
#######################################################
#                                                     #
#                        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_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS168_1-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           -
LGA    E     350      I     351           #
LGA    -       -      V     352           -
LGA    I     351      D     353           #
LGA    V     352      F     354          3.691
LGA    D     353      Y     355          4.128
LGA    F     354      L     356          3.183
LGA    Y     355      P     357          4.588
LGA    L     356      P     358           #
LGA    P     357      E     359           -
LGA    P     358      G     360           -
LGA    E     359      C     361           -
LGA    G     360      S     362           -
LGA    C     361      Y     363           -
LGA    S     362      R     364           -
LGA    Y     363      L     365           -
LGA    R     364      A     366           -
LGA    L     365      -       -           -
LGA    A     366      -       -           -
LGA    V     367      V     367           #
LGA    V     368      V     368          4.362
LGA    T     369      T     369          2.801
LGA    I     370      I     370          5.264
LGA    K     371      K     371          5.787
LGA    K     372      -       -           -
LGA    Q     373      K     372          5.504
LGA    Y     374      Q     373          4.264
LGA    A     375      Y     374          1.946
LGA    G     376      A     375          2.960
LGA    H     377      G     376          4.029
LGA    A     378      H     377          2.931
LGA    K     379      A     378          1.948
LGA    R     380      K     379          1.575
LGA    V     381      R     380          1.374
LGA    M     382      V     381          0.603
LGA    M     383      M     382          0.547
LGA    G     384      M     383          0.322
LGA    V     385      G     384          1.187
LGA    W     386      V     385          1.465
LGA    S     387      W     386          1.914
LGA    F     388      S     387          2.011
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    L     389      M     393          1.343
LGA    R     390      Y     394          2.957
LGA    -       -      T     395           -
LGA    Q     391      K     396          0.359
LGA    F     392      F     397          3.185
LGA    M     393      -       -           -
LGA    Y     394      -       -           -
LGA    T     395      -       -           -
LGA    K     396      -       -           -
LGA    F     397      -       -           -
LGA    V     398      -       -           -
LGA    I     399      -       -           -
LGA    V     400      V     398           #
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    C     401      N     406           #
LGA    D     402      A     407          1.782
LGA    D     403      R     408          1.995
LGA    D     404      D     409           #
LGA    V     405      -       -           -
LGA    N     406      -       -           -
LGA    A     407      W     410          2.037
LGA    R     408      N     411          3.013
LGA    D     409      D     412          5.327
LGA    W     410      V     413           #
LGA    N     411      I     414          4.796
LGA    D     412      W     415          3.848
LGA    V     413      A     416          4.262
LGA    I     414      -       -           -
LGA    W     415      I     417          2.019
LGA    A     416      T     418           -
LGA    I     417      T     419           -
LGA    T     418      -       -           -
LGA    T     419      -       -           -
LGA    R     420      R     420           #
LGA    M     421      M     421          3.664
LGA    D     422      D     422          2.628
LGA    P     423      P     423          2.558
LGA    A     424      A     424          0.795
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    R     425      T     427          2.381
LGA    D     426      V     428          1.650
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    T     427      G     452          3.478
LGA    V     428      L     453           -
LGA    L     429      D     454           -
LGA    V     430      A     455           -
LGA    E     431      T     456           -
LGA    N     432      N     457           -
LGA    T     433      K     458           -
LGA    P     434      W     459           -
LGA    I     435      P     460           -
LGA    D     436      G     461           -
LGA    Y     437      E     462           -
LGA    L     438      T     463           -
LGA    D     439      Q     464           -
LGA    F     440      R     465           -
LGA    A     441      E     466           -
LGA    S     442      W     467           -
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     44    3.14    25.00     22.648     1.358

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.960370 * X  +   0.202940 * Y  +  -0.191063 * Z  +  61.269924
  Y_new =  -0.194047 * X  +  -0.005283 * Y  +  -0.980978 * Z  +  75.479553
  Z_new =  -0.200089 * X  +   0.979177 * Y  +   0.034306 * Z  +  52.771957 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.535775   -1.605817  [ DEG:    87.9934    -92.0066 ]
  Theta =   0.201448    2.940144  [ DEG:    11.5421    168.4579 ]
  Phi   =  -0.199370    2.942223  [ DEG:   -11.4230    168.5770 ]
 
# 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_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS168_1-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   44   3.14   25.00  22.648
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS168_1-D3
PFRMAT TS
TARGET T0356
MODEL 1
PARENT N/A
ATOM    348  CA  PHE   348      47.547  67.246  57.618  1.00 25.00           C
ATOM    349  CA  PRO   349      49.196  63.803  57.526  1.00 25.00           C
ATOM    350  CA  GLU   350      52.906  64.594  57.075  1.00 25.00           C
ATOM    351  CA  ILE   351      56.105  65.688  58.682  1.00 25.00           C
ATOM    352  CA  VAL   352      56.204  67.262  62.173  1.00 25.00           C
ATOM    353  CA  ASP   353      55.208  65.656  65.445  1.00 25.00           C
ATOM    354  CA  PHE   354      54.100  68.719  67.502  1.00 25.00           C
ATOM    355  CA  TYR   355      54.617  68.263  71.247  1.00 25.00           C
ATOM    356  CA  LEU   356      53.570  71.050  73.573  1.00 25.00           C
ATOM    357  CA  PRO   357      50.084  70.389  72.195  1.00 25.00           C
ATOM    358  CA  PRO   358      47.503  73.048  72.743  1.00 25.00           C
ATOM    359  CA  GLU   359      46.083  76.455  71.754  1.00 25.00           C
ATOM    360  CA  GLY   360      45.635  76.272  68.016  1.00 25.00           C
ATOM    361  CA  CYS   361      49.252  75.420  67.276  1.00 25.00           C
ATOM    362  CA  SER   362      52.143  73.955  69.352  1.00 25.00           C
ATOM    363  CA  TYR   363      55.496  74.599  71.093  1.00 25.00           C
ATOM    364  CA  ARG   364      56.999  71.884  68.877  1.00 25.00           C
ATOM    365  CA  LEU   365      57.411  71.408  65.094  1.00 25.00           C
ATOM    366  CA  ALA   366      54.155  71.130  63.153  1.00 25.00           C
ATOM    367  CA  VAL   367      50.867  73.089  62.710  1.00 25.00           C
ATOM    368  CA  VAL   368      48.576  71.220  60.277  1.00 25.00           C
ATOM    369  CA  THR   369      46.595  72.068  57.219  1.00 25.00           C
ATOM    370  CA  ILE   370      44.096  72.445  54.344  1.00 25.00           C
ATOM    371  CA  LYS   371      42.091  72.047  51.179  1.00 25.00           C
ATOM    372  CA  LYS   372      42.025  68.504  52.573  1.00 25.00           C
ATOM    373  CA  GLN   373      42.335  66.269  49.556  1.00 25.00           C
ATOM    374  CA  TYR   374      45.581  68.008  48.653  1.00 25.00           C
ATOM    375  CA  ALA   375      47.125  66.441  45.602  1.00 25.00           C
ATOM    376  CA  GLY   376      46.577  62.736  46.403  1.00 25.00           C
ATOM    377  CA  HIS   377      50.188  61.958  45.390  1.00 25.00           C
ATOM    378  CA  ALA   378      51.454  64.797  47.627  1.00 25.00           C
ATOM    379  CA  LYS   379      49.375  63.453  50.550  1.00 25.00           C
ATOM    380  CA  ARG   380      50.804  59.945  49.984  1.00 25.00           C
ATOM    381  CA  VAL   381      54.358  61.372  49.945  1.00 25.00           C
ATOM    382  CA  MET   382      53.667  63.248  53.211  1.00 25.00           C
ATOM    383  CA  MET   383      52.325  60.034  54.803  1.00 25.00           C
ATOM    384  CA  GLY   384      55.454  58.137  53.670  1.00 25.00           C
ATOM    385  CA  VAL   385      57.681  60.874  55.159  1.00 25.00           C
ATOM    386  CA  TRP   386      55.750  60.684  58.460  1.00 25.00           C
ATOM    387  CA  SER   387      56.165  56.877  58.512  1.00 25.00           C
ATOM    388  CA  PHE   388      59.924  57.253  57.879  1.00 25.00           C
ATOM    389  CA  LEU   389      59.697  55.910  61.401  1.00 25.00           C
ATOM    390  CA  ARG   390      56.508  55.235  63.353  1.00 25.00           C
ATOM    391  CA  GLN   391      52.985  54.524  64.582  1.00 25.00           C
ATOM    392  CA  PHE   392      52.768  58.362  64.673  1.00 25.00           C
ATOM    393  CA  MET   393      54.319  59.167  68.038  1.00 25.00           C
ATOM    394  CA  TYR   394      57.667  60.263  66.634  1.00 25.00           C
ATOM    395  CA  THR   395      60.824  58.162  66.232  1.00 25.00           C
ATOM    396  CA  LYS   396      61.075  58.279  70.052  1.00 25.00           C
ATOM    397  CA  PHE   397      59.442  61.608  71.041  1.00 25.00           C
ATOM    398  CA  VAL   398      56.167  63.139  70.018  1.00 25.00           C
ATOM    399  CA  ILE   399      52.771  63.904  68.588  1.00 25.00           C
ATOM    400  CA  VAL   400      50.705  65.339  65.758  1.00 25.00           C
ATOM    401  CA  CYS   401      49.493  68.910  65.186  1.00 25.00           C
ATOM    402  CA  ASP   402      47.060  71.788  65.603  1.00 25.00           C
ATOM    403  CA  ASP   403      46.057  69.862  68.697  1.00 25.00           C
ATOM    404  CA  ASP   404      46.580  66.079  68.620  1.00 25.00           C
ATOM    405  CA  VAL   405      46.884  65.696  72.398  1.00 25.00           C
ATOM    406  CA  ASN   406      43.145  65.502  71.855  1.00 25.00           C
ATOM    407  CA  ALA   407      40.553  66.358  69.208  1.00 25.00           C
ATOM    408  CA  ARG   408      37.631  68.100  71.044  1.00 25.00           C
ATOM    409  CA  ASP   409      35.908  70.786  68.923  1.00 25.00           C
ATOM    410  CA  TRP   410      36.009  70.228  65.174  1.00 25.00           C
ATOM    411  CA  ASN   411      35.159  67.418  62.716  1.00 25.00           C
ATOM    412  CA  ASP   412      37.765  68.754  60.249  1.00 25.00           C
ATOM    413  CA  VAL   413      40.384  68.871  63.040  1.00 25.00           C
ATOM    414  CA  ILE   414      39.541  65.264  64.016  1.00 25.00           C
ATOM    415  CA  TRP   415      39.889  64.169  60.362  1.00 25.00           C
ATOM    416  CA  ALA   416      43.285  65.925  60.133  1.00 25.00           C
ATOM    417  CA  ILE   417      44.431  64.180  63.343  1.00 25.00           C
ATOM    418  CA  THR   418      43.311  60.799  61.934  1.00 25.00           C
ATOM    419  CA  THR   419      45.227  61.489  58.690  1.00 25.00           C
ATOM    420  CA  ARG   420      42.420  61.936  56.133  1.00 25.00           C
ATOM    421  CA  MET   421      39.573  61.997  53.670  1.00 25.00           C
ATOM    422  CA  ASP   422      37.016  59.602  55.051  1.00 25.00           C
ATOM    423  CA  PRO   423      37.237  55.791  55.155  1.00 25.00           C
ATOM    424  CA  ALA   424      38.335  52.189  55.771  1.00 25.00           C
ATOM    425  CA  ARG   425      42.065  52.652  56.366  1.00 25.00           C
ATOM    426  CA  ASP   426      45.888  52.594  56.345  1.00 25.00           C
ATOM    427  CA  THR   427      48.714  54.875  55.475  1.00 25.00           C
ATOM    428  CA  VAL   428      51.445  54.783  52.781  1.00 25.00           C
ATOM    429  CA  LEU   429      54.375  53.366  50.877  1.00 25.00           C
ATOM    430  CA  VAL   430      57.745  51.893  51.784  1.00 25.00           C
ATOM    431  CA  GLU   431      58.235  48.416  50.499  1.00 25.00           C
ATOM    432  CA  ASN   432      61.826  47.810  49.309  1.00 25.00           C
ATOM    433  CA  THR   433      63.636  51.121  48.596  1.00 25.00           C
ATOM    434  CA  PRO   434      63.750  51.194  44.840  1.00 25.00           C
ATOM    435  CA  ILE   435      62.429  54.730  44.054  1.00 25.00           C
ATOM    436  CA  ASP   436      61.705  58.405  44.703  1.00 25.00           C
ATOM    437  CA  TYR   437      61.967  58.882  48.491  1.00 25.00           C
ATOM    438  CA  LEU   438      64.254  61.636  49.868  1.00 25.00           C
ATOM    439  CA  ASP   439      67.296  59.912  48.422  1.00 25.00           C
ATOM    440  CA  PHE   440      69.387  57.923  50.958  1.00 25.00           C
ATOM    441  CA  ALA   441      72.831  58.867  49.715  1.00 25.00           C
ATOM    442  CA  SER   442      75.973  56.764  49.835  1.00 25.00           C
ATOM    443  CA  PRO   443      78.572  57.453  52.505  1.00 25.00           C
ATOM    444  CA  VAL   444      81.098  60.281  52.487  1.00 25.00           C
ATOM    445  CA  SER   445      79.435  63.668  52.783  1.00 25.00           C
ATOM    446  CA  GLY   446      77.639  66.787  53.965  1.00 25.00           C
ATOM    447  CA  LEU   447      74.692  66.744  56.426  1.00 25.00           C
ATOM    448  CA  GLY   448      73.129  69.062  59.042  1.00 25.00           C
ATOM    449  CA  SER   449      69.795  70.621  57.943  1.00 25.00           C
ATOM    450  CA  LYS   450      66.226  69.622  58.770  1.00 25.00           C
ATOM    451  CA  MET   451      63.820  71.938  57.050  1.00 25.00           C
ATOM    452  CA  GLY   452      64.143  73.449  53.598  1.00 25.00           C
ATOM    453  CA  LEU   453      62.964  76.611  51.873  1.00 25.00           C
ATOM    454  CA  ASP   454      60.505  78.824  49.976  1.00 25.00           C
ATOM    455  CA  ALA   455      62.851  81.663  50.765  1.00 25.00           C
ATOM    456  CA  THR   456      61.162  84.242  48.502  1.00 25.00           C
ATOM    457  CA  ASN   457      63.024  87.394  47.355  1.00 25.00           C
ATOM    458  CA  LYS   458      64.337  86.922  43.863  1.00 25.00           C
ATOM    459  CA  TRP   459      67.445  88.487  42.298  1.00 25.00           C
ATOM    460  CA  PRO   460      66.816  92.177  42.945  1.00 25.00           C
ATOM    461  CA  GLY   461      64.514  95.077  42.069  1.00 25.00           C
ATOM    462  CA  GLU   462      63.249  98.420  43.363  1.00 25.00           C
ATOM    463  CA  THR   463      61.758 101.852  43.101  1.00 25.00           C
ATOM    464  CA  GLN   464      59.136 103.079  45.597  1.00 25.00           C
ATOM    465  CA  ARG   465      56.709 101.477  43.177  1.00 25.00           C
ATOM    466  CA  GLU   466      55.734 104.603  41.177  1.00 25.00           C
ATOM    467  CA  TRP   467      56.666 102.235  38.320  1.00 25.00           C
TER
END
