
#######################################################
#                                                     #
#                        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 T0356TS599_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS599_4-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      P     349           -
LGA    E     350      E     350           -
LGA    I     351      I     351           -
LGA    V     352      V     352           -
LGA    D     353      D     353           -
LGA    F     354      F     354           -
LGA    Y     355      Y     355           -
LGA    -       -      L     356           -
LGA    -       -      P     357           -
LGA    -       -      P     358           -
LGA    L     356      E     359          2.442
LGA    -       -      G     360           -
LGA    P     357      C     361          1.981
LGA    P     358      S     362          1.929
LGA    E     359      Y     363          3.107
LGA    G     360      R     364          2.764
LGA    C     361      L     365          2.622
LGA    S     362      -       -           -
LGA    Y     363      -       -           -
LGA    R     364      -       -           -
LGA    L     365      -       -           -
LGA    A     366      A     366          4.178
LGA    V     367      V     367          3.524
LGA    V     368      V     368          3.531
LGA    T     369      T     369          3.119
LGA    I     370      I     370          4.177
LGA    K     371      -       -           -
LGA    K     372      -       -           -
LGA    Q     373      K     371          5.787
LGA    Y     374      K     372          2.115
LGA    A     375      Q     373          4.395
LGA    G     376      Y     374          4.553
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    H     377      H     377          4.427
LGA    A     378      A     378          3.476
LGA    K     379      K     379          2.693
LGA    R     380      R     380          1.077
LGA    V     381      V     381          1.860
LGA    M     382      M     382          1.210
LGA    M     383      M     383          0.902
LGA    G     384      G     384          2.571
LGA    V     385      V     385          2.354
LGA    W     386      W     386          2.171
LGA    S     387      S     387          4.268
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    F     388      M     393          4.463
LGA    L     389      Y     394          4.866
LGA    R     390      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      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    Q     391      T     433          2.601
LGA    F     392      P     434          4.010
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    M     393      G     448          3.967
LGA    Y     394      S     449          4.565
LGA    T     395      K     450          1.334
LGA    K     396      M     451          1.273
LGA    F     397      G     452          1.329
LGA    V     398      L     453          1.335
LGA    I     399      D     454          0.473
LGA    V     400      A     455          1.554
LGA    C     401      T     456          1.537
LGA    D     402      N     457          2.804
LGA    D     403      K     458           -
LGA    D     404      W     459           -
LGA    V     405      P     460           -
LGA    N     406      G     461           -
LGA    A     407      E     462           -
LGA    R     408      T     463           -
LGA    D     409      Q     464           -
LGA    W     410      R     465           -
LGA    N     411      E     466           -
LGA    D     412      W     467           -
LGA    V     413      -       -           -
LGA    I     414      -       -           -
LGA    W     415      -       -           -
LGA    A     416      -       -           -
LGA    I     417      -       -           -
LGA    T     418      -       -           -
LGA    T     419      -       -           -
LGA    R     420      -       -           -
LGA    M     421      -       -           -
LGA    D     422      -       -           -
LGA    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    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    3.12    40.00     19.913     1.243

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.411353 * X  +   0.856662 * Y  +  -0.311318 * Z  +  41.414486
  Y_new =   0.479287 * X  +  -0.493817 * Y  +  -0.725554 * Z  +  49.639088
  Z_new =  -0.775289 * X  +   0.149248 * Y  +  -0.613720 * Z  +  41.790291 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.903037   -0.238555  [ DEG:   166.3318    -13.6682 ]
  Theta =   0.887172    2.254421  [ DEG:    50.8312    129.1688 ]
  Phi   =   0.861526   -2.280066  [ DEG:    49.3618   -130.6382 ]
 
# 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: T0356TS599_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS599_4-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   3.12   40.00  19.913
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS599_4-D3
PFRMAT TS                                                                       
TARGET T0356                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM    348  CA  PHE   348      35.170  55.690  77.562  1.00  0.00              
ATOM    349  CA  PRO   349      32.520  58.396  77.163  1.00  0.00              
ATOM    350  CA  GLU   350      32.428  59.912  80.658  1.00  0.00              
ATOM    351  CA  ILE   351      36.026  60.416  80.124  1.00  0.00              
ATOM    352  CA  VAL   352      37.542  63.657  82.458  1.00  0.00              
ATOM    353  CA  ASP   353      40.659  63.222  81.564  1.00  0.00              
ATOM    354  CA  PHE   354      43.728  61.923  79.832  1.00  0.00              
ATOM    355  CA  TYR   355      47.135  61.267  79.906  1.00  0.00              
ATOM    356  CA  LEU   356      49.663  61.090  77.131  1.00  0.00              
ATOM    357  CA  PRO   357      52.827  59.869  76.030  1.00  0.00              
ATOM    358  CA  PRO   358      54.665  61.974  73.989  1.00  0.00              
ATOM    359  CA  GLU   359      56.741  59.619  72.253  1.00  0.00              
ATOM    360  CA  GLY   360      54.461  57.099  71.479  1.00  0.00              
ATOM    361  CA  CYS   361      52.334  59.424  69.358  1.00  0.00              
ATOM    362  CA  SER   362      55.126  61.063  67.559  1.00  0.00              
ATOM    363  CA  TYR   363      57.157  57.943  66.618  1.00  0.00              
ATOM    364  CA  ARG   364      54.196  56.397  65.349  1.00  0.00              
ATOM    365  CA  LEU   365      50.878  57.907  64.115  1.00  0.00              
ATOM    366  CA  ALA   366      50.410  60.563  61.533  1.00  0.00              
ATOM    367  CA  VAL   367      47.934  63.039  60.848  1.00  0.00              
ATOM    368  CA  VAL   368      48.199  64.936  57.857  1.00  0.00              
ATOM    369  CA  THR   369      45.955  68.159  56.839  1.00  0.00              
ATOM    370  CA  ILE   370      45.548  68.757  53.489  1.00  0.00              
ATOM    371  CA  LYS   371      44.046  72.034  51.958  1.00  0.00              
ATOM    372  CA  LYS   372      41.502  70.162  49.094  1.00  0.00              
ATOM    373  CA  GLN   373      44.164  72.714  46.980  1.00  0.00              
ATOM    374  CA  TYR   374      47.426  71.381  48.165  1.00  0.00              
ATOM    375  CA  ALA   375      46.415  67.606  48.809  1.00  0.00              
ATOM    376  CA  GLY   376      49.221  65.535  47.075  1.00  0.00              
ATOM    377  CA  HIS   377      51.776  67.046  49.501  1.00  0.00              
ATOM    378  CA  ALA   378      50.192  65.691  52.105  1.00  0.00              
ATOM    379  CA  LYS   379      50.298  62.476  51.515  1.00  0.00              
ATOM    380  CA  ARG   380      53.548  62.550  50.445  1.00  0.00              
ATOM    381  CA  VAL   381      55.121  63.836  53.421  1.00  0.00              
ATOM    382  CA  MET   382      53.245  61.233  55.466  1.00  0.00              
ATOM    383  CA  MET   383      54.644  58.549  53.334  1.00  0.00              
ATOM    384  CA  GLY   384      58.295  59.339  53.900  1.00  0.00              
ATOM    385  CA  VAL   385      57.592  59.625  57.175  1.00  0.00              
ATOM    386  CA  TRP   386      56.014  56.794  57.898  1.00  0.00              
ATOM    387  CA  SER   387      58.610  54.850  55.931  1.00  0.00              
ATOM    388  CA  PHE   388      61.383  56.582  57.995  1.00  0.00              
ATOM    389  CA  LEU   389      61.338  54.804  61.293  1.00  0.00              
ATOM    390  CA  ARG   390      63.022  51.598  61.464  1.00  0.00              
ATOM    391  CA  GLN   391      59.989  49.378  60.175  1.00  0.00              
ATOM    392  CA  PHE   392      56.834  51.037  61.754  1.00  0.00              
ATOM    393  CA  MET   393      55.408  50.426  64.828  1.00  0.00              
ATOM    394  CA  TYR   394      52.236  51.724  65.167  1.00  0.00              
ATOM    395  CA  THR   395      51.642  52.996  62.237  1.00  0.00              
ATOM    396  CA  LYS   396      48.584  54.371  61.607  1.00  0.00              
ATOM    397  CA  PHE   397      47.692  57.870  58.884  1.00  0.00              
ATOM    398  CA  VAL   398      45.088  59.294  58.984  1.00  0.00              
ATOM    399  CA  ILE   399      44.495  61.579  55.732  1.00  0.00              
ATOM    400  CA  VAL   400      42.198  64.575  55.955  1.00  0.00              
ATOM    401  CA  CYS   401      40.970  66.573  52.777  1.00  0.00              
ATOM    402  CA  ASP   402      39.749  69.449  53.021  1.00  0.00              
ATOM    403  CA  ASP   403      40.154  73.183  51.697  1.00  0.00              
ATOM    404  CA  ASP   404      37.419  74.752  53.904  1.00  0.00              
ATOM    405  CA  VAL   405      39.716  74.679  56.538  1.00  0.00              
ATOM    406  CA  ASN   406      40.008  77.259  59.672  1.00  0.00              
ATOM    407  CA  ALA   407      42.078  76.231  62.542  1.00  0.00              
ATOM    408  CA  ARG   408      42.099  77.397  65.717  1.00  0.00              
ATOM    409  CA  ASP   409      45.187  77.476  67.299  1.00  0.00              
ATOM    410  CA  TRP   410      47.317  75.500  64.907  1.00  0.00              
ATOM    411  CA  ASN   411      50.433  77.499  64.450  1.00  0.00              
ATOM    412  CA  ASP   412      51.212  77.452  68.122  1.00  0.00              
ATOM    413  CA  VAL   413      50.425  73.937  68.803  1.00  0.00              
ATOM    414  CA  ILE   414      52.528  72.657  66.314  1.00  0.00              
ATOM    415  CA  TRP   415      55.335  74.725  67.349  1.00  0.00              
ATOM    416  CA  ALA   416      55.309  73.001  70.598  1.00  0.00              
ATOM    417  CA  ILE   417      55.279  69.490  70.083  1.00  0.00              
ATOM    418  CA  THR   418      58.182  69.644  67.163  1.00  0.00              
ATOM    419  CA  THR   419      60.605  71.611  69.462  1.00  0.00              
ATOM    420  CA  ARG   420      59.836  69.005  72.096  1.00  0.00              
ATOM    421  CA  MET   421      60.396  66.216  69.955  1.00  0.00              
ATOM    422  CA  ASP   422      63.171  65.004  67.815  1.00  0.00              
ATOM    423  CA  PRO   423      63.103  66.517  64.459  1.00  0.00              
ATOM    424  CA  ALA   424      63.304  62.683  62.874  1.00  0.00              
ATOM    425  CA  ARG   425      59.988  61.695  64.927  1.00  0.00              
ATOM    426  CA  ASP   426      57.091  62.947  62.719  1.00  0.00              
ATOM    427  CA  THR   427      54.712  65.857  63.066  1.00  0.00              
ATOM    428  CA  VAL   428      50.929  65.623  62.844  1.00  0.00              
ATOM    429  CA  LEU   429      48.928  68.386  61.064  1.00  0.00              
ATOM    430  CA  VAL   430      45.254  68.535  62.033  1.00  0.00              
ATOM    431  CA  GLU   431      42.603  69.633  59.501  1.00  0.00              
ATOM    432  CA  ASN   432      39.514  70.765  60.798  1.00  0.00              
ATOM    433  CA  THR   433      40.845  71.470  64.293  1.00  0.00              
ATOM    434  CA  PRO   434      39.299  73.208  67.036  1.00  0.00              
ATOM    435  CA  ILE   435      42.043  74.491  69.094  1.00  0.00              
ATOM    436  CA  ASP   436      40.795  73.884  72.832  1.00  0.00              
ATOM    437  CA  TYR   437      41.599  73.607  76.068  1.00  0.00              
ATOM    438  CA  LEU   438      39.854  70.606  77.634  1.00  0.00              
ATOM    439  CA  ASP   439      40.393  71.239  81.268  1.00  0.00              
ATOM    440  CA  PHE   440      40.376  67.930  83.357  1.00  0.00              
ATOM    441  CA  ALA   441      36.772  68.330  84.831  1.00  0.00              
ATOM    442  CA  SER   442      34.496  68.546  82.152  1.00  0.00              
ATOM    443  CA  PRO   443      32.051  66.084  81.078  1.00  0.00              
ATOM    444  CA  VAL   444      32.348  66.162  77.507  1.00  0.00              
ATOM    445  CA  SER   445      32.802  62.801  76.650  1.00  0.00              
ATOM    446  CA  GLY   446      34.209  63.269  73.062  1.00  0.00              
ATOM    447  CA  LEU   447      35.983  66.251  72.976  1.00  0.00              
ATOM    448  CA  GLY   448      38.726  66.530  70.838  1.00  0.00              
ATOM    449  CA  SER   449      40.150  69.765  72.424  1.00  0.00              
ATOM    450  CA  LYS   450      43.218  70.476  71.133  1.00  0.00              
ATOM    451  CA  MET   451      45.811  72.409  73.162  1.00  0.00              
ATOM    452  CA  GLY   452      49.462  72.695  72.409  1.00  0.00              
ATOM    453  CA  LEU   453      51.450  72.506  75.883  1.00  0.00              
ATOM    454  CA  ASP   454      48.858  70.374  76.775  1.00  0.00              
ATOM    455  CA  ALA   455      49.841  68.005  74.445  1.00  0.00              
ATOM    456  CA  THR   456      53.694  67.964  75.171  1.00  0.00              
ATOM    457  CA  ASN   457      53.353  67.674  78.624  1.00  0.00              
ATOM    458  CA  LYS   458      50.725  65.249  79.851  1.00  0.00              
ATOM    459  CA  TRP   459      51.265  62.798  82.033  1.00  0.00              
ATOM    460  CA  PRO   460      52.583  63.706  85.493  1.00  0.00              
ATOM    461  CA  GLY   461      54.798  60.810  86.207  1.00  0.00              
ATOM    462  CA  GLU   462      55.679  61.077  89.793  1.00  0.00              
ATOM    463  CA  THR   463      53.164  61.971  92.077  1.00  0.00              
ATOM    464  CA  GLN   464      50.119  59.498  92.410  1.00  0.00              
ATOM    465  CA  ARG   465      52.749  56.720  92.380  1.00  0.00              
ATOM    466  CA  GLU   466      51.245  53.804  90.472  1.00  0.00              
ATOM    467  CA  TRP   467      48.292  54.960  88.636  1.00  0.00              
TER                                                                             
END
