
#######################################################
#                                                     #
#                        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  120 (  120),  selected  120 , name T0356TS168_5-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS168_5-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348           -
LGA    -       -      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    -       -      V     352           -
LGA    -       -      D     353           -
LGA    -       -      F     354           -
LGA    -       -      Y     355           -
LGA    P     349      L     356           #
LGA    E     350      P     357           -
LGA    I     351      P     358          3.846
LGA    V     352      E     359          4.471
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    -       -      R     364           -
LGA    D     353      L     365           #
LGA    F     354      A     366           -
LGA    Y     355      V     367           #
LGA    L     356      V     368           -
LGA    P     357      -       -           -
LGA    P     358      -       -           -
LGA    E     359      -       -           -
LGA    G     360      -       -           -
LGA    C     361      -       -           -
LGA    S     362      -       -           -
LGA    Y     363      -       -           -
LGA    R     364      -       -           -
LGA    L     365      -       -           -
LGA    A     366      T     369          2.519
LGA    V     367      I     370          2.142
LGA    V     368      K     371           #
LGA    T     369      K     372           -
LGA    I     370      Q     373           -
LGA    K     371      Y     374           -
LGA    K     372      A     375           -
LGA    Q     373      -       -           -
LGA    Y     374      -       -           -
LGA    A     375      G     376          2.951
LGA    G     376      H     377          1.821
LGA    H     377      A     378          1.181
LGA    A     378      K     379          1.556
LGA    K     379      R     380          1.520
LGA    R     380      V     381          1.080
LGA    V     381      M     382          0.887
LGA    M     382      M     383          0.627
LGA    M     383      G     384          1.548
LGA    G     384      V     385          1.890
LGA    V     385      W     386          1.809
LGA    W     386      S     387          1.929
LGA    S     387      F     388          1.014
LGA    F     388      L     389          1.731
LGA    -       -      R     390           -
LGA    L     389      Q     391          4.922
LGA    R     390      F     392           #
LGA    Q     391      M     393          3.857
LGA    F     392      Y     394          4.392
LGA    M     393      -       -           -
LGA    Y     394      -       -           -
LGA    T     395      -       -           -
LGA    K     396      T     395           #
LGA    F     397      K     396           #
LGA    V     398      F     397          2.526
LGA    I     399      V     398          1.863
LGA    V     400      I     399          1.722
LGA    C     401      V     400          1.998
LGA    D     402      C     401          2.028
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    D     403      D     404          5.151
LGA    D     404      V     405          3.064
LGA    V     405      N     406           -
LGA    N     406      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    A     407      D     412           #
LGA    R     408      V     413           -
LGA    -       -      I     414           -
LGA    D     409      W     415          4.798
LGA    W     410      A     416          4.578
LGA    -       -      I     417           -
LGA    N     411      T     418          2.222
LGA    D     412      T     419          1.402
LGA    V     413      R     420          3.651
LGA    I     414      M     421          2.813
LGA    W     415      D     422          4.590
LGA    A     416      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    I     417      D     454          2.705
LGA    T     418      A     455           #
LGA    T     419      T     456           #
LGA    -       -      N     457           -
LGA    R     420      K     458          1.779
LGA    M     421      W     459          0.755
LGA    D     422      P     460          3.730
LGA    -       -      G     461           -
LGA    P     423      E     462          4.867
LGA    A     424      T     463           -
LGA    R     425      Q     464           -
LGA    D     426      R     465           -
LGA    T     427      E     466           -
LGA    V     428      W     467           -
LGA    L     429      -       -           -
LGA    V     430      -       -           -
LGA    E     431      -       -           -
LGA    N     432      -       -           -
LGA    T     433      -       -           -
LGA    P     434      -       -           -
LGA    I     435      -       -           -
LGA    D     436      -       -           -
LGA    Y     437      -       -           -
LGA    L     438      -       -           -
LGA    D     439      -       -           -
LGA    F     440      -       -           -
LGA    A     441      -       -           -
LGA    S     442      -       -           -
LGA    P     443      -       -           -
LGA    V     444      -       -           -
LGA    S     445      -       -           -
LGA    G     446      -       -           -
LGA    L     447      -       -           -
LGA    G     448      -       -           -
LGA    S     449      -       -           -
LGA    K     450      -       -           -
LGA    M     451      -       -           -
LGA    G     452      -       -           -
LGA    L     453      -       -           -
LGA    D     454      -       -           -
LGA    A     455      -       -           -
LGA    T     456      -       -           -
LGA    N     457      -       -           -
LGA    K     458      -       -           -
LGA    W     459      -       -           -
LGA    P     460      -       -           -
LGA    G     461      -       -           -
LGA    E     462      -       -           -
LGA    T     463      -       -           -
LGA    Q     464      -       -           -
LGA    R     465      -       -           -
LGA    E     466      -       -           -
LGA    W     467      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  120  120    5.0     40    2.92     5.00     21.962     1.326

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.700533 * X  +   0.703078 * Y  +   0.122209 * Z  +  57.604465
  Y_new =  -0.106612 * X  +   0.272441 * Y  +  -0.956248 * Z  +  69.232124
  Z_new =  -0.705611 * X  +   0.656854 * Y  +   0.265811 * Z  +  54.165741 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.186268   -1.955324  [ DEG:    67.9682   -112.0318 ]
  Theta =   0.783285    2.358308  [ DEG:    44.8789    135.1211 ]
  Phi   =  -0.151029    2.990564  [ DEG:    -8.6533    171.3467 ]
 
# 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: T0356TS168_5-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS168_5-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  120  120   5.0   40   2.92    5.00  21.962
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS168_5-D3
PFRMAT TS
TARGET T0356
MODEL 5
PARENT N/A
ATOM    348  CA  PHE   348      55.800  57.408  67.174  1.00 25.00           C
ATOM    349  CA  PRO   349      55.554  60.978  68.474  1.00 25.00           C
ATOM    350  CA  GLU   350      57.474  60.792  71.723  1.00 25.00           C
ATOM    351  CA  ILE   351      54.603  61.623  74.081  1.00 25.00           C
ATOM    352  CA  VAL   352      51.812  61.745  71.585  1.00 25.00           C
ATOM    353  CA  ASP   353      48.055  61.046  71.605  1.00 25.00           C
ATOM    354  CA  PHE   354      45.538  63.334  69.983  1.00 25.00           C
ATOM    355  CA  TYR   355      42.815  65.842  70.787  1.00 25.00           C
ATOM    356  CA  LEU   356      40.631  67.328  67.987  1.00 25.00           C
ATOM    357  CA  PRO   357      38.386  64.224  68.088  1.00 25.00           C
ATOM    358  CA  PRO   358      36.004  65.997  70.480  1.00 25.00           C
ATOM    359  CA  GLU   359      34.269  67.708  67.519  1.00 25.00           C
ATOM    360  CA  GLY   360      36.896  69.543  65.475  1.00 25.00           C
ATOM    361  CA  CYS   361      39.733  72.007  64.627  1.00 25.00           C
ATOM    362  CA  SER   362      41.764  74.819  63.005  1.00 25.00           C
ATOM    363  CA  TYR   363      44.429  77.346  63.719  1.00 25.00           C
ATOM    364  CA  ARG   364      47.091  76.291  61.179  1.00 25.00           C
ATOM    365  CA  LEU   365      46.777  75.610  57.485  1.00 25.00           C
ATOM    366  CA  ALA   366      47.287  71.903  56.784  1.00 25.00           C
ATOM    367  CA  VAL   367      47.552  69.317  54.058  1.00 25.00           C
ATOM    368  CA  VAL   368      49.906  66.367  54.417  1.00 25.00           C
ATOM    369  CA  THR   369      49.798  63.010  56.111  1.00 25.00           C
ATOM    370  CA  ILE   370      48.290  59.811  57.432  1.00 25.00           C
ATOM    371  CA  LYS   371      49.725  56.506  56.224  1.00 25.00           C
ATOM    372  CA  LYS   372      46.117  55.366  56.555  1.00 25.00           C
ATOM    373  CA  GLN   373      45.021  54.078  53.103  1.00 25.00           C
ATOM    374  CA  TYR   374      45.661  57.363  51.321  1.00 25.00           C
ATOM    375  CA  ALA   375      46.941  58.902  48.099  1.00 25.00           C
ATOM    376  CA  GLY   376      48.414  62.405  48.576  1.00 25.00           C
ATOM    377  CA  HIS   377      48.139  62.029  52.377  1.00 25.00           C
ATOM    378  CA  ALA   378      49.890  58.628  52.194  1.00 25.00           C
ATOM    379  CA  LYS   379      52.687  60.155  50.070  1.00 25.00           C
ATOM    380  CA  ARG   380      53.095  62.997  52.604  1.00 25.00           C
ATOM    381  CA  VAL   381      53.286  60.454  55.462  1.00 25.00           C
ATOM    382  CA  MET   382      55.941  58.466  53.547  1.00 25.00           C
ATOM    383  CA  MET   383      57.957  61.671  52.968  1.00 25.00           C
ATOM    384  CA  GLY   384      57.730  62.516  56.697  1.00 25.00           C
ATOM    385  CA  VAL   385      58.923  58.989  57.594  1.00 25.00           C
ATOM    386  CA  TRP   386      61.865  59.339  55.167  1.00 25.00           C
ATOM    387  CA  SER   387      62.780  62.716  56.726  1.00 25.00           C
ATOM    388  CA  PHE   388      62.650  61.163  60.225  1.00 25.00           C
ATOM    389  CA  LEU   389      60.861  58.179  61.786  1.00 25.00           C
ATOM    390  CA  ARG   390      62.090  54.561  62.047  1.00 25.00           C
ATOM    391  CA  GLN   391      61.709  55.363  65.780  1.00 25.00           C
ATOM    392  CA  PHE   392      60.479  58.718  66.938  1.00 25.00           C
ATOM    393  CA  MET   393      60.357  57.493  70.495  1.00 25.00           C
ATOM    394  CA  TYR   394      57.466  55.127  71.106  1.00 25.00           C
ATOM    395  CA  THR   395      54.180  56.719  72.212  1.00 25.00           C
ATOM    396  CA  LYS   396      51.457  57.140  69.608  1.00 25.00           C
ATOM    397  CA  PHE   397      50.075  59.613  67.105  1.00 25.00           C
ATOM    398  CA  VAL   398      47.598  58.065  64.644  1.00 25.00           C
ATOM    399  CA  ILE   399      48.235  60.916  62.197  1.00 25.00           C
ATOM    400  CA  VAL   400      47.230  63.364  59.493  1.00 25.00           C
ATOM    401  CA  CYS   401      45.493  65.768  57.113  1.00 25.00           C
ATOM    402  CA  ASP   402      43.058  68.743  57.516  1.00 25.00           C
ATOM    403  CA  ASP   403      41.116  70.497  60.315  1.00 25.00           C
ATOM    404  CA  ASP   404      40.922  73.688  58.276  1.00 25.00           C
ATOM    405  CA  VAL   405      37.127  73.549  57.835  1.00 25.00           C
ATOM    406  CA  ASN   406      33.649  74.570  58.856  1.00 25.00           C
ATOM    407  CA  ALA   407      33.623  71.209  60.558  1.00 25.00           C
ATOM    408  CA  ARG   408      30.758  70.425  62.958  1.00 25.00           C
ATOM    409  CA  ASP   409      31.257  66.667  63.372  1.00 25.00           C
ATOM    410  CA  TRP   410      34.712  65.144  62.888  1.00 25.00           C
ATOM    411  CA  ASN   411      32.957  63.102  60.165  1.00 25.00           C
ATOM    412  CA  ASP   412      34.031  65.658  57.522  1.00 25.00           C
ATOM    413  CA  VAL   413      37.642  65.482  58.785  1.00 25.00           C
ATOM    414  CA  ILE   414      37.543  61.658  58.610  1.00 25.00           C
ATOM    415  CA  TRP   415      36.196  61.833  55.029  1.00 25.00           C
ATOM    416  CA  ALA   416      38.992  64.267  54.069  1.00 25.00           C
ATOM    417  CA  ILE   417      41.599  61.918  55.605  1.00 25.00           C
ATOM    418  CA  THR   418      40.127  58.969  53.653  1.00 25.00           C
ATOM    419  CA  THR   419      40.261  61.012  50.417  1.00 25.00           C
ATOM    420  CA  ARG   420      40.395  64.645  49.234  1.00 25.00           C
ATOM    421  CA  MET   421      39.109  66.091  46.038  1.00 25.00           C
ATOM    422  CA  ASP   422      40.950  64.193  43.257  1.00 25.00           C
ATOM    423  CA  PRO   423      43.757  61.785  43.992  1.00 25.00           C
ATOM    424  CA  ALA   424      45.894  63.662  41.490  1.00 25.00           C
ATOM    425  CA  ARG   425      49.331  62.868  42.732  1.00 25.00           C
ATOM    426  CA  ASP   426      51.970  61.883  45.329  1.00 25.00           C
ATOM    427  CA  THR   427      53.119  64.777  47.575  1.00 25.00           C
ATOM    428  CA  VAL   428      56.405  66.088  48.843  1.00 25.00           C
ATOM    429  CA  LEU   429      59.772  64.396  49.665  1.00 25.00           C
ATOM    430  CA  VAL   430      63.417  64.720  48.637  1.00 25.00           C
ATOM    431  CA  GLU   431      66.139  66.505  46.625  1.00 25.00           C
ATOM    432  CA  ASN   432      69.686  67.780  45.919  1.00 25.00           C
ATOM    433  CA  THR   433      70.556  71.387  45.179  1.00 25.00           C
ATOM    434  CA  PRO   434      73.778  70.994  47.236  1.00 25.00           C
ATOM    435  CA  ILE   435      72.076  69.935  50.443  1.00 25.00           C
ATOM    436  CA  ASP   436      74.491  67.262  51.600  1.00 25.00           C
ATOM    437  CA  TYR   437      71.695  65.846  53.728  1.00 25.00           C
ATOM    438  CA  LEU   438      71.564  68.376  56.550  1.00 25.00           C
ATOM    439  CA  ASP   439      72.564  71.346  58.670  1.00 25.00           C
ATOM    440  CA  PHE   440      70.704  74.619  59.095  1.00 25.00           C
ATOM    441  CA  ALA   441      71.579  78.185  57.973  1.00 25.00           C
ATOM    442  CA  SER   442      75.218  78.768  56.934  1.00 25.00           C
ATOM    443  CA  PRO   443      76.388  82.347  57.692  1.00 25.00           C
ATOM    444  CA  VAL   444      74.164  85.423  57.622  1.00 25.00           C
ATOM    445  CA  SER   445      71.152  85.780  59.839  1.00 25.00           C
ATOM    446  CA  GLY   446      68.224  85.137  62.146  1.00 25.00           C
ATOM    447  CA  LEU   447      67.530  81.412  62.055  1.00 25.00           C
ATOM    448  CA  GLY   448      64.101  80.264  63.271  1.00 25.00           C
ATOM    449  CA  SER   449      62.660  77.074  64.660  1.00 25.00           C
ATOM    450  CA  LYS   450      60.423  74.198  63.497  1.00 25.00           C
ATOM    451  CA  MET   451      58.466  75.416  60.430  1.00 25.00           C
ATOM    452  CA  GLY   452      58.934  72.707  57.863  1.00 25.00           C
ATOM    453  CA  LEU   453      58.886  72.441  54.057  1.00 25.00           C
ATOM    454  CA  ASP   454      57.394  72.018  50.590  1.00 25.00           C
ATOM    455  CA  ALA   455      56.225  74.906  48.406  1.00 25.00           C
ATOM    456  CA  THR   456      54.907  77.517  45.980  1.00 25.00           C
ATOM    457  CA  ASN   457      55.131  77.021  42.268  1.00 25.00           C
ATOM    458  CA  LYS   458      57.346  75.344  39.643  1.00 25.00           C
ATOM    459  CA  TRP   459      55.857  77.232  36.722  1.00 25.00           C
ATOM    460  CA  PRO   460      56.517  75.661  33.284  1.00 25.00           C
ATOM    461  CA  GLY   461      59.024  73.669  31.192  1.00 25.00           C
ATOM    462  CA  GLU   462      59.548  70.155  29.916  1.00 25.00           C
ATOM    463  CA  THR   463      62.166  67.461  29.260  1.00 25.00           C
ATOM    464  CA  GLN   464      59.907  64.647  30.507  1.00 25.00           C
ATOM    465  CA  ARG   465      62.932  62.794  29.151  1.00 25.00           C
ATOM    466  CA  GLU   466      62.291  59.894  31.521  1.00 25.00           C
ATOM    467  CA  TRP   467      62.652  57.562  28.564  1.00 25.00           C
TER
END
