
#######################################################
#                                                     #
#                        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 T0356TS393_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS393_2-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      -       -           -
LGA    P     349      -       -           -
LGA    E     350      -       -           -
LGA    I     351      -       -           -
LGA    V     352      -       -           -
LGA    D     353      F     348          3.668
LGA    F     354      P     349           -
LGA    Y     355      -       -           -
LGA    L     356      -       -           -
LGA    P     357      -       -           -
LGA    P     358      -       -           -
LGA    E     359      -       -           -
LGA    G     360      -       -           -
LGA    C     361      -       -           -
LGA    S     362      E     350          2.777
LGA    Y     363      -       -           -
LGA    R     364      I     351           #
LGA    L     365      V     352          4.443
LGA    A     366      D     353          2.480
LGA    V     367      F     354          1.929
LGA    V     368      Y     355          4.412
LGA    -       -      L     356           -
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    T     369      L     365          5.000
LGA    I     370      A     366          2.922
LGA    K     371      -       -           -
LGA    K     372      -       -           -
LGA    Q     373      -       -           -
LGA    Y     374      -       -           -
LGA    A     375      V     367           #
LGA    G     376      V     368           -
LGA    -       -      T     369           -
LGA    -       -      I     370           -
LGA    -       -      K     371           -
LGA    -       -      K     372           -
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    H     377      A     378          4.183
LGA    A     378      K     379           -
LGA    K     379      R     380           -
LGA    R     380      V     381           #
LGA    V     381      M     382          1.647
LGA    M     382      -       -           -
LGA    M     383      -       -           -
LGA    G     384      M     383          1.357
LGA    V     385      G     384          2.950
LGA    W     386      V     385          4.535
LGA    S     387      W     386          4.099
LGA    F     388      S     387          2.489
LGA    L     389      -       -           -
LGA    R     390      -       -           -
LGA    Q     391      -       -           -
LGA    F     392      -       -           -
LGA    M     393      -       -           -
LGA    Y     394      F     388          2.844
LGA    T     395      L     389          4.088
LGA    K     396      R     390           -
LGA    F     397      Q     391           -
LGA    V     398      F     392           -
LGA    I     399      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    V     400      I     399           #
LGA    C     401      V     400           #
LGA    D     402      C     401           #
LGA    D     403      D     402          3.790
LGA    D     404      D     403          3.408
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      D     404          3.556
LGA    I     414      V     405          3.548
LGA    W     415      N     406           -
LGA    A     416      -       -           -
LGA    I     417      A     407           #
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    T     418      V     413          2.021
LGA    T     419      I     414          4.358
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    R     420      I     417          2.969
LGA    M     421      T     418          3.250
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    D     422      M     421          1.468
LGA    P     423      D     422          3.251
LGA    A     424      P     423          1.399
LGA    R     425      A     424          3.059
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    D     426      T     427          1.596
LGA    T     427      V     428          1.059
LGA    V     428      L     429          4.111
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    L     429      S     449          4.396
LGA    V     430      K     450          3.803
LGA    E     431      M     451           #
LGA    N     432      G     452           -
LGA    T     433      L     453           -
LGA    P     434      D     454           -
LGA    I     435      A     455           -
LGA    D     436      T     456           -
LGA    Y     437      N     457           -
LGA    L     438      K     458           -
LGA    D     439      W     459           -
LGA    F     440      P     460           -
LGA    A     441      G     461           -
LGA    S     442      E     462           -
LGA    P     443      T     463           -
LGA    V     444      Q     464           -
LGA    S     445      R     465           -
LGA    G     446      E     466           -
LGA    L     447      W     467           -
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     34    3.32     5.88     15.712     0.994

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.700713 * X  +   0.651577 * Y  +   0.290601 * Z  +  56.457108
  Y_new =   0.567179 * X  +  -0.755845 * Y  +   0.327119 * Z  +  68.071808
  Z_new =   0.432792 * X  +  -0.064394 * Y  +  -0.899191 * Z  +  74.130051 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.070102    0.071491  [ DEG:  -175.9039      4.0961 ]
  Theta =  -0.447588   -2.694005  [ DEG:   -25.6449   -154.3551 ]
  Phi   =   0.680465   -2.461127  [ DEG:    38.9878   -141.0122 ]
 
# 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: T0356TS393_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS393_2-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   34   3.32    5.88  15.712
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS393_2-D3
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM    348  CA  PHE   348      69.053  68.424  56.100  1.00 25.00           C
ATOM    349  CA  PRO   349      66.688  65.761  54.862  1.00 25.00           C
ATOM    350  CA  GLU   350      65.077  65.720  51.421  1.00 25.00           C
ATOM    351  CA  ILE   351      63.334  68.910  52.429  1.00 25.00           C
ATOM    352  CA  VAL   352      59.812  67.996  51.452  1.00 25.00           C
ATOM    353  CA  ASP   353      56.557  66.361  50.241  1.00 25.00           C
ATOM    354  CA  PHE   354      54.143  63.997  52.061  1.00 25.00           C
ATOM    355  CA  TYR   355      51.259  66.286  51.207  1.00 25.00           C
ATOM    356  CA  LEU   356      48.230  64.995  53.016  1.00 25.00           C
ATOM    357  CA  PRO   357      46.160  65.428  49.869  1.00 25.00           C
ATOM    358  CA  PRO   358      46.802  68.030  47.207  1.00 25.00           C
ATOM    359  CA  GLU   359      45.837  71.606  48.040  1.00 25.00           C
ATOM    360  CA  GLY   360      45.734  70.932  51.801  1.00 25.00           C
ATOM    361  CA  CYS   361      48.269  71.583  54.595  1.00 25.00           C
ATOM    362  CA  SER   362      51.386  73.407  53.242  1.00 25.00           C
ATOM    363  CA  TYR   363      54.991  74.330  52.443  1.00 25.00           C
ATOM    364  CA  ARG   364      58.414  73.376  53.877  1.00 25.00           C
ATOM    365  CA  LEU   365      55.817  72.873  56.608  1.00 25.00           C
ATOM    366  CA  ALA   366      53.157  71.523  58.959  1.00 25.00           C
ATOM    367  CA  VAL   367      51.560  70.172  62.170  1.00 25.00           C
ATOM    368  CA  VAL   368      52.152  66.479  61.841  1.00 25.00           C
ATOM    369  CA  THR   369      52.849  64.464  64.958  1.00 25.00           C
ATOM    370  CA  ILE   370      51.067  62.010  67.296  1.00 25.00           C
ATOM    371  CA  LYS   371      49.231  59.413  69.422  1.00 25.00           C
ATOM    372  CA  LYS   372      46.262  57.703  67.797  1.00 25.00           C
ATOM    373  CA  GLN   373      43.660  57.401  65.101  1.00 25.00           C
ATOM    374  CA  TYR   374      45.121  60.168  62.871  1.00 25.00           C
ATOM    375  CA  ALA   375      43.373  62.040  60.024  1.00 25.00           C
ATOM    376  CA  GLY   376      44.215  59.254  57.535  1.00 25.00           C
ATOM    377  CA  HIS   377      46.121  61.752  55.345  1.00 25.00           C
ATOM    378  CA  ALA   378      48.066  62.988  58.405  1.00 25.00           C
ATOM    379  CA  LYS   379      48.933  59.377  59.342  1.00 25.00           C
ATOM    380  CA  ARG   380      50.137  58.712  55.767  1.00 25.00           C
ATOM    381  CA  VAL   381      52.300  61.870  55.882  1.00 25.00           C
ATOM    382  CA  MET   382      53.794  60.755  59.227  1.00 25.00           C
ATOM    383  CA  MET   383      54.561  57.300  57.760  1.00 25.00           C
ATOM    384  CA  GLY   384      56.249  58.932  54.735  1.00 25.00           C
ATOM    385  CA  VAL   385      58.344  61.136  57.062  1.00 25.00           C
ATOM    386  CA  TRP   386      59.377  58.056  59.090  1.00 25.00           C
ATOM    387  CA  SER   387      60.372  56.238  55.869  1.00 25.00           C
ATOM    388  CA  PHE   388      62.443  59.267  54.769  1.00 25.00           C
ATOM    389  CA  LEU   389      65.295  57.189  53.381  1.00 25.00           C
ATOM    390  CA  ARG   390      64.960  53.976  55.393  1.00 25.00           C
ATOM    391  CA  GLN   391      67.139  53.369  58.461  1.00 25.00           C
ATOM    392  CA  PHE   392      67.142  56.711  60.306  1.00 25.00           C
ATOM    393  CA  MET   393      63.929  58.242  58.916  1.00 25.00           C
ATOM    394  CA  TYR   394      64.112  61.970  58.653  1.00 25.00           C
ATOM    395  CA  THR   395      62.282  64.829  56.878  1.00 25.00           C
ATOM    396  CA  LYS   396      60.524  64.023  53.633  1.00 25.00           C
ATOM    397  CA  PHE   397      57.599  66.113  55.022  1.00 25.00           C
ATOM    398  CA  VAL   398      54.574  68.378  54.567  1.00 25.00           C
ATOM    399  CA  ILE   399      51.294  68.246  56.438  1.00 25.00           C
ATOM    400  CA  VAL   400      48.248  67.319  58.524  1.00 25.00           C
ATOM    401  CA  CYS   401      47.976  70.903  59.579  1.00 25.00           C
ATOM    402  CA  ASP   402      44.982  72.235  61.548  1.00 25.00           C
ATOM    403  CA  ASP   403      44.628  73.496  58.014  1.00 25.00           C
ATOM    404  CA  ASP   404      45.962  77.034  58.247  1.00 25.00           C
ATOM    405  CA  VAL   405      47.340  77.392  54.671  1.00 25.00           C
ATOM    406  CA  ASN   406      44.635  76.867  52.007  1.00 25.00           C
ATOM    407  CA  ALA   407      41.087  76.771  53.402  1.00 25.00           C
ATOM    408  CA  ARG   408      37.604  76.389  51.845  1.00 25.00           C
ATOM    409  CA  ASP   409      36.238  77.806  55.096  1.00 25.00           C
ATOM    410  CA  TRP   410      37.769  76.683  58.448  1.00 25.00           C
ATOM    411  CA  ASN   411      35.142  74.320  59.927  1.00 25.00           C
ATOM    412  CA  ASP   412      35.944  71.709  57.242  1.00 25.00           C
ATOM    413  CA  VAL   413      39.681  72.026  58.017  1.00 25.00           C
ATOM    414  CA  ILE   414      38.970  71.574  61.752  1.00 25.00           C
ATOM    415  CA  TRP   415      36.870  68.462  61.002  1.00 25.00           C
ATOM    416  CA  ALA   416      39.699  67.040  58.847  1.00 25.00           C
ATOM    417  CA  ILE   417      42.207  67.693  61.667  1.00 25.00           C
ATOM    418  CA  THR   418      39.896  65.934  64.163  1.00 25.00           C
ATOM    419  CA  THR   419      39.581  62.938  61.796  1.00 25.00           C
ATOM    420  CA  ARG   420      38.546  60.566  58.975  1.00 25.00           C
ATOM    421  CA  MET   421      35.909  63.147  58.362  1.00 25.00           C
ATOM    422  CA  ASP   422      35.674  60.773  55.367  1.00 25.00           C
ATOM    423  CA  PRO   423      34.333  58.248  57.822  1.00 25.00           C
ATOM    424  CA  ALA   424      36.166  54.921  57.561  1.00 25.00           C
ATOM    425  CA  ARG   425      39.629  54.309  56.211  1.00 25.00           C
ATOM    426  CA  ASP   426      42.925  54.773  54.395  1.00 25.00           C
ATOM    427  CA  THR   427      46.538  54.532  55.412  1.00 25.00           C
ATOM    428  CA  VAL   428      48.202  54.203  58.784  1.00 25.00           C
ATOM    429  CA  LEU   429      49.870  51.778  61.186  1.00 25.00           C
ATOM    430  CA  VAL   430      50.885  48.922  63.475  1.00 25.00           C
ATOM    431  CA  GLU   431      48.350  46.509  61.886  1.00 25.00           C
ATOM    432  CA  ASN   432      46.335  43.886  63.741  1.00 25.00           C
ATOM    433  CA  THR   433      45.098  42.772  67.148  1.00 25.00           C
ATOM    434  CA  PRO   434      41.754  44.170  68.335  1.00 25.00           C
ATOM    435  CA  ILE   435      42.005  47.117  70.769  1.00 25.00           C
ATOM    436  CA  ASP   436      41.687  50.876  70.072  1.00 25.00           C
ATOM    437  CA  TYR   437      44.704  51.010  72.306  1.00 25.00           C
ATOM    438  CA  LEU   438      44.594  54.456  73.815  1.00 25.00           C
ATOM    439  CA  ASP   439      44.937  53.283  77.399  1.00 25.00           C
ATOM    440  CA  PHE   440      41.928  55.390  78.427  1.00 25.00           C
ATOM    441  CA  ALA   441      41.217  54.415  82.022  1.00 25.00           C
ATOM    442  CA  SER   442      39.801  54.807  85.503  1.00 25.00           C
ATOM    443  CA  PRO   443      37.810  58.052  85.814  1.00 25.00           C
ATOM    444  CA  VAL   444      36.393  61.357  84.553  1.00 25.00           C
ATOM    445  CA  SER   445      37.672  64.618  85.986  1.00 25.00           C
ATOM    446  CA  GLY   446      39.709  64.791  82.781  1.00 25.00           C
ATOM    447  CA  LEU   447      43.047  66.588  82.031  1.00 25.00           C
ATOM    448  CA  GLY   448      46.126  66.616  79.750  1.00 25.00           C
ATOM    449  CA  SER   449      47.880  67.577  76.528  1.00 25.00           C
ATOM    450  CA  LYS   450      50.783  69.649  75.150  1.00 25.00           C
ATOM    451  CA  MET   451      53.231  72.504  74.963  1.00 25.00           C
ATOM    452  CA  GLY   452      55.906  74.242  72.960  1.00 25.00           C
ATOM    453  CA  LEU   453      57.393  75.542  69.692  1.00 25.00           C
ATOM    454  CA  ASP   454      57.775  75.217  65.911  1.00 25.00           C
ATOM    455  CA  ALA   455      56.829  78.304  63.897  1.00 25.00           C
ATOM    456  CA  THR   456      56.325  81.661  62.136  1.00 25.00           C
ATOM    457  CA  ASN   457      56.550  85.063  60.611  1.00 25.00           C
ATOM    458  CA  LYS   458      55.004  88.554  60.218  1.00 25.00           C
ATOM    459  CA  TRP   459      55.594  92.269  60.486  1.00 25.00           C
ATOM    460  CA  PRO   460      51.911  92.963  61.038  1.00 25.00           C
ATOM    461  CA  GLY   461      48.413  91.848  61.752  1.00 25.00           C
ATOM    462  CA  GLU   462      45.111  93.586  62.620  1.00 25.00           C
ATOM    463  CA  THR   463      44.781  96.469  65.136  1.00 25.00           C
ATOM    464  CA  GLN   464      42.769  96.050  68.281  1.00 25.00           C
ATOM    465  CA  ARG   465      42.372  95.308  72.045  1.00 25.00           C
ATOM    466  CA  GLU   466      44.164  92.034  72.762  1.00 25.00           C
ATOM    467  CA  TRP   467      43.268  88.318  72.578  1.00 25.00           C
TER
END
