
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0356AL381_5-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL381_5-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     376      -       -           -
LGA    H     377      -       -           -
LGA    A     378      -       -           -
LGA    K     379      -       -           -
LGA    R     380      F     348           #
LGA    V     381      P     349          3.577
LGA    M     382      E     350           -
LGA    M     383      I     351          5.013
LGA    G     384      V     352           -
LGA    V     385      D     353           -
LGA    W     386      -       -           -
LGA    S     387      F     354          5.091
LGA    F     388      Y     355           -
LGA    L     389      -       -           -
LGA    R     390      L     356           #
LGA    Q     391      P     357           -
LGA    F     392      P     358           -
LGA    M     393      E     359           -
LGA    Y     394      G     360           -
LGA    -       -      C     361           -
LGA    -       -      S     362           -
LGA    T     395      Y     363          2.872
LGA    -       -      R     364           -
LGA    K     396      L     365          1.968
LGA    F     397      A     366          1.311
LGA    V     398      V     367          1.190
LGA    I     399      V     368          1.578
LGA    V     400      T     369          1.761
LGA    C     401      I     370          1.791
LGA    D     402      K     371          1.578
LGA    D     403      K     372          1.021
LGA    D     404      Q     373           #
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    A     416      H     377          4.366
LGA    I     417      -       -           -
LGA    T     418      A     378          2.296
LGA    T     419      K     379          3.603
LGA    R     420      R     380          2.279
LGA    M     421      V     381          3.160
LGA    D     422      M     382          1.912
LGA    P     423      M     383          4.830
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    -       -      W     386           -
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      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    A     424      V     428          2.783
LGA    R     425      L     429          3.102
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    D     426      G     452          0.515
LGA    T     427      L     453          0.614
LGA    V     428      D     454          1.491
LGA    L     429      A     455          1.398
LGA    V     430      T     456          3.316
LGA    E     431      N     457          4.646
LGA    N     432      K     458          2.693
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)   46  120    5.0     28    2.88     7.14     15.133     0.938

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624093 * X  +   0.693896 * Y  +  -0.359189 * Z  + 101.971092
  Y_new =  -0.604111 * X  +  -0.720065 * Y  +  -0.341404 * Z  + 225.397308
  Z_new =  -0.495539 * X  +   0.003922 * Y  +   0.868577 * Z  + -86.801186 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.004516   -3.137077  [ DEG:     0.2587   -179.7413 ]
  Theta =   0.518455    2.623138  [ DEG:    29.7053    150.2947 ]
  Phi   =  -2.372462    0.769130  [ DEG:  -135.9321     44.0679 ]
 
# 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: T0356AL381_5-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL381_5-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46  120   5.0   28   2.88    7.14  15.133
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL381_5-D3
REMARK Aligment from pdb entry: 1e9rA
ATOM      1  N   GLY   376      55.777  82.538  49.312  1.00  0.00              
ATOM      2  CA  GLY   376      56.972  82.156  48.590  1.00  0.00              
ATOM      3  C   GLY   376      58.263  82.230  49.365  1.00  0.00              
ATOM      4  O   GLY   376      59.312  81.915  48.811  1.00  0.00              
ATOM      5  N   HIS   377      58.205  82.623  50.634  1.00  0.00              
ATOM      6  CA  HIS   377      59.422  82.720  51.433  1.00  0.00              
ATOM      7  C   HIS   377      59.959  81.371  51.925  1.00  0.00              
ATOM      8  O   HIS   377      61.090  81.292  52.405  1.00  0.00              
ATOM      9  N   ALA   378      59.160  80.313  51.808  1.00  0.00              
ATOM     10  CA  ALA   378      59.630  79.001  52.225  1.00  0.00              
ATOM     11  C   ALA   378      58.975  78.342  53.427  1.00  0.00              
ATOM     12  O   ALA   378      59.487  77.344  53.934  1.00  0.00              
ATOM     13  N   LYS   379      57.842  78.877  53.878  1.00  0.00              
ATOM     14  CA  LYS   379      57.145  78.319  55.031  1.00  0.00              
ATOM     15  C   LYS   379      56.817  76.825  54.888  1.00  0.00              
ATOM     16  O   LYS   379      57.054  76.031  55.803  1.00  0.00              
ATOM     17  N   ARG   380      56.266  76.443  53.743  1.00  0.00              
ATOM     18  CA  ARG   380      55.895  75.050  53.521  1.00  0.00              
ATOM     19  C   ARG   380      57.112  74.149  53.560  1.00  0.00              
ATOM     20  O   ARG   380      57.045  73.035  54.074  1.00  0.00              
ATOM     21  N   VAL   381      58.225  74.633  53.019  1.00  0.00              
ATOM     22  CA  VAL   381      59.470  73.866  53.003  1.00  0.00              
ATOM     23  C   VAL   381      59.918  73.606  54.438  1.00  0.00              
ATOM     24  O   VAL   381      60.251  72.481  54.808  1.00  0.00              
ATOM     25  N   MET   382      59.914  74.657  55.249  1.00  0.00              
ATOM     26  CA  MET   382      60.326  74.539  56.638  1.00  0.00              
ATOM     27  C   MET   382      59.426  73.562  57.392  1.00  0.00              
ATOM     28  O   MET   382      59.912  72.702  58.125  1.00  0.00              
ATOM     29  N   MET   383      58.115  73.694  57.217  1.00  0.00              
ATOM     30  CA  MET   383      57.177  72.810  57.902  1.00  0.00              
ATOM     31  C   MET   383      57.330  71.371  57.446  1.00  0.00              
ATOM     32  O   MET   383      57.158  70.451  58.241  1.00  0.00              
ATOM     33  N   GLY   384      57.641  71.181  56.166  1.00  0.00              
ATOM     34  CA  GLY   384      57.820  69.843  55.606  1.00  0.00              
ATOM     35  C   GLY   384      59.031  69.184  56.269  1.00  0.00              
ATOM     36  O   GLY   384      58.968  68.019  56.668  1.00  0.00              
ATOM     37  N   VAL   385      60.122  69.937  56.395  1.00  0.00              
ATOM     38  CA  VAL   385      61.331  69.429  57.034  1.00  0.00              
ATOM     39  C   VAL   385      61.077  69.063  58.491  1.00  0.00              
ATOM     40  O   VAL   385      61.510  68.021  58.966  1.00  0.00              
ATOM     41  N   TRP   386      60.380  69.932  59.207  1.00  0.00              
ATOM     42  CA  TRP   386      60.078  69.679  60.608  1.00  0.00              
ATOM     43  C   TRP   386      59.253  68.411  60.767  1.00  0.00              
ATOM     44  O   TRP   386      59.560  67.558  61.593  1.00  0.00              
ATOM     45  N   SER   387      58.194  68.291  59.973  1.00  0.00              
ATOM     46  CA  SER   387      57.327  67.122  60.034  1.00  0.00              
ATOM     47  C   SER   387      58.140  65.864  59.757  1.00  0.00              
ATOM     48  O   SER   387      58.060  64.878  60.490  1.00  0.00              
ATOM     49  N   PHE   388      58.932  65.920  58.689  1.00  0.00              
ATOM     50  CA  PHE   388      59.771  64.806  58.281  1.00  0.00              
ATOM     51  C   PHE   388      60.660  64.303  59.413  1.00  0.00              
ATOM     52  O   PHE   388      60.599  63.132  59.787  1.00  0.00              
ATOM     53  N   LEU   389      61.482  65.194  59.959  1.00  0.00              
ATOM     54  CA  LEU   389      62.381  64.829  61.049  1.00  0.00              
ATOM     55  C   LEU   389      61.616  64.362  62.284  1.00  0.00              
ATOM     56  O   LEU   389      62.149  63.614  63.104  1.00  0.00              
ATOM     57  N   ARG   390      60.368  64.803  62.413  1.00  0.00              
ATOM     58  CA  ARG   390      59.563  64.390  63.546  1.00  0.00              
ATOM     59  C   ARG   390      59.088  62.975  63.302  1.00  0.00              
ATOM     60  O   ARG   390      58.921  62.175  64.222  1.00  0.00              
ATOM     61  N   GLN   391      58.869  62.668  62.032  1.00  0.00              
ATOM     62  CA  GLN   391      58.424  61.337  61.648  1.00  0.00              
ATOM     63  C   GLN   391      59.573  60.362  61.845  1.00  0.00              
ATOM     64  O   GLN   391      59.374  59.250  62.331  1.00  0.00              
ATOM     65  N   PHE   392      60.777  60.792  61.474  1.00  0.00              
ATOM     66  CA  PHE   392      61.959  59.952  61.632  1.00  0.00              
ATOM     67  C   PHE   392      62.130  59.559  63.093  1.00  0.00              
ATOM     68  O   PHE   392      62.671  58.498  63.403  1.00  0.00              
ATOM     69  N   MET   393      61.662  60.417  63.991  1.00  0.00              
ATOM     70  CA  MET   393      61.773  60.146  65.416  1.00  0.00              
ATOM     71  C   MET   393      60.598  59.292  65.896  1.00  0.00              
ATOM     72  O   MET   393      60.567  58.853  67.048  1.00  0.00              
ATOM     73  N   TYR   394      59.633  59.068  65.006  1.00  0.00              
ATOM     74  CA  TYR   394      58.477  58.256  65.347  1.00  0.00              
ATOM     75  C   TYR   394      57.366  58.985  66.073  1.00  0.00              
ATOM     76  O   TYR   394      56.566  58.368  66.774  1.00  0.00              
ATOM     77  N   THR   395      57.312  60.300  65.899  1.00  0.00              
ATOM     78  CA  THR   395      56.296  61.121  66.548  1.00  0.00              
ATOM     79  C   THR   395      54.974  61.090  65.790  1.00  0.00              
ATOM     80  O   THR   395      54.959  61.009  64.555  1.00  0.00              
ATOM     81  N   LYS   396      53.869  61.133  66.531  1.00  0.00              
ATOM     82  CA  LYS   396      52.554  61.167  65.907  1.00  0.00              
ATOM     83  C   LYS   396      52.233  62.635  65.631  1.00  0.00              
ATOM     84  O   LYS   396      52.695  63.525  66.348  1.00  0.00              
ATOM     85  N   PHE   397      51.439  62.890  64.596  1.00  0.00              
ATOM     86  CA  PHE   397      51.094  64.259  64.257  1.00  0.00              
ATOM     87  C   PHE   397      49.856  64.427  63.387  1.00  0.00              
ATOM     88  O   PHE   397      49.472  63.525  62.636  1.00  0.00              
ATOM     89  N   VAL   398      49.228  65.591  63.526  1.00  0.00              
ATOM     90  CA  VAL   398      48.057  65.957  62.751  1.00  0.00              
ATOM     91  C   VAL   398      48.587  67.041  61.826  1.00  0.00              
ATOM     92  O   VAL   398      49.284  67.943  62.270  1.00  0.00              
ATOM     93  N   ILE   399      48.267  66.952  60.545  1.00  0.00              
ATOM     94  CA  ILE   399      48.757  67.929  59.599  1.00  0.00              
ATOM     95  C   ILE   399      47.655  68.520  58.763  1.00  0.00              
ATOM     96  O   ILE   399      46.918  67.794  58.110  1.00  0.00              
ATOM     97  N   VAL   400      47.532  69.842  58.809  1.00  0.00              
ATOM     98  CA  VAL   400      46.558  70.555  57.997  1.00  0.00              
ATOM     99  C   VAL   400      47.362  70.642  56.716  1.00  0.00              
ATOM    100  O   VAL   400      48.257  71.471  56.565  1.00  0.00              
ATOM    101  N   CYS   401      47.025  69.741  55.803  1.00  0.00              
ATOM    102  CA  CYS   401      47.751  69.566  54.560  1.00  0.00              
ATOM    103  C   CYS   401      47.032  69.950  53.267  1.00  0.00              
ATOM    104  O   CYS   401      46.278  69.158  52.705  1.00  0.00              
ATOM    105  N   ASP   402      47.272  71.181  52.775  1.00  0.00              
ATOM    106  CA  ASP   402      46.655  71.682  51.543  1.00  0.00              
ATOM    107  C   ASP   402      47.092  70.852  50.341  1.00  0.00              
ATOM    108  O   ASP   402      48.288  70.619  50.142  1.00  0.00              
ATOM    109  N   ASP   403      46.120  70.410  49.548  1.00  0.00              
ATOM    110  CA  ASP   403      46.387  69.619  48.351  1.00  0.00              
ATOM    111  C   ASP   403      47.047  68.280  48.624  1.00  0.00              
ATOM    112  O   ASP   403      47.627  67.683  47.721  1.00  0.00              
ATOM    113  N   ASP   404      46.967  67.812  49.864  1.00  0.00              
ATOM    114  CA  ASP   404      47.562  66.533  50.213  1.00  0.00              
ATOM    115  C   ASP   404      49.046  66.392  49.905  1.00  0.00              
ATOM    116  O   ASP   404      49.531  65.281  49.726  1.00  0.00              
ATOM    117  N   ALA   416      49.772  67.505  49.849  1.00  0.00              
ATOM    118  CA  ALA   416      51.198  67.468  49.554  1.00  0.00              
ATOM    119  C   ALA   416      51.979  66.600  50.542  1.00  0.00              
ATOM    120  O   ALA   416      52.752  65.737  50.137  1.00  0.00              
ATOM    121  N   ILE   417      51.787  66.821  51.836  1.00  0.00              
ATOM    122  CA  ILE   417      52.497  66.030  52.825  1.00  0.00              
ATOM    123  C   ILE   417      51.994  64.598  52.884  1.00  0.00              
ATOM    124  O   ILE   417      52.738  63.686  53.236  1.00  0.00              
ATOM    125  N   THR   418      50.728  64.405  52.539  1.00  0.00              
ATOM    126  CA  THR   418      50.131  63.074  52.532  1.00  0.00              
ATOM    127  C   THR   418      50.817  62.245  51.459  1.00  0.00              
ATOM    128  O   THR   418      51.151  61.077  51.676  1.00  0.00              
ATOM    129  N   THR   419      51.027  62.863  50.302  1.00  0.00              
ATOM    130  CA  THR   419      51.648  62.186  49.174  1.00  0.00              
ATOM    131  C   THR   419      53.097  61.811  49.441  1.00  0.00              
ATOM    132  O   THR   419      53.591  60.828  48.895  1.00  0.00              
ATOM    133  N   ARG   420      53.776  62.583  50.286  1.00  0.00              
ATOM    134  CA  ARG   420      55.181  62.323  50.586  1.00  0.00              
ATOM    135  C   ARG   420      55.413  61.458  51.817  1.00  0.00              
ATOM    136  O   ARG   420      56.310  60.619  51.818  1.00  0.00              
ATOM    137  N   MET   421      54.610  61.664  52.858  1.00  0.00              
ATOM    138  CA  MET   421      54.797  60.939  54.114  1.00  0.00              
ATOM    139  C   MET   421      53.679  60.014  54.548  1.00  0.00              
ATOM    140  O   MET   421      53.782  59.351  55.578  1.00  0.00              
ATOM    141  N   ASP   422      52.608  59.963  53.771  1.00  0.00              
ATOM    142  CA  ASP   422      51.492  59.112  54.131  1.00  0.00              
ATOM    143  C   ASP   422      51.778  57.619  54.140  1.00  0.00              
ATOM    144  O   ASP   422      52.146  57.035  53.121  1.00  0.00              
ATOM    145  N   PRO   423      51.612  56.997  55.301  1.00  0.00              
ATOM    146  CA  PRO   423      51.825  55.567  55.439  1.00  0.00              
ATOM    147  C   PRO   423      50.458  54.927  55.316  1.00  0.00              
ATOM    148  O   PRO   423      49.439  55.616  55.281  1.00  0.00              
ATOM    149  N   ALA   424      50.445  53.605  55.284  1.00  0.00              
ATOM    150  CA  ALA   424      49.215  52.844  55.147  1.00  0.00              
ATOM    151  C   ALA   424      48.278  52.915  56.364  1.00  0.00              
ATOM    152  O   ALA   424      47.054  52.909  56.227  1.00  0.00              
ATOM    153  N   ARG   425      48.862  52.983  57.552  1.00  0.00              
ATOM    154  CA  ARG   425      48.088  53.051  58.782  1.00  0.00              
ATOM    155  C   ARG   425      47.582  54.465  59.092  1.00  0.00              
ATOM    156  O   ARG   425      46.884  54.682  60.082  1.00  0.00              
ATOM    157  N   ASP   426      47.922  55.426  58.243  1.00  0.00              
ATOM    158  CA  ASP   426      47.503  56.792  58.484  1.00  0.00              
ATOM    159  C   ASP   426      46.069  57.119  58.087  1.00  0.00              
ATOM    160  O   ASP   426      45.465  56.437  57.263  1.00  0.00              
ATOM    161  N   THR   427      45.549  58.180  58.699  1.00  0.00              
ATOM    162  CA  THR   427      44.190  58.658  58.502  1.00  0.00              
ATOM    163  C   THR   427      44.102  59.852  57.564  1.00  0.00              
ATOM    164  O   THR   427      45.017  60.659  57.485  1.00  0.00              
ATOM    165  N   VAL   428      42.983  59.949  56.855  1.00  0.00              
ATOM    166  CA  VAL   428      42.730  61.056  55.939  1.00  0.00              
ATOM    167  C   VAL   428      41.333  61.582  56.210  1.00  0.00              
ATOM    168  O   VAL   428      40.391  60.811  56.356  1.00  0.00              
ATOM    169  N   LEU   429      41.220  62.898  56.310  1.00  0.00              
ATOM    170  CA  LEU   429      39.940  63.546  56.498  1.00  0.00              
ATOM    171  C   LEU   429      39.846  64.557  55.368  1.00  0.00              
ATOM    172  O   LEU   429      40.610  65.522  55.308  1.00  0.00              
ATOM    173  N   VAL   430      38.925  64.285  54.448  1.00  0.00              
ATOM    174  CA  VAL   430      38.683  65.110  53.263  1.00  0.00              
ATOM    175  C   VAL   430      37.379  64.566  52.681  1.00  0.00              
ATOM    176  O   VAL   430      37.337  63.445  52.165  1.00  0.00              
ATOM    177  N   GLU   431      36.299  65.356  52.748  1.00  0.00              
ATOM    178  CA  GLU   431      35.010  64.906  52.226  1.00  0.00              
ATOM    179  C   GLU   431      34.983  64.435  50.785  1.00  0.00              
ATOM    180  O   GLU   431      34.105  63.666  50.399  1.00  0.00              
ATOM    181  N   ASN   432      35.954  64.872  49.994  1.00  0.00              
ATOM    182  CA  ASN   432      35.976  64.493  48.595  1.00  0.00              
ATOM    183  C   ASN   432      37.070  63.515  48.182  1.00  0.00              
ATOM    184  O   ASN   432      37.301  63.314  46.995  1.00  0.00              
END
