
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0356AL242_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL242_1-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R     425      F     348           -
LGA    -       -      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    D     426      V     352          3.454
LGA    T     427      D     353          3.067
LGA    V     428      F     354          3.707
LGA    -       -      Y     355           -
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    -       -      L     365           -
LGA    -       -      A     366           -
LGA    -       -      V     367           -
LGA    -       -      V     368           -
LGA    L     429      T     369          1.793
LGA    V     430      I     370          3.954
LGA    E     431      K     371           -
LGA    N     432      K     372           -
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    -       -      R     380           -
LGA    T     433      V     381          3.885
LGA    P     434      M     382           -
LGA    I     435      M     383           -
LGA    -       -      G     384           -
LGA    D     436      V     385          1.860
LGA    Y     437      W     386          0.914
LGA    L     438      S     387          3.392
LGA    D     439      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    F     440      F     392           #
LGA    A     441      M     393          4.073
LGA    S     442      Y     394          1.635
LGA    P     443      -       -           -
LGA    V     444      -       -           -
LGA    S     445      T     395          2.539
LGA    G     446      K     396          2.057
LGA    L     447      F     397          1.558
LGA    G     448      V     398          2.943
LGA    S     449      -       -           -
LGA    K     450      -       -           -
LGA    M     451      I     399          2.282
LGA    G     452      V     400          4.484
LGA    L     453      -       -           -
LGA    D     454      -       -           -
LGA    A     455      -       -           -
LGA    T     456      -       -           -
LGA    N     457      C     401          2.520
LGA    K     458      D     402          4.176
LGA    W     459      D     403          2.915
LGA    P     460      D     404          1.582
LGA    G     461      V     405          1.823
LGA    E     462      N     406          0.655
LGA    -       -      A     407           -
LGA    T     463      R     408          4.616
LGA    Q     464      D     409          1.419
LGA    R     465      W     410          3.992
LGA    E     466      N     411          1.831
LGA    W     467      D     412          3.019
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)   43  120    5.0     28    2.94     0.00     14.086     0.922

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.009761 * X  +   0.641603 * Y  +  -0.766975 * Z  +  51.468403
  Y_new =  -0.284175 * X  +   0.733606 * Y  +   0.617306 * Z  +  66.675316
  Z_new =   0.958723 * X  +   0.223980 * Y  +   0.175167 * Z  +  65.193626 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.907087   -2.234505  [ DEG:    51.9723   -128.0277 ]
  Theta =  -1.282476   -1.859117  [ DEG:   -73.4805   -106.5195 ]
  Phi   =  -1.605130    1.536463  [ DEG:   -91.9672     88.0328 ]
 
# 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: T0356AL242_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL242_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43  120   5.0   28   2.94    0.00  14.086
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL242_1-D3
REMARK Aligment from pdb entry: 2fj6_A
ATOM      1  N   ARG   425      52.352  79.904  63.090  1.00  0.00              
ATOM      2  CA  ARG   425      51.959  78.474  62.924  1.00  0.00              
ATOM      3  C   ARG   425      52.132  78.069  61.463  1.00  0.00              
ATOM      4  O   ARG   425      52.259  78.923  60.584  1.00  0.00              
ATOM      5  N   ASP   426      52.133  76.763  61.210  1.00  0.00              
ATOM      6  CA  ASP   426      52.288  76.255  59.851  1.00  0.00              
ATOM      7  C   ASP   426      51.569  74.916  59.689  1.00  0.00              
ATOM      8  O   ASP   426      52.114  73.868  60.034  1.00  0.00              
ATOM      9  N   THR   427      50.343  74.977  59.158  1.00  0.00              
ATOM     10  CA  THR   427      49.507  73.788  58.923  1.00  0.00              
ATOM     11  C   THR   427      50.098  72.524  59.550  1.00  0.00              
ATOM     12  O   THR   427      51.051  71.946  59.023  1.00  0.00              
ATOM     13  N   VAL   428      49.518  72.095  60.669  1.00  0.00              
ATOM     14  CA  VAL   428      49.990  70.897  61.360  1.00  0.00              
ATOM     15  C   VAL   428      50.180  69.745  60.374  1.00  0.00              
ATOM     16  O   VAL   428      51.077  68.918  60.540  1.00  0.00              
ATOM     17  N   LEU   429      49.337  69.705  59.343  1.00  0.00              
ATOM     18  CA  LEU   429      49.428  68.655  58.333  1.00  0.00              
ATOM     19  C   LEU   429      50.765  68.739  57.600  1.00  0.00              
ATOM     20  O   LEU   429      51.433  67.725  57.392  1.00  0.00              
ATOM     21  N   VAL   430      51.151  69.954  57.213  1.00  0.00              
ATOM     22  CA  VAL   430      52.412  70.159  56.505  1.00  0.00              
ATOM     23  C   VAL   430      53.593  69.891  57.425  1.00  0.00              
ATOM     24  O   VAL   430      54.579  69.278  57.017  1.00  0.00              
ATOM     25  N   GLU   431      53.493  70.337  58.673  1.00  0.00              
ATOM     26  CA  GLU   431      54.572  70.096  59.615  1.00  0.00              
ATOM     27  C   GLU   431      54.803  68.595  59.664  1.00  0.00              
ATOM     28  O   GLU   431      55.928  68.114  59.527  1.00  0.00              
ATOM     29  N   ASN   432      53.701  67.869  59.824  1.00  0.00              
ATOM     30  CA  ASN   432      53.730  66.416  59.850  1.00  0.00              
ATOM     31  C   ASN   432      54.289  65.859  58.539  1.00  0.00              
ATOM     32  O   ASN   432      54.869  64.771  58.525  1.00  0.00              
ATOM     33  N   THR   433      54.099  66.594  57.433  1.00  0.00              
ATOM     34  CA  THR   433      54.587  66.125  56.134  1.00  0.00              
ATOM     35  C   THR   433      56.099  65.912  56.162  1.00  0.00              
ATOM     36  O   THR   433      56.635  65.119  55.388  1.00  0.00              
ATOM     37  N   PRO   434      56.781  66.617  57.060  1.00  0.00              
ATOM     38  CA  PRO   434      58.231  66.486  57.179  1.00  0.00              
ATOM     39  C   PRO   434      58.593  65.149  57.825  1.00  0.00              
ATOM     40  O   PRO   434      59.733  64.692  57.735  1.00  0.00              
ATOM     41  N   ILE   435      57.611  64.534  58.482  1.00  0.00              
ATOM     42  CA  ILE   435      57.816  63.258  59.150  1.00  0.00              
ATOM     43  C   ILE   435      57.026  62.152  58.456  1.00  0.00              
ATOM     44  O   ILE   435      56.384  61.331  59.113  1.00  0.00              
ATOM     45  N   ASP   436      57.078  62.131  57.125  1.00  0.00              
ATOM     46  CA  ASP   436      56.361  61.113  56.356  1.00  0.00              
ATOM     47  C   ASP   436      56.804  59.718  56.750  1.00  0.00              
ATOM     48  O   ASP   436      56.225  58.718  56.324  1.00  0.00              
ATOM     49  N   TYR   437      57.824  59.689  57.578  1.00  0.00              
ATOM     50  CA  TYR   437      58.400  58.447  58.092  1.00  0.00              
ATOM     51  C   TYR   437      58.196  57.288  57.116  1.00  0.00              
ATOM     52  O   TYR   437      57.309  56.456  57.307  1.00  0.00              
ATOM     53  N   LEU   438      58.997  57.215  56.086  1.00  0.00              
ATOM     54  CA  LEU   438      58.894  56.122  55.075  1.00  0.00              
ATOM     55  C   LEU   438      59.227  54.762  55.686  1.00  0.00              
ATOM     56  O   LEU   438      59.145  53.730  55.021  1.00  0.00              
ATOM     57  N   ASP   439      59.587  54.785  56.969  1.00  0.00              
ATOM     58  CA  ASP   439      59.919  53.572  57.706  1.00  0.00              
ATOM     59  C   ASP   439      59.469  53.726  59.160  1.00  0.00              
ATOM     60  O   ASP   439      60.287  53.949  60.053  1.00  0.00              
ATOM     61  N   PHE   440      58.182  53.631  59.396  1.00  0.00              
ATOM     62  CA  PHE   440      57.587  53.778  60.758  1.00  0.00              
ATOM     63  C   PHE   440      58.372  53.032  61.834  1.00  0.00              
ATOM     64  O   PHE   440      58.834  51.911  61.616  1.00  0.00              
ATOM     65  N   ALA   441      58.509  53.667  62.997  1.00  0.00              
ATOM     66  CA  ALA   441      59.231  53.070  64.117  1.00  0.00              
ATOM     67  C   ALA   441      58.666  53.580  65.440  1.00  0.00              
ATOM     68  O   ALA   441      58.183  52.799  66.262  1.00  0.00              
ATOM     69  N   SER   442      58.727  54.895  65.634  1.00  0.00              
ATOM     70  CA  SER   442      58.219  55.509  66.856  1.00  0.00              
ATOM     71  C   SER   442      56.713  55.729  66.757  1.00  0.00              
ATOM     72  O   SER   442      56.145  55.696  65.665  1.00  0.00              
ATOM     73  N   PRO   443      56.075  55.954  67.904  1.00  0.00              
ATOM     74  CA  PRO   443      54.634  56.180  67.941  1.00  0.00              
ATOM     75  C   PRO   443      54.238  57.306  66.989  1.00  0.00              
ATOM     76  O   PRO   443      53.253  57.199  66.261  1.00  0.00              
ATOM     77  N   VAL   444      55.011  58.388  67.006  1.00  0.00              
ATOM     78  CA  VAL   444      54.730  59.530  66.141  1.00  0.00              
ATOM     79  C   VAL   444      54.925  59.162  64.670  1.00  0.00              
ATOM     80  O   VAL   444      54.234  59.684  63.794  1.00  0.00              
ATOM     81  N   SER   445      55.882  58.273  64.408  1.00  0.00              
ATOM     82  CA  SER   445      56.175  57.857  63.040  1.00  0.00              
ATOM     83  C   SER   445      54.992  57.120  62.414  1.00  0.00              
ATOM     84  O   SER   445      54.553  57.468  61.315  1.00  0.00              
ATOM     85  N   GLY   446      54.474  56.114  63.119  1.00  0.00              
ATOM     86  CA  GLY   446      53.335  55.346  62.615  1.00  0.00              
ATOM     87  C   GLY   446      52.134  56.263  62.402  1.00  0.00              
ATOM     88  O   GLY   446      51.392  56.118  61.428  1.00  0.00              
ATOM     89  N   LEU   447      51.960  57.213  63.317  1.00  0.00              
ATOM     90  CA  LEU   447      50.858  58.163  63.229  1.00  0.00              
ATOM     91  C   LEU   447      50.993  59.018  61.971  1.00  0.00              
ATOM     92  O   LEU   447      50.011  59.274  61.273  1.00  0.00              
ATOM     93  N   GLY   448      52.219  59.462  61.695  1.00  0.00              
ATOM     94  CA  GLY   448      52.481  60.297  60.526  1.00  0.00              
ATOM     95  C   GLY   448      51.970  59.636  59.248  1.00  0.00              
ATOM     96  O   GLY   448      51.258  60.263  58.462  1.00  0.00              
ATOM     97  N   SER   449      52.333  58.369  59.043  1.00  0.00              
ATOM     98  CA  SER   449      51.894  57.646  57.848  1.00  0.00              
ATOM     99  C   SER   449      50.370  57.597  57.790  1.00  0.00              
ATOM    100  O   SER   449      49.775  57.761  56.724  1.00  0.00              
ATOM    101  N   LYS   450      49.747  57.373  58.944  1.00  0.00              
ATOM    102  CA  LYS   450      48.292  57.307  59.021  1.00  0.00              
ATOM    103  C   LYS   450      47.677  58.649  58.629  1.00  0.00              
ATOM    104  O   LYS   450      46.772  58.710  57.796  1.00  0.00              
ATOM    105  N   MET   451      48.180  59.719  59.240  1.00  0.00              
ATOM    106  CA  MET   451      47.684  61.065  58.960  1.00  0.00              
ATOM    107  C   MET   451      47.816  61.403  57.476  1.00  0.00              
ATOM    108  O   MET   451      46.982  62.118  56.922  1.00  0.00              
ATOM    109  N   GLY   452      48.866  60.886  56.839  1.00  0.00              
ATOM    110  CA  GLY   452      49.091  61.146  55.418  1.00  0.00              
ATOM    111  C   GLY   452      47.890  60.689  54.592  1.00  0.00              
ATOM    112  O   GLY   452      47.592  61.262  53.542  1.00  0.00              
ATOM    113  N   LEU   453      47.205  59.656  55.076  1.00  0.00              
ATOM    114  CA  LEU   453      46.042  59.125  54.381  1.00  0.00              
ATOM    115  C   LEU   453      44.789  59.908  54.765  1.00  0.00              
ATOM    116  O   LEU   453      43.723  59.716  54.180  1.00  0.00              
ATOM    117  N   ASP   454      44.930  60.798  55.745  1.00  0.00              
ATOM    118  CA  ASP   454      43.810  61.614  56.194  1.00  0.00              
ATOM    119  C   ASP   454      43.623  62.807  55.258  1.00  0.00              
ATOM    120  O   ASP   454      43.903  63.950  55.622  1.00  0.00              
ATOM    121  N   ALA   455      43.150  62.528  54.046  1.00  0.00              
ATOM    122  CA  ALA   455      42.928  63.577  53.056  1.00  0.00              
ATOM    123  C   ALA   455      41.852  64.553  53.530  1.00  0.00              
ATOM    124  O   ALA   455      41.685  65.631  52.957  1.00  0.00              
ATOM    125  N   THR   456      41.125  64.167  54.578  1.00  0.00              
ATOM    126  CA  THR   456      40.065  65.013  55.120  1.00  0.00              
ATOM    127  C   THR   456      40.570  65.824  56.313  1.00  0.00              
ATOM    128  O   THR   456      39.833  66.640  56.869  1.00  0.00              
ATOM    129  N   ASN   457      41.827  65.600  56.698  1.00  0.00              
ATOM    130  CA  ASN   457      42.416  66.321  57.826  1.00  0.00              
ATOM    131  C   ASN   457      42.171  67.825  57.683  1.00  0.00              
ATOM    132  O   ASN   457      42.292  68.374  56.588  1.00  0.00              
ATOM    133  N   LYS   458      41.831  68.497  58.759  1.00  0.00              
ATOM    134  CA  LYS   458      41.570  69.971  58.740  1.00  0.00              
ATOM    135  C   LYS   458      42.850  70.780  58.504  1.00  0.00              
ATOM    136  O   LYS   458      43.327  71.485  59.394  1.00  0.00              
ATOM    137  N   TRP   459      43.399  70.666  57.296  1.00  0.00              
ATOM    138  CA  TRP   459      44.624  71.382  56.938  1.00  0.00              
ATOM    139  C   TRP   459      44.445  72.889  57.111  1.00  0.00              
ATOM    140  O   TRP   459      45.382  73.594  57.487  1.00  0.00              
ATOM    141  N   PRO   460      43.237  73.374  56.828  1.00  0.00              
ATOM    142  CA  PRO   460      42.943  74.800  56.944  1.00  0.00              
ATOM    143  C   PRO   460      42.287  75.113  58.291  1.00  0.00              
ATOM    144  O   PRO   460      41.352  75.912  58.367  1.00  0.00              
ATOM    145  N   GLY   461      42.792  74.484  59.354  1.00  0.00              
ATOM    146  CA  GLY   461      42.257  74.701  60.694  1.00  0.00              
ATOM    147  C   GLY   461      43.016  73.845  61.697  1.00  0.00              
ATOM    148  O   GLY   461      42.849  72.626  61.739  1.00  0.00              
ATOM    149  N   GLU   462      43.850  74.490  62.508  1.00  0.00              
ATOM    150  CA  GLU   462      44.624  73.772  63.506  1.00  0.00              
ATOM    151  C   GLU   462      44.311  74.309  64.894  1.00  0.00              
ATOM    152  O   GLU   462      44.722  75.412  65.259  1.00  0.00              
ATOM    153  N   THR   463      43.589  73.508  65.659  1.00  0.00              
ATOM    154  CA  THR   463      43.217  73.874  67.014  1.00  0.00              
ATOM    155  C   THR   463      43.223  72.626  67.890  1.00  0.00              
ATOM    156  O   THR   463      42.611  71.616  67.544  1.00  0.00              
ATOM    157  N   GLN   464      43.935  72.697  69.007  1.00  0.00              
ATOM    158  CA  GLN   464      44.041  71.561  69.916  1.00  0.00              
ATOM    159  C   GLN   464      42.675  70.942  70.222  1.00  0.00              
ATOM    160  O   GLN   464      42.493  69.737  70.073  1.00  0.00              
ATOM    161  N   ARG   465      41.734  71.765  70.671  1.00  0.00              
ATOM    162  CA  ARG   465      40.397  71.275  71.024  1.00  0.00              
ATOM    163  C   ARG   465      39.655  70.693  69.819  1.00  0.00              
ATOM    164  O   ARG   465      39.129  69.582  69.885  1.00  0.00              
ATOM    165  N   GLU   466      39.596  71.457  68.733  1.00  0.00              
ATOM    166  CA  GLU   466      38.889  71.019  67.530  1.00  0.00              
ATOM    167  C   GLU   466      39.475  69.723  66.974  1.00  0.00              
ATOM    168  O   GLU   466      38.746  68.760  66.727  1.00  0.00              
ATOM    169  N   TRP   467      40.788  69.706  66.773  1.00  0.00              
ATOM    170  CA  TRP   467      41.451  68.524  66.236  1.00  0.00              
ATOM    171  C   TRP   467      41.412  67.373  67.244  1.00  0.00              
ATOM    172  O   TRP   467      41.276  66.213  66.857  1.00  0.00              
END
