963  83.793  15.773  1.00  1.00
ATOM    448  N   ALA   253      -9.802  85.888  16.994  1.00  1.00
ATOM    449  CA  ALA   253      -9.346  86.618  18.167  1.00  1.00
ATOM    450  C   ALA   253     -10.385  86.580  19.280  1.00  1.00
ATOM    451  O   ALA   253     -11.590  86.671  19.032  1.00  1.00
ATOM    452  CB  ALA   253      -9.012  88.069  17.800  1.00  1.00
ATOM    453  N   VAL   256      -9.911  86.432  20.511  1.00  1.00
ATOM    454  CA  VAL   256     -10.801  86.387  21.662  1.00  1.00
ATOM    455  C   VAL   256     -11.460  87.741  21.903  1.00  1.00
ATOM    456  O   VAL   256     -10.816  88.783  21.797  1.00  1.00
ATOM    457  CB  VAL   256     -10.018  85.983  22.917  1.00  1.00
ATOM    458  N   ASP   257     -12.754  87.701  22.210  1.00  1.00
ATOM    459  CA  ASP   257     -13.559  88.875  22.536  1.00  1.00
ATOM    460  C   ASP   257     -14.916  88.310  22.948  1.00  1.00
ATOM    461  O   ASP   257     -15.279  87.206  22.545  1.00  1.00
ATOM    462  CB  ASP   257     -13.717  89.817  21.334  1.00  1.00
ATOM    463  N   LEU   258     -15.655  89.042  23.774  1.00  1.00
ATOM    464  CA  LEU   258     -16.962  88.562  24.207  1.00  1.00
ATOM    465  C   LEU   258     -17.843  88.309  22.989  1.00  1.00
ATOM    466  O   LEU   258     -18.565  87.313  22.923  1.00  1.00
ATOM    467  CB  LEU   258     -17.619  89.585  25.123  1.00  1.00
ATOM    468  N   ALA   259     -17.767  89.216  22.022  1.00  1.00
ATOM    469  CA  ALA   259     -18.562  89.112  20.809  1.00  1.00
ATOM    470  C   ALA   259     -18.216  87.880  19.986  1.00  1.00
ATOM    471  O   ALA   259     -19.104  87.176  19.510  1.00  1.00
ATOM    472  CB  ALA   259     -18.375  90.353  19.934  1.00  1.00
ATOM    473  N   ALA   260     -16.926  87.616  19.814  1.00  1.00
ATOM    474  CA  ALA   260     -16.526  86.462  19.022  1.00  1.00
ATOM    475  C   ALA   260     -16.805  85.140  19.712  1.00  1.00
ATOM    476  O   ALA   260     -17.206  84.177  19.063  1.00  1.00
ATOM    477  CB  ALA   260     -15.049  86.554  18.637  1.00  1.00
ATOM    478  N   VAL   261     -16.603  85.087  21.024  1.00  1.00
ATOM    479  CA  VAL   261     -16.853  83.853  21.756  1.00  1.00
ATOM    480  C   VAL   261     -18.323  83.491  21.622  1.00  1.00
ATOM    481  O   VAL   261     -18.668  82.335  21.368  1.00  1.00
ATOM    482  CB  VAL   261     -16.463  84.000  23.237  1.00  1.00
ATOM    483  N   THR   262     -19.179  84.499  21.755  1.00  1.00
ATOM    484  CA  THR   262     -20.621  84.316  21.644  1.00  1.00
ATOM    485  C   THR   262     -21.002  83.834  20.247  1.00  1.00
ATOM    486  O   THR   262     -21.771  82.884  20.090  1.00  1.00
ATOM    487  CB  THR   262     -21.341  85.635  21.934  1.00  1.00
ATOM    488  N   ARG   263     -20.462  84.501  19.233  1.00  1.00
ATOM    489  CA  ARG   263     -20.746  84.160  17.844  1.00  1.00
ATOM    490  C   ARG   263     -20.291  82.745  17.495  1.00  1.00
ATOM    491  O   ARG   263     -21.011  81.996  16.831  1.00  1.00
ATOM    492  CB  ARG   263     -20.073  85.170  16.915  1.00  1.00
ATOM    493  N   VAL   264     -19.100  82.375  17.951  1.00  1.00
ATOM    494  CA  VAL   264     -18.555  81.052  17.663  1.00  1.00
ATOM    495  C   VAL   264     -19.390  79.915  18.235  1.00  1.00
ATOM    496  O   VAL   264     -19.687  78.943  17.544  1.00  1.00
ATOM    497  CB  VAL   264     -17.117  80.918  18.206  1.00  1.00
ATOM    498  N   LEU   265     -19.757  80.035  19.504  1.00  1.00
ATOM    499  CA  LEU   265     -20.545  79.003  20.163  1.00  1.00
ATOM    500  C   LEU   265     -21.942  78.926  19.556  1.00  1.00
ATOM    501  O   LEU   265     -22.515  77.846  19.420  1.00  1.00
ATOM    502  CB  LEU   265     -20.632  79.268  21.677  1.00  1.00
TER
END
