
#######################################################
#                                                     #
#                        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   67 (   67),  selected   67 , name T0356TS677_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS677_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          1.744
LGA    P     349      P     349          1.202
LGA    E     350      E     350          1.570
LGA    I     351      I     351          1.404
LGA    V     352      V     352          2.181
LGA    D     353      D     353          2.457
LGA    F     354      F     354          2.921
LGA    Y     355      Y     355          2.648
LGA    L     356      L     356          2.545
LGA    P     357      P     357          2.262
LGA    P     358      P     358           -
LGA    E     359      E     359           -
LGA    G     360      -       -           -
LGA    C     361      -       -           -
LGA    S     362      G     360          4.082
LGA    Y     363      C     361           #
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    R     364      R     364          3.097
LGA    L     365      L     365          3.069
LGA    A     366      A     366          3.169
LGA    V     367      V     367          3.100
LGA    V     368      V     368          2.904
LGA    T     369      T     369          2.841
LGA    I     370      I     370          2.239
LGA    K     371      K     371          2.872
LGA    K     372      K     372           #
LGA    Q     373      Q     373          3.544
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    Y     374      H     377          3.460
LGA    A     375      A     378          3.598
LGA    G     376      K     379          2.959
LGA    H     377      R     380          1.507
LGA    A     378      V     381          1.444
LGA    K     379      M     382          2.359
LGA    R     380      M     383          1.560
LGA    V     381      G     384          1.409
LGA    M     382      V     385          1.953
LGA    M     383      W     386          2.402
LGA    G     384      S     387          2.329
LGA    V     385      F     388          2.218
LGA    W     386      L     389          2.375
LGA    S     387      R     390          2.504
LGA    F     388      Q     391           #
LGA    L     389      F     392          5.660
LGA    R     390      M     393          4.395
LGA    Q     391      Y     394          3.929
LGA    F     392      T     395          3.870
LGA    M     393      K     396          1.506
LGA    K     396      F     397          0.863
LGA    F     397      V     398          2.247
LGA    V     398      I     399          1.938
LGA    I     399      V     400          2.535
LGA    V     400      C     401          1.268
LGA    C     401      D     402          2.911
LGA    -       -      D     403           -
LGA    D     402      D     404          1.647
LGA    D     403      V     405          2.379
LGA    N     406      N     406          2.268
LGA    A     407      A     407           #
LGA    R     408      -       -           -
LGA    D     409      -       -           -
LGA    W     410      -       -           -
LGA    N     411      -       -           -
LGA    D     412      -       -           -
LGA    V     413      -       -           -
LGA    I     414      R     408          3.420
LGA    W     415      D     409          5.481
LGA    A     416      W     410          4.211
LGA    I     417      N     411          3.691
LGA    -       -      D     412           -
LGA    T     418      V     413          4.311
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)   67  120    5.0     53    2.88    41.51     27.533     1.778

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.544224 * X  +  -0.225840 * Y  +  -0.807971 * Z  +  59.620247
  Y_new =  -0.430515 * X  +  -0.901787 * Y  +  -0.037918 * Z  + 113.966484
  Z_new =  -0.720054 * X  +   0.368479 * Y  +  -0.588002 * Z  +  86.272942 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.581798   -0.559794  [ DEG:   147.9261    -32.0739 ]
  Theta =   0.803880    2.337713  [ DEG:    46.0589    133.9411 ]
  Phi   =  -0.669267    2.472326  [ DEG:   -38.3462    141.6538 ]
 
# 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: T0356TS677_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   67  120   5.0   53   2.88   41.51  27.533
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_1-D3
PFRMAT TS
TARGET T0356
MODEL  1
PARENT 2D1Q_A
ATOM    463  CA  PHE   348      57.958  70.319  53.352  1.00 99.00
ATOM    464  CA  PRO   349      57.128  72.561  50.333  1.00 38.00
ATOM    465  CA  GLU   350      53.508  71.284  50.134  1.00 45.00
ATOM    466  CA  ILE   351      52.779  71.714  53.868  1.00 62.00
ATOM    467  CA  VAL   352      51.644  75.093  55.122  1.00 47.00
ATOM    468  CA  ASP   353      50.965  74.178  58.766  1.00 27.00
ATOM    469  CA  PHE   354      51.097  71.055  60.945  1.00 40.00
ATOM    470  CA  TYR   355      50.360  69.856  64.470  1.00 29.00
ATOM    471  CA  LEU   356      51.302  66.620  66.246  1.00 27.00
ATOM    472  CA  PRO   357      49.826  64.678  69.198  1.00 47.00
ATOM    477  CA  PRO   358      46.750  49.210  73.314  1.00 50.00
ATOM    478  CA  GLU   359      50.221  47.910  72.287  1.00 63.00
ATOM    479  CA  GLY   360      52.492  50.966  72.389  1.00 60.00
ATOM    480  CA  CYS   361      50.615  53.321  74.758  1.00 47.00
ATOM    481  CA  SER   362      50.754  56.297  72.367  1.00 57.00
ATOM    482  CA  TYR   363      51.390  56.735  68.605  1.00 58.00
ATOM    483  CA  ARG   364      52.506  60.004  66.984  1.00 41.00
ATOM    484  CA  LEU   365      49.900  61.326  64.587  1.00 55.00
ATOM    485  CA  ALA   366      49.571  64.601  62.698  1.00 60.00
ATOM    486  CA  VAL   367      47.104  67.118  61.333  1.00 49.00
ATOM    487  CA  VAL   368      48.353  68.765  58.138  1.00 54.00
ATOM    488  CA  THR   369      47.319  71.888  56.198  1.00 55.00
ATOM    489  CA  ILE   370      48.509  71.831  52.579  1.00 55.00
ATOM    490  CA  LYS   371      49.461  74.903  50.525  1.00 70.00
ATOM    491  CA  LYS   372      46.508  75.996  48.352  1.00 92.00
ATOM    492  CA  GLN   373      46.410  73.988  45.109  1.00 99.00
ATOM    496  CA  TYR   374      48.175  61.559  50.443  1.00 99.00
ATOM    497  CA  ALA   375      48.359  60.243  54.029  1.00 99.00
ATOM    498  CA  GLY   376      51.062  57.766  52.934  1.00 99.00
ATOM    499  CA  HIS   377      53.155  60.414  51.129  1.00 99.00
ATOM    500  CA  ALA   378      53.367  62.478  54.327  1.00 99.00
ATOM    501  CA  LYS   379      54.227  59.323  56.345  1.00 99.00
ATOM    502  CA  ARG   380      56.928  58.189  53.853  1.00 99.00
ATOM    503  CA  VAL   381      58.579  61.639  53.816  1.00 99.00
ATOM    504  CA  MET   382      58.697  61.727  57.663  1.00 99.00
ATOM    505  CA  MET   383      60.047  58.150  57.846  1.00 99.00
ATOM    506  CA  GLY   384      62.953  59.065  55.548  1.00 86.00
ATOM    507  CA  VAL   385      64.056  61.930  57.851  1.00 83.00
ATOM    508  CA  TRP   386      63.636  60.689  61.454  1.00 99.00
ATOM    509  CA  SER   387      64.503  57.617  63.520  1.00 99.00
ATOM    510  CA  PHE   388      62.143  54.640  63.883  1.00 99.00
ATOM    511  CA  LEU   389      60.451  55.795  67.111  1.00 99.00
ATOM    512  CA  ARG   390      59.403  59.198  65.709  1.00 99.00
ATOM    513  CA  GLN   391      57.450  57.698  62.735  1.00 99.00
ATOM    514  CA  PHE   392      53.840  58.815  62.313  1.00 99.00
ATOM    515  CA  MET   393      52.314  55.458  63.218  1.00 99.00
ATOM    516  CA  LYS   396      49.137  57.190  64.418  1.00 99.00
ATOM    517  CA  PHE   397      48.126  58.494  60.985  1.00 99.00
ATOM    518  CA  VAL   398      47.803  61.797  59.128  1.00 99.00
ATOM    519  CA  ILE   399      44.640  63.866  58.654  1.00 99.00
ATOM    520  CA  VAL   400      44.281  66.860  56.364  1.00 99.00
ATOM    521  CA  CYS   401      42.522  69.921  57.818  1.00 99.00
ATOM    522  CA  ASP   402      41.712  73.576  56.982  1.00 99.00
ATOM    523  CA  ASP   403      43.255  74.881  60.221  1.00 99.00
ATOM    525  CA  ASN   406      43.965  73.960  66.215  1.00 87.00
ATOM    526  CA  ALA   407      46.185  76.448  68.090  1.00 81.00
ATOM    527  CA  ARG   408      46.075  78.916  70.958  1.00 53.00
ATOM    528  CA  ASP   409      46.474  82.641  70.440  1.00 53.00
ATOM    529  CA  TRP   410      50.249  82.632  70.993  1.00 38.00
ATOM    530  CA  ASN   411      50.892  79.638  68.767  1.00 54.00
ATOM    531  CA  ASP   412      50.649  76.655  71.135  1.00 75.00
ATOM    532  CA  VAL   413      49.163  73.483  69.627  1.00 85.00
ATOM    533  CA  ILE   414      45.899  72.227  71.125  1.00 77.00
ATOM    534  CA  TRP   415      46.947  68.587  71.601  1.00 99.00
ATOM    535  CA  ALA   416      43.456  67.678  72.925  1.00 93.00
ATOM    536  CA  ILE   417      41.738  68.987  69.794  1.00 93.00
ATOM    537  CA  THR   418      44.191  67.033  67.550  1.00 93.00
TER
END
