
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0347AL333_5-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_5-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      -       -           -
LGA    P     135      D     134          1.125
LGA    F     136      P     135          1.863
LGA    R     137      F     136          2.300
LGA    S     138      R     137          1.284
LGA    L     139      S     138          1.406
LGA    A     140      L     139          2.371
LGA    G     141      A     140          1.725
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    A     142      L     143          2.161
LGA    L     143      R     144          0.900
LGA    R     144      M     145          2.658
LGA    M     145      A     146          3.243
LGA    A     146      G     147          1.771
LGA    G     147      G     148          4.240
LGA    G     148      Y     149          2.384
LGA    I     153      A     150           #
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    I     154      W     161          4.090
LGA    P     155      A     162           #
LGA    -       -      D     163           -
LGA    A     162      F     164          1.089
LGA    D     163      L     165          2.445
LGA    F     164      R     166          4.907
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    D     172      A     181          4.084
LGA    L     173      L     182          2.748
LGA    L     174      A     183          3.060
LGA    S     175      E     184          1.678
LGA    D     176      A     185          3.632
LGA    S     177      M     186          3.326
LGA    -       -      K     187           -
LGA    -       -      L     188           -
LGA    F     178      A     189          2.240
LGA    D     179      K     190          4.619
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    D     180      G     199          4.310
LGA    A     181      W     200          5.206
LGA    L     182      C     201           #
LGA    A     183      -       -           -
LGA    E     184      -       -           -
LGA    A     185      G     202          2.637
LGA    M     186      V     203          3.548
LGA    K     187      E     204           -
LGA    W     200      -       -           -
LGA    C     201      -       -           -
LGA    G     202      -       -           -
LGA    V     203      -       -           -
LGA    E     204      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   71    5.0     30    3.01     6.67     27.753     0.964

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.724584 * X  +   0.215916 * Y  +  -0.654491 * Z  +  39.304173
  Y_new =   0.670506 * X  +  -0.440460 * Y  +   0.597007 * Z  + -25.717930
  Z_new =  -0.159373 * X  +  -0.871421 * Y  +  -0.463923 * Z  +  34.188427 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.060007    1.081585  [ DEG:  -118.0297     61.9703 ]
  Theta =   0.160056    2.981537  [ DEG:     9.1705    170.8295 ]
  Phi   =   0.746654   -2.394938  [ DEG:    42.7801   -137.2199 ]
 
# 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: T0347AL333_5-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_5-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   71   5.0   30   3.01    6.67  27.753
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_5-D2
REMARK Aligment from pdb entry: 1qmv_A
ATOM    401  N   ASP   134       4.449  58.894   0.136  1.00  0.00              
ATOM    402  CA  ASP   134       5.402  57.970   0.808  1.00  0.00              
ATOM    403  C   ASP   134       5.886  56.912  -0.150  1.00  0.00              
ATOM    404  O   ASP   134       7.067  56.538  -0.176  1.00  0.00              
ATOM    405  N   PRO   135       5.030  56.369  -1.031  1.00  0.00              
ATOM    406  CA  PRO   135       5.486  55.388  -1.990  1.00  0.00              
ATOM    407  C   PRO   135       6.547  56.013  -2.907  1.00  0.00              
ATOM    408  O   PRO   135       7.523  55.351  -3.248  1.00  0.00              
ATOM    409  N   PHE   136       6.311  57.235  -3.379  1.00  0.00              
ATOM    410  CA  PHE   136       7.302  57.918  -4.209  1.00  0.00              
ATOM    411  C   PHE   136       8.597  58.159  -3.413  1.00  0.00              
ATOM    412  O   PHE   136       9.649  57.906  -3.983  1.00  0.00              
ATOM    413  N   ARG   137       8.523  58.609  -2.174  1.00  0.00              
ATOM    414  CA  ARG   137       9.738  58.830  -1.365  1.00  0.00              
ATOM    415  C   ARG   137      10.556  57.569  -1.255  1.00  0.00              
ATOM    416  O   ARG   137      11.780  57.538  -1.402  1.00  0.00              
ATOM    417  N   SER   138       9.885  56.432  -1.005  1.00  0.00              
ATOM    418  CA  SER   138      10.532  55.143  -0.870  1.00  0.00              
ATOM    419  C   SER   138      11.107  54.659  -2.186  1.00  0.00              
ATOM    420  O   SER   138      12.214  54.098  -2.204  1.00  0.00              
ATOM    421  N   LEU   139      10.405  54.857  -3.308  1.00  0.00              
ATOM    422  CA  LEU   139      11.012  54.489  -4.591  1.00  0.00              
ATOM    423  C   LEU   139      12.287  55.327  -4.846  1.00  0.00              
ATOM    424  O   LEU   139      13.293  54.786  -5.280  1.00  0.00              
ATOM    425  N   ALA   140      12.202  56.621  -4.579  1.00  0.00              
ATOM    426  CA  ALA   140      13.370  57.501  -4.819  1.00  0.00              
ATOM    427  C   ALA   140      14.559  57.061  -3.956  1.00  0.00              
ATOM    428  O   ALA   140      15.717  57.020  -4.401  1.00  0.00              
ATOM    429  N   GLY   141      14.229  56.789  -2.696  1.00  0.00              
ATOM    430  CA  GLY   141      15.251  56.317  -1.744  1.00  0.00              
ATOM    431  C   GLY   141      15.902  55.022  -2.174  1.00  0.00              
ATOM    432  O   GLY   141      17.137  54.915  -2.134  1.00  0.00              
ATOM    433  N   ALA   142      18.187  55.686  -5.060  1.00  0.00              
ATOM    434  CA  ALA   142      19.396  56.418  -4.660  1.00  0.00              
ATOM    435  C   ALA   142      20.409  55.472  -4.018  1.00  0.00              
ATOM    436  O   ALA   142      21.589  55.404  -4.427  1.00  0.00              
ATOM    437  N   LEU   143      19.955  54.648  -3.055  1.00  0.00              
ATOM    438  CA  LEU   143      20.862  53.722  -2.382  1.00  0.00              
ATOM    439  C   LEU   143      21.409  52.686  -3.355  1.00  0.00              
ATOM    440  O   LEU   143      22.567  52.262  -3.199  1.00  0.00              
ATOM    441  N   ARG   144      20.658  52.310  -4.394  1.00  0.00              
ATOM    442  CA  ARG   144      21.177  51.319  -5.329  1.00  0.00              
ATOM    443  C   ARG   144      22.338  51.987  -6.130  1.00  0.00              
ATOM    444  O   ARG   144      23.302  51.320  -6.467  1.00  0.00              
ATOM    445  N   MET   145      22.121  53.244  -6.467  1.00  0.00              
ATOM    446  CA  MET   145      23.037  53.980  -7.331  1.00  0.00              
ATOM    447  C   MET   145      24.279  54.487  -6.628  1.00  0.00              
ATOM    448  O   MET   145      25.392  54.230  -7.112  1.00  0.00              
ATOM    449  N   ALA   146      24.127  55.156  -5.495  1.00  0.00              
ATOM    450  CA  ALA   146      25.242  55.727  -4.764  1.00  0.00              
ATOM    451  C   ALA   146      25.908  54.883  -3.705  1.00  0.00              
ATOM    452  O   ALA   146      26.934  55.293  -3.139  1.00  0.00              
ATOM    453  N   GLY   147      25.322  53.770  -3.294  1.00  0.00              
ATOM    454  CA  GLY   147      25.872  52.897  -2.279  1.00  0.00              
ATOM    455  C   GLY   147      26.046  53.593  -0.938  1.00  0.00              
ATOM    456  O   GLY   147      26.989  53.353  -0.184  1.00  0.00              
ATOM    457  N   GLY   148      25.176  54.522  -0.637  1.00  0.00              
ATOM    458  CA  GLY   148      25.072  55.267   0.596  1.00  0.00              
ATOM    459  C   GLY   148      23.717  54.837   1.184  1.00  0.00              
ATOM    460  O   GLY   148      23.031  54.080   0.473  1.00  0.00              
ATOM    461  N   ILE   153      23.420  55.195   2.427  1.00  0.00              
ATOM    462  CA  ILE   153      22.122  54.692   2.949  1.00  0.00              
ATOM    463  C   ILE   153      21.308  55.907   3.336  1.00  0.00              
ATOM    464  O   ILE   153      21.840  56.969   3.653  1.00  0.00              
ATOM    465  N   ILE   154      19.978  55.738   3.300  1.00  0.00              
ATOM    466  CA  ILE   154      19.133  56.902   3.614  1.00  0.00              
ATOM    467  C   ILE   154      18.619  56.942   5.028  1.00  0.00              
ATOM    468  O   ILE   154      17.857  56.077   5.490  1.00  0.00              
ATOM    469  N   PRO   155      18.877  58.020   5.749  1.00  0.00              
ATOM    470  CA  PRO   155      18.365  58.236   7.069  1.00  0.00              
ATOM    471  C   PRO   155      16.838  58.329   7.125  1.00  0.00              
ATOM    472  O   PRO   155      16.140  58.512   6.106  1.00  0.00              
ATOM    473  N   ALA   162      16.341  58.301   8.367  1.00  0.00              
ATOM    474  CA  ALA   162      14.923  58.470   8.587  1.00  0.00              
ATOM    475  C   ALA   162      14.443  59.760   7.916  1.00  0.00              
ATOM    476  O   ALA   162      15.053  60.830   8.104  1.00  0.00              
ATOM    477  N   ASP   163      13.319  59.689   7.222  1.00  0.00              
ATOM    478  CA  ASP   163      12.688  60.863   6.624  1.00  0.00              
ATOM    479  C   ASP   163      13.365  61.363   5.356  1.00  0.00              
ATOM    480  O   ASP   163      12.920  62.378   4.789  1.00  0.00              
ATOM    481  N   PHE   164      14.365  60.685   4.837  1.00  0.00              
ATOM    482  CA  PHE   164      15.087  61.156   3.658  1.00  0.00              
ATOM    483  C   PHE   164      14.143  61.488   2.494  1.00  0.00              
ATOM    484  O   PHE   164      13.207  60.760   2.204  1.00  0.00              
ATOM    485  N   ASP   172      14.457  62.543   1.758  1.00  0.00              
ATOM    486  CA  ASP   172      13.794  62.998   0.558  1.00  0.00              
ATOM    487  C   ASP   172      14.906  63.481  -0.376  1.00  0.00              
ATOM    488  O   ASP   172      15.982  63.804   0.138  1.00  0.00              
ATOM    489  N   LEU   173      14.700  63.479  -1.668  1.00  0.00              
ATOM    490  CA  LEU   173      15.714  63.948  -2.618  1.00  0.00              
ATOM    491  C   LEU   173      16.260  65.266  -2.092  1.00  0.00              
ATOM    492  O   LEU   173      15.498  66.113  -1.621  1.00  0.00              
ATOM    493  N   LEU   174      17.591  65.384  -2.053  1.00  0.00              
ATOM    494  CA  LEU   174      18.232  66.577  -1.521  1.00  0.00              
ATOM    495  C   LEU   174      18.695  66.421  -0.081  1.00  0.00              
ATOM    496  O   LEU   174      19.459  67.255   0.433  1.00  0.00              
ATOM    497  N   SER   175      18.276  65.332   0.587  1.00  0.00              
ATOM    498  CA  SER   175      18.663  65.174   1.983  1.00  0.00              
ATOM    499  C   SER   175      20.051  64.549   2.081  1.00  0.00              
ATOM    500  O   SER   175      20.482  63.869   1.150  1.00  0.00              
ATOM    501  N   ASP   176      20.694  64.744   3.232  1.00  0.00              
ATOM    502  CA  ASP   176      22.000  64.097   3.415  1.00  0.00              
ATOM    503  C   ASP   176      21.871  62.580   3.510  1.00  0.00              
ATOM    504  O   ASP   176      20.836  62.082   3.976  1.00  0.00              
ATOM    505  N   SER   177      22.877  61.840   3.066  1.00  0.00              
ATOM    506  CA  SER   177      22.899  60.382   3.192  1.00  0.00              
ATOM    507  C   SER   177      24.131  60.024   4.034  1.00  0.00              
ATOM    508  O   SER   177      24.848  60.932   4.494  1.00  0.00              
ATOM    509  N   PHE   178      24.273  58.763   4.375  1.00  0.00              
ATOM    510  CA  PHE   178      25.372  58.297   5.234  1.00  0.00              
ATOM    511  C   PHE   178      26.181  57.243   4.518  1.00  0.00              
ATOM    512  O   PHE   178      25.599  56.359   3.874  1.00  0.00              
ATOM    513  N   ASP   179      27.514  57.318   4.604  1.00  0.00              
ATOM    514  CA  ASP   179      28.332  56.281   3.950  1.00  0.00              
ATOM    515  C   ASP   179      28.435  55.189   5.025  1.00  0.00              
ATOM    516  O   ASP   179      28.812  55.515   6.155  1.00  0.00              
ATOM    517  N   ASP   180      27.986  53.994   4.695  1.00  0.00              
ATOM    518  CA  ASP   180      27.824  52.901   5.631  1.00  0.00              
ATOM    519  C   ASP   180      29.065  52.133   6.042  1.00  0.00              
ATOM    520  O   ASP   180      29.179  50.930   5.824  1.00  0.00              
ATOM    521  N   ALA   181      29.982  52.861   6.674  1.00  0.00              
ATOM    522  CA  ALA   181      31.184  52.258   7.259  1.00  0.00              
ATOM    523  C   ALA   181      31.534  53.133   8.458  1.00  0.00              
ATOM    524  O   ALA   181      31.106  54.288   8.565  1.00  0.00              
ATOM    525  N   LEU   182      32.178  52.564   9.480  1.00  0.00              
ATOM    526  CA  LEU   182      32.342  53.274  10.750  1.00  0.00              
ATOM    527  C   LEU   182      33.040  54.624  10.608  1.00  0.00              
ATOM    528  O   LEU   182      32.573  55.647  11.152  1.00  0.00              
ATOM    529  N   ALA   183      34.148  54.652   9.889  1.00  0.00              
ATOM    530  CA  ALA   183      34.914  55.897   9.783  1.00  0.00              
ATOM    531  C   ALA   183      34.208  56.950   8.927  1.00  0.00              
ATOM    532  O   ALA   183      34.106  58.103   9.343  1.00  0.00              
ATOM    533  N   GLU   184      33.714  56.596   7.757  1.00  0.00              
ATOM    534  CA  GLU   184      33.064  57.563   6.860  1.00  0.00              
ATOM    535  C   GLU   184      31.726  58.054   7.376  1.00  0.00              
ATOM    536  O   GLU   184      31.290  59.173   7.063  1.00  0.00              
ATOM    537  N   ALA   185      31.071  57.317   8.274  1.00  0.00              
ATOM    538  CA  ALA   185      29.789  57.781   8.810  1.00  0.00              
ATOM    539  C   ALA   185      29.919  58.962   9.754  1.00  0.00              
ATOM    540  O   ALA   185      28.966  59.699  10.010  1.00  0.00              
ATOM    541  N   MET   186      31.103  59.203  10.317  1.00  0.00              
ATOM    542  CA  MET   186      31.362  60.299  11.232  1.00  0.00              
ATOM    543  C   MET   186      31.078  61.673  10.623  1.00  0.00              
ATOM    544  O   MET   186      30.621  62.622  11.272  1.00  0.00              
ATOM    545  N   LYS   187      31.265  61.780   9.322  1.00  0.00              
ATOM    546  CA  LYS   187      30.915  62.993   8.548  1.00  0.00              
ATOM    547  C   LYS   187      29.456  63.344   8.728  1.00  0.00              
ATOM    548  O   LYS   187      29.151  64.510   9.044  1.00  0.00              
ATOM    549  N   TRP   200      28.528  62.378   8.592  1.00  0.00              
ATOM    550  CA  TRP   200      27.121  62.655   8.837  1.00  0.00              
ATOM    551  C   TRP   200      26.931  62.991  10.304  1.00  0.00              
ATOM    552  O   TRP   200      26.318  64.008  10.644  1.00  0.00              
ATOM    553  N   CYS   201      27.363  62.150  11.256  1.00  0.00              
ATOM    554  CA  CYS   201      27.061  62.383  12.660  1.00  0.00              
ATOM    555  C   CYS   201      27.603  63.693  13.224  1.00  0.00              
ATOM    556  O   CYS   201      26.925  64.307  14.059  1.00  0.00              
ATOM    557  N   GLY   202      28.777  64.128  12.792  1.00  0.00              
ATOM    558  CA  GLY   202      29.316  65.405  13.284  1.00  0.00              
ATOM    559  C   GLY   202      28.579  66.564  12.632  1.00  0.00              
ATOM    560  O   GLY   202      28.216  67.516  13.324  1.00  0.00              
ATOM    561  N   VAL   203      28.189  66.436  11.367  1.00  0.00              
ATOM    562  CA  VAL   203      27.411  67.467  10.696  1.00  0.00              
ATOM    563  C   VAL   203      26.024  67.636  11.301  1.00  0.00              
ATOM    564  O   VAL   203      25.548  68.762  11.483  1.00  0.00              
ATOM    565  N   GLU   204      25.340  66.520  11.592  1.00  0.00              
ATOM    566  CA  GLU   204      23.967  66.639  12.079  1.00  0.00              
ATOM    567  C   GLU   204      23.792  66.757  13.564  1.00  0.00              
ATOM    568  O   GLU   204      22.652  66.786  14.052  1.00  0.00              
END
