
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0320TS599_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS599_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    N     228      L     236           #
LGA    N     229      R     237          4.516
LGA    S     230      K     238          4.237
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    L     231      N     242          4.718
LGA    P     232      P     243          2.421
LGA    N     233      A     244          0.794
LGA    P     234      L     245          3.110
LGA    H     235      H     246          2.487
LGA    L     236      F     247          3.492
LGA    R     237      E     248          3.353
LGA    K     238      W     249          2.716
LGA    D     239      E     250           #
LGA    S     240      -       -           -
LGA    N     241      -       -           -
LGA    N     242      -       -           -
LGA    P     243      -       -           -
LGA    A     244      -       -           -
LGA    L     245      I     251          1.253
LGA    H     246      I     252           -
LGA    F     247      H     253           -
LGA    E     248      A     254           -
LGA    W     249      F     255           -
LGA    E     250      G     256           -
LGA    I     251      K     257           -
LGA    I     252      D     258           -
LGA    H     253      R     263           -
LGA    A     254      S     264           -
LGA    F     255      S     265           -
LGA    G     256      A     266           -
LGA    K     257      I     267           -
LGA    D     258      N     268           -
LGA    A     259      T     269           -
LGA    E     260      -       -           -
LGA    G     261      -       -           -
LGA    E     262      -       -           -
LGA    R     263      -       -           -
LGA    S     264      -       -           -
LGA    S     265      -       -           -
LGA    A     266      -       -           -
LGA    I     267      -       -           -
LGA    N     268      -       -           -
LGA    T     269      -       -           -
LGA    S     270      -       -           -
LGA    P     271      -       -           -
LGA    I     272      -       -           -
LGA    S     273      -       -           -
LGA    V     274      -       -           -
LGA    V     275      S     270           #
LGA    D     276      P     271           #
LGA    K     277      I     272          3.162
LGA    E     278      S     273          2.972
LGA    -       -      V     274           -
LGA    R     279      V     275          1.606
LGA    F     280      D     276          1.051
LGA    S     281      K     277          0.843
LGA    K     282      E     278          1.440
LGA    Y     283      R     279          1.438
LGA    H     284      F     280          1.077
LGA    D     285      S     281          1.505
LGA    -       -      K     282           -
LGA    N     286      Y     283          4.256
LGA    Y     287      H     284          1.699
LGA    -       -      D     285           -
LGA    Y     288      N     286          3.521
LGA    P     289      Y     287          3.983
LGA    G     290      Y     288          4.755
LGA    W     291      P     289          5.014
LGA    Y     292      G     290          5.240
LGA    L     293      W     291          3.568
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    V     294      V     294          2.708
LGA    -       -      D     295           -
LGA    D     295      D     296           #
LGA    D     296      T     297           -
LGA    T     297      L     298           -
LGA    L     298      E     299           -
LGA    E     299      R     300           -
LGA    R     300      A     301           -
LGA    A     301      G     302           -
LGA    G     302      R     303           -
LGA    R     303      I     304           -
LGA    I     304      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   73    5.0     29    3.17    10.34     24.928     0.888

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.850396 * X  +   0.161591 * Y  +   0.500715 * Z  +  13.258543
  Y_new =  -0.210700 * X  +   0.767437 * Y  +  -0.605513 * Z  +  21.472979
  Z_new =  -0.482112 * X  +  -0.620426 * Y  +  -0.618578 * Z  +   9.855147 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.354703    0.786890  [ DEG:  -134.9145     45.0855 ]
  Theta =   0.503064    2.638528  [ DEG:    28.8235    151.1765 ]
  Phi   =  -2.898716    0.242876  [ DEG:  -166.0842     13.9158 ]
 
# 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: T0320TS599_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   73   5.0   29   3.17   10.34  24.928
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_2-D2
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    228  CA  ASN   228      10.662  17.406  -0.391  1.00  0.00              
ATOM    229  CA  ASN   229      10.850  14.123  -2.359  1.00  0.00              
ATOM    230  CA  SER   230      10.972  11.611   0.522  1.00  0.00              
ATOM    231  CA  LEU   231       7.781  12.678   2.229  1.00  0.00              
ATOM    232  CA  PRO   232       4.889  10.216   1.651  1.00  0.00              
ATOM    233  CA  ASN   233       3.283   9.773   4.988  1.00  0.00              
ATOM    234  CA  PRO   234       0.266  11.983   4.587  1.00  0.00              
ATOM    235  CA  HIS   235      -0.307  13.069   8.071  1.00  0.00              
ATOM    236  CA  LEU   236      -1.640  16.699   8.450  1.00  0.00              
ATOM    237  CA  ARG   237      -3.839  17.388  11.330  1.00  0.00              
ATOM    238  CA  LYS   238      -5.380  20.766  12.111  1.00  0.00              
ATOM    239  CA  ASP   239      -7.454  20.739  15.308  1.00  0.00              
ATOM    240  CA  SER   240      -8.982  24.025  15.543  1.00  0.00              
ATOM    241  CA  ASN   241      -7.613  27.072  17.225  1.00  0.00              
ATOM    242  CA  ASN   242      -5.030  28.569  14.941  1.00  0.00              
ATOM    243  CA  PRO   243      -5.779  26.621  11.877  1.00  0.00              
ATOM    244  CA  ALA   244      -2.268  25.543  11.086  1.00  0.00              
ATOM    245  CA  LEU   245      -1.654  22.352   9.210  1.00  0.00              
ATOM    246  CA  HIS   246       0.562  19.661  10.404  1.00  0.00              
ATOM    247  CA  PHE   247       2.684  17.986   7.781  1.00  0.00              
ATOM    248  CA  GLU   248       3.802  14.539   8.503  1.00  0.00              
ATOM    249  CA  TRP   249       7.256  13.310   7.490  1.00  0.00              
ATOM    250  CA  GLU   250       8.341   9.794   8.415  1.00  0.00              
ATOM    251  CA  ILE   251      11.802   9.274   9.787  1.00  0.00              
ATOM    252  CA  ILE   252      13.503   6.159   8.554  1.00  0.00              
ATOM    253  CA  HIS   253      16.481   5.425  10.713  1.00  0.00              
ATOM    254  CA  ALA   254      19.108   6.784   8.276  1.00  0.00              
ATOM    255  CA  PHE   255      17.620  10.283   8.173  1.00  0.00              
ATOM    256  CA  GLY   256      17.334  10.855  11.908  1.00  0.00              
ATOM    257  CA  LYS   257      20.995   9.850  12.460  1.00  0.00              
ATOM    258  CA  ASP   258      23.131  11.598   9.892  1.00  0.00              
ATOM    259  CA  ALA   259      21.577  15.064   9.768  1.00  0.00              
ATOM    260  CA  GLU   260      21.049  15.658  13.448  1.00  0.00              
ATOM    261  CA  GLY   261      24.573  14.916  14.601  1.00  0.00              
ATOM    262  CA  GLU   262      26.032  17.218  11.912  1.00  0.00              
ATOM    263  CA  ARG   263      23.727  20.125  12.859  1.00  0.00              
ATOM    264  CA  SER   264      24.249  19.793  16.678  1.00  0.00              
ATOM    265  CA  SER   265      28.010  19.729  16.066  1.00  0.00              
ATOM    266  CA  ALA   266      28.307  22.835  14.075  1.00  0.00              
ATOM    267  CA  ILE   267      25.888  24.882  16.256  1.00  0.00              
ATOM    268  CA  ASN   268      27.606  28.157  16.542  1.00  0.00              
ATOM    269  CA  THR   269      26.703  29.248  20.079  1.00  0.00              
ATOM    270  CA  SER   270      24.353  32.036  19.651  1.00  0.00              
ATOM    271  CA  PRO   271      21.233  30.520  21.195  1.00  0.00              
ATOM    272  CA  ILE   272      19.177  30.855  18.071  1.00  0.00              
ATOM    273  CA  SER   273      21.363  31.424  15.081  1.00  0.00              
ATOM    274  CA  VAL   274      19.935  33.115  12.109  1.00  0.00              
ATOM    275  CA  VAL   275      21.289  32.260   8.868  1.00  0.00              
ATOM    276  CA  ASP   276      21.184  34.741   6.032  1.00  0.00              
ATOM    277  CA  LYS   277      18.763  33.865   3.312  1.00  0.00              
ATOM    278  CA  GLU   278      21.230  34.658   0.653  1.00  0.00              
ATOM    279  CA  ARG   279      23.876  32.182   1.824  1.00  0.00              
ATOM    280  CA  PHE   280      21.816  28.979   2.160  1.00  0.00              
ATOM    281  CA  SER   281      19.730  29.469  -0.978  1.00  0.00              
ATOM    282  CA  LYS   282      22.623  30.133  -3.329  1.00  0.00              
ATOM    283  CA  TYR   283      24.776  27.130  -2.526  1.00  0.00              
ATOM    284  CA  HIS   284      21.850  24.712  -2.689  1.00  0.00              
ATOM    285  CA  ASP   285      20.230  25.773  -6.009  1.00  0.00              
ATOM    286  CA  ASN   286      18.540  22.558  -6.655  1.00  0.00              
ATOM    287  CA  TYR   287      17.708  21.345  -3.230  1.00  0.00              
ATOM    288  CA  TYR   288      18.354  17.653  -3.136  1.00  0.00              
ATOM    289  CA  PRO   289      17.526  16.006   0.070  1.00  0.00              
ATOM    290  CA  GLY   290      14.390  14.036   0.753  1.00  0.00              
ATOM    291  CA  TRP   291      13.513  15.242   4.198  1.00  0.00              
ATOM    292  CA  TYR   292      12.353  12.698   6.719  1.00  0.00              
ATOM    293  CA  LEU   293      10.755  14.645   9.662  1.00  0.00              
ATOM    294  CA  VAL   294      10.837  12.759  12.868  1.00  0.00              
ATOM    295  CA  ASP   295       8.697  12.882  15.865  1.00  0.00              
ATOM    296  CA  ASP   296      11.278  14.671  17.981  1.00  0.00              
ATOM    297  CA  THR   297      11.326  17.611  15.466  1.00  0.00              
ATOM    298  CA  LEU   298       7.500  17.896  15.324  1.00  0.00              
ATOM    299  CA  GLU   299       7.198  17.762  19.090  1.00  0.00              
ATOM    300  CA  ARG   300       9.815  20.481  19.678  1.00  0.00              
ATOM    301  CA  ALA   301       8.077  22.757  17.175  1.00  0.00              
ATOM    302  CA  GLY   302       4.663  22.283  18.917  1.00  0.00              
ATOM    303  CA  ARG   303       2.666  21.195  15.941  1.00  0.00              
ATOM    304  CA  ILE   304      -0.453  23.738  17.393  1.00  0.00              
TER                                                                             
END
