
#######################################################
#                                                     #
#                        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   51 (  204),  selected   51 , name T0295AL380_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL380_5-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     181      T     181          4.844
LGA    N     182      N     182          0.646
LGA    F     183      F     183          0.948
LGA    D     184      D     184          0.675
LGA    E     185      E     185          1.117
LGA    W     186      W     186          1.027
LGA    D     187      D     187          1.093
LGA    N     188      N     188          1.062
LGA    L     189      L     189          1.177
LGA    L     190      L     190          0.932
LGA    R     191      R     191          0.300
LGA    I     192      I     192          1.397
LGA    C     193      C     193          1.856
LGA    F     194      F     194          1.563
LGA    S     195      S     195          1.597
LGA    -       -      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    -       -      T     200           -
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    R     196      A     203           #
LGA    K     197      I     204          5.475
LGA    R     198      F     205          2.827
LGA    K     199      K     206           #
LGA    -       -      R     207           -
LGA    -       -      N     208           -
LGA    -       -      A     209           -
LGA    T     200      V     210          2.667
LGA    -       -      L     211           -
LGA    -       -      N     212           -
LGA    -       -      M     213           -
LGA    L     201      L     214          3.679
LGA    -       -      E     215           -
LGA    -       -      H     216           -
LGA    H     202      N     217           #
LGA    -       -      Y     218           -
LGA    -       -      K     219           -
LGA    -       -      N     220           -
LGA    -       -      W     221           -
LGA    -       -      C     222           -
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      N     225           -
LGA    -       -      K     226           -
LGA    -       -      Q     227           -
LGA    -       -      V     228           -
LGA    -       -      P     229           -
LGA    -       -      V     230           -
LGA    -       -      N     231           -
LGA    -       -      F     232           -
LGA    -       -      P     233           -
LGA    A     203      F     234          3.917
LGA    I     204      K     235          1.759
LGA    F     205      K     236          1.484
LGA    K     206      Y     237          3.089
LGA    R     207      C     238          3.319
LGA    N     208      L     239          2.281
LGA    A     209      D     240          1.152
LGA    V     210      V     241          0.969
LGA    L     211      L     242          0.988
LGA    N     212      E     243          1.624
LGA    M     213      H     244          1.666
LGA    L     214      L     245          1.351
LGA    C     248      D     246          1.853
LGA    E     249      M     247          1.503
LGA    K     250      C     248          4.398
LGA    R     251      E     249          1.526
LGA    S     252      K     250          2.871
LGA    I     253      R     251          2.700
LGA    N     254      S     252           #
LGA    -       -      I     253           -
LGA    L     255      N     254          4.993
LGA    D     256      L     255          2.965
LGA    E     257      D     256          2.390
LGA    -       -      E     257           -
LGA    N     258      N     258          2.825
LGA    D     259      D     259          2.742
LGA    F     260      F     260          2.446
LGA    L     261      L     261          2.073
LGA    K     262      K     262          1.725
LGA    L     263      L     263          1.405
LGA    L     264      L     264          1.256
LGA    -       -      L     265           -
LGA    -       -      E     266           -
LGA    -       -      F     267           -
LGA    -       -      N     268           -
LGA    -       -      K     269           -
LGA    -       -      K     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   51   95    5.0     47    2.41    55.32     34.911     1.873

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.674965 * X  +  -0.725434 * Y  +   0.134788 * Z  +  27.196598
  Y_new =   0.726131 * X  +  -0.620639 * Y  +   0.295873 * Z  +  -2.267062
  Z_new =  -0.130982 * X  +   0.297578 * Y  +   0.945670 * Z  + -25.345081 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.304865   -2.836728  [ DEG:    17.4675   -162.5325 ]
  Theta =   0.131359    3.010233  [ DEG:     7.5263    172.4737 ]
  Phi   =   2.319692   -0.821901  [ DEG:   132.9086    -47.0914 ]
 
# 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: T0295AL380_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL380_5-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   95   5.0   47   2.41   55.32  34.911
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL380_5-D2
REMARK Aligment from pdb entry: 1qamA
ATOM    689  N   THR   181      20.042  12.705  13.155  1.00  0.00              
ATOM    690  CA  THR   181      18.843  13.373  13.635  1.00  0.00              
ATOM    691  C   THR   181      19.078  14.874  13.517  1.00  0.00              
ATOM    692  O   THR   181      18.141  15.664  13.443  1.00  0.00              
ATOM    693  N   ASN   182      20.540  16.449  10.930  1.00  0.00              
ATOM    694  CA  ASN   182      20.219  16.925   9.587  1.00  0.00              
ATOM    695  C   ASN   182      18.781  16.643   9.143  1.00  0.00              
ATOM    696  O   ASN   182      18.472  16.705   7.956  1.00  0.00              
ATOM    697  N   PHE   183      17.907  16.349  10.097  1.00  0.00              
ATOM    698  CA  PHE   183      16.510  16.044   9.794  1.00  0.00              
ATOM    699  C   PHE   183      15.782  17.084   8.944  1.00  0.00              
ATOM    700  O   PHE   183      15.288  16.771   7.857  1.00  0.00              
ATOM    701  N   ASP   184      15.709  18.316   9.443  1.00  0.00              
ATOM    702  CA  ASP   184      15.006  19.382   8.736  1.00  0.00              
ATOM    703  C   ASP   184      15.702  19.751   7.438  1.00  0.00              
ATOM    704  O   ASP   184      15.056  19.974   6.418  1.00  0.00              
ATOM    705  N   GLU   185      17.027  19.800   7.481  1.00  0.00              
ATOM    706  CA  GLU   185      17.820  20.149   6.315  1.00  0.00              
ATOM    707  C   GLU   185      17.667  19.082   5.229  1.00  0.00              
ATOM    708  O   GLU   185      17.632  19.396   4.040  1.00  0.00              
ATOM    709  N   TRP   186      17.561  17.822   5.637  1.00  0.00              
ATOM    710  CA  TRP   186      17.399  16.728   4.681  1.00  0.00              
ATOM    711  C   TRP   186      16.002  16.767   4.052  1.00  0.00              
ATOM    712  O   TRP   186      15.834  16.536   2.853  1.00  0.00              
ATOM    713  N   ASP   187      15.001  17.047   4.879  1.00  0.00              
ATOM    714  CA  ASP   187      13.626  17.107   4.411  1.00  0.00              
ATOM    715  C   ASP   187      13.459  18.202   3.361  1.00  0.00              
ATOM    716  O   ASP   187      12.765  18.012   2.358  1.00  0.00              
ATOM    717  N   ASN   188      14.103  19.344   3.589  1.00  0.00              
ATOM    718  CA  ASN   188      14.035  20.467   2.656  1.00  0.00              
ATOM    719  C   ASN   188      14.740  20.102   1.349  1.00  0.00              
ATOM    720  O   ASN   188      14.189  20.285   0.259  1.00  0.00              
ATOM    721  N   LEU   189      15.959  19.576   1.469  1.00  0.00              
ATOM    722  CA  LEU   189      16.753  19.197   0.305  1.00  0.00              
ATOM    723  C   LEU   189      16.018  18.187  -0.582  1.00  0.00              
ATOM    724  O   LEU   189      15.972  18.343  -1.803  1.00  0.00              
ATOM    725  N   LEU   190      15.457  17.151   0.038  1.00  0.00              
ATOM    726  CA  LEU   190      14.724  16.127  -0.701  1.00  0.00              
ATOM    727  C   LEU   190      13.603  16.726  -1.551  1.00  0.00              
ATOM    728  O   LEU   190      13.510  16.465  -2.753  1.00  0.00              
ATOM    729  N   ARG   191      12.753  17.520  -0.907  1.00  0.00              
ATOM    730  CA  ARG   191      11.619  18.146  -1.580  1.00  0.00              
ATOM    731  C   ARG   191      12.047  19.051  -2.723  1.00  0.00              
ATOM    732  O   ARG   191      11.519  18.944  -3.833  1.00  0.00              
ATOM    733  N   ILE   192      13.001  19.939  -2.467  1.00  0.00              
ATOM    734  CA  ILE   192      13.470  20.812  -3.532  1.00  0.00              
ATOM    735  C   ILE   192      14.141  20.031  -4.651  1.00  0.00              
ATOM    736  O   ILE   192      14.029  20.400  -5.816  1.00  0.00              
ATOM    737  N   CYS   193      14.806  18.932  -4.321  1.00  0.00              
ATOM    738  CA  CYS   193      15.453  18.141  -5.360  1.00  0.00              
ATOM    739  C   CYS   193      14.458  17.385  -6.237  1.00  0.00              
ATOM    740  O   CYS   193      14.589  17.376  -7.459  1.00  0.00              
ATOM    741  N   PHE   194      13.463  16.756  -5.626  1.00  0.00              
ATOM    742  CA  PHE   194      12.491  16.006  -6.413  1.00  0.00              
ATOM    743  C   PHE   194      11.638  16.943  -7.267  1.00  0.00              
ATOM    744  O   PHE   194      11.169  16.555  -8.331  1.00  0.00              
ATOM    745  N   SER   195      11.455  18.175  -6.802  1.00  0.00              
ATOM    746  CA  SER   195      10.676  19.171  -7.538  1.00  0.00              
ATOM    747  C   SER   195      11.533  19.901  -8.555  1.00  0.00              
ATOM    748  O   SER   195      11.049  20.791  -9.252  1.00  0.00              
ATOM    749  N   ARG   196      12.806  19.526  -8.630  1.00  0.00              
ATOM    750  CA  ARG   196      13.751  20.142  -9.555  1.00  0.00              
ATOM    751  C   ARG   196      13.913  21.652  -9.350  1.00  0.00              
ATOM    752  O   ARG   196      14.213  22.392 -10.291  1.00  0.00              
ATOM    753  N   LYS   197      13.720  22.103  -8.117  1.00  0.00              
ATOM    754  CA  LYS   197      13.890  23.513  -7.797  1.00  0.00              
ATOM    755  C   LYS   197      15.357  23.691  -7.419  1.00  0.00              
ATOM    756  O   LYS   197      15.685  24.209  -6.351  1.00  0.00              
ATOM    757  N   ARG   198      16.235  23.256  -8.315  1.00  0.00              
ATOM    758  CA  ARG   198      17.668  23.306  -8.082  1.00  0.00              
ATOM    759  C   ARG   198      18.200  24.641  -7.582  1.00  0.00              
ATOM    760  O   ARG   198      19.016  24.680  -6.659  1.00  0.00              
ATOM    761  N   LYS   199      17.736  25.733  -8.178  1.00  0.00              
ATOM    762  CA  LYS   199      18.193  27.067  -7.804  1.00  0.00              
ATOM    763  C   LYS   199      18.049  27.395  -6.316  1.00  0.00              
ATOM    764  O   LYS   199      18.775  28.234  -5.788  1.00  0.00              
ATOM    765  N   THR   200      17.125  26.731  -5.636  1.00  0.00              
ATOM    766  CA  THR   200      16.927  26.993  -4.220  1.00  0.00              
ATOM    767  C   THR   200      17.902  26.223  -3.336  1.00  0.00              
ATOM    768  O   THR   200      17.968  26.466  -2.130  1.00  0.00              
ATOM    769  N   LEU   201      18.665  25.306  -3.928  1.00  0.00              
ATOM    770  CA  LEU   201      19.621  24.511  -3.156  1.00  0.00              
ATOM    771  C   LEU   201      21.059  24.558  -3.666  1.00  0.00              
ATOM    772  O   LEU   201      21.994  24.296  -2.915  1.00  0.00              
ATOM    773  N   HIS   202      21.244  24.893  -4.936  1.00  0.00              
ATOM    774  CA  HIS   202      22.585  24.963  -5.508  1.00  0.00              
ATOM    775  C   HIS   202      22.753  26.134  -6.465  1.00  0.00              
ATOM    776  O   HIS   202      21.841  26.462  -7.225  1.00  0.00              
ATOM    777  N   ALA   203      23.923  26.763  -6.422  1.00  0.00              
ATOM    778  CA  ALA   203      24.215  27.830  -7.365  1.00  0.00              
ATOM    779  C   ALA   203      24.583  26.990  -8.584  1.00  0.00              
ATOM    780  O   ALA   203      24.765  25.778  -8.450  1.00  0.00              
ATOM    781  N   ILE   204      24.692  27.592  -9.762  1.00  0.00              
ATOM    782  CA  ILE   204      25.010  26.797 -10.939  1.00  0.00              
ATOM    783  C   ILE   204      26.329  26.073 -10.801  1.00  0.00              
ATOM    784  O   ILE   204      26.485  24.941 -11.251  1.00  0.00              
ATOM    785  N   PHE   205      27.288  26.729 -10.172  1.00  0.00              
ATOM    786  CA  PHE   205      28.598  26.124 -10.002  1.00  0.00              
ATOM    787  C   PHE   205      28.617  24.978  -9.022  1.00  0.00              
ATOM    788  O   PHE   205      29.249  23.952  -9.272  1.00  0.00              
ATOM    789  N   LYS   206      27.925  25.153  -7.908  1.00  0.00              
ATOM    790  CA  LYS   206      27.844  24.111  -6.909  1.00  0.00              
ATOM    791  C   LYS   206      27.112  22.928  -7.532  1.00  0.00              
ATOM    792  O   LYS   206      27.502  21.775  -7.345  1.00  0.00              
ATOM    793  N   ARG   207      26.063  23.219  -8.297  1.00  0.00              
ATOM    794  CA  ARG   207      25.267  22.174  -8.940  1.00  0.00              
ATOM    795  C   ARG   207      26.137  21.255  -9.798  1.00  0.00              
ATOM    796  O   ARG   207      26.146  20.043  -9.610  1.00  0.00              
ATOM    797  N   ASN   208      26.860  21.843 -10.746  1.00  0.00              
ATOM    798  CA  ASN   208      27.740  21.094 -11.635  1.00  0.00              
ATOM    799  C   ASN   208      28.833  20.339 -10.881  1.00  0.00              
ATOM    800  O   ASN   208      29.061  19.152 -11.127  1.00  0.00              
ATOM    801  N   ALA   209      29.515  21.029  -9.973  1.00  0.00              
ATOM    802  CA  ALA   209      30.569  20.404  -9.183  1.00  0.00              
ATOM    803  C   ALA   209      30.019  19.230  -8.384  1.00  0.00              
ATOM    804  O   ALA   209      30.643  18.171  -8.315  1.00  0.00              
ATOM    805  N   VAL   210      28.848  19.427  -7.786  1.00  0.00              
ATOM    806  CA  VAL   210      28.214  18.389  -6.987  1.00  0.00              
ATOM    807  C   VAL   210      27.885  17.167  -7.834  1.00  0.00              
ATOM    808  O   VAL   210      28.116  16.037  -7.406  1.00  0.00              
ATOM    809  N   LEU   211      27.351  17.388  -9.034  1.00  0.00              
ATOM    810  CA  LEU   211      27.009  16.275  -9.912  1.00  0.00              
ATOM    811  C   LEU   211      28.251  15.492 -10.320  1.00  0.00              
ATOM    812  O   LEU   211      28.272  14.264 -10.234  1.00  0.00              
ATOM    813  N   ASN   212      29.286  16.198 -10.765  1.00  0.00              
ATOM    814  CA  ASN   212      30.511  15.520 -11.164  1.00  0.00              
ATOM    815  C   ASN   212      31.117  14.838  -9.947  1.00  0.00              
ATOM    816  O   ASN   212      31.609  13.712 -10.037  1.00  0.00              
ATOM    817  N   MET   213      31.067  15.514  -8.804  1.00  0.00              
ATOM    818  CA  MET   213      31.631  14.937  -7.599  1.00  0.00              
ATOM    819  C   MET   213      30.898  13.669  -7.186  1.00  0.00              
ATOM    820  O   MET   213      31.503  12.757  -6.625  1.00  0.00              
ATOM    821  N   LEU   214      29.600  13.605  -7.469  1.00  0.00              
ATOM    822  CA  LEU   214      28.812  12.431  -7.111  1.00  0.00              
ATOM    823  C   LEU   214      28.874  11.368  -8.207  1.00  0.00              
ATOM    824  O   LEU   214      28.431  10.237  -8.015  1.00  0.00              
ATOM    825  N   CYS   248      29.425  11.739  -9.358  1.00  0.00              
ATOM    826  CA  CYS   248      29.526  10.803 -10.463  1.00  0.00              
ATOM    827  C   CYS   248      28.209  10.634 -11.199  1.00  0.00              
ATOM    828  O   CYS   248      27.966   9.601 -11.823  1.00  0.00              
ATOM    829  N   GLU   249      27.353  11.648 -11.122  1.00  0.00              
ATOM    830  CA  GLU   249      26.058  11.609 -11.789  1.00  0.00              
ATOM    831  C   GLU   249      26.167  12.199 -13.193  1.00  0.00              
ATOM    832  O   GLU   249      26.358  13.402 -13.349  1.00  0.00              
ATOM    833  N   LYS   250      26.048  11.350 -14.209  1.00  0.00              
ATOM    834  CA  LYS   250      26.131  11.809 -15.595  1.00  0.00              
ATOM    835  C   LYS   250      24.748  11.950 -16.216  1.00  0.00              
ATOM    836  O   LYS   250      24.577  12.616 -17.237  1.00  0.00              
ATOM    837  N   ARG   251      23.763  11.316 -15.591  1.00  0.00              
ATOM    838  CA  ARG   251      22.389  11.366 -16.069  1.00  0.00              
ATOM    839  C   ARG   251      21.433  11.665 -14.922  1.00  0.00              
ATOM    840  O   ARG   251      21.121  10.795 -14.109  1.00  0.00              
ATOM    841  N   SER   252      20.982  12.915 -14.866  1.00  0.00              
ATOM    842  CA  SER   252      20.062  13.375 -13.834  1.00  0.00              
ATOM    843  C   SER   252      18.775  12.581 -13.746  1.00  0.00              
ATOM    844  O   SER   252      18.119  12.571 -12.705  1.00  0.00              
ATOM    845  N   ILE   253      18.406  11.918 -14.835  1.00  0.00              
ATOM    846  CA  ILE   253      17.162  11.168 -14.848  1.00  0.00              
ATOM    847  C   ILE   253      17.326   9.784 -14.245  1.00  0.00              
ATOM    848  O   ILE   253      16.374   9.010 -14.175  1.00  0.00              
ATOM    849  N   ASN   254      18.536   9.471 -13.797  1.00  0.00              
ATOM    850  CA  ASN   254      18.773   8.166 -13.204  1.00  0.00              
ATOM    851  C   ASN   254      19.928   8.191 -12.209  1.00  0.00              
ATOM    852  O   ASN   254      21.079   7.970 -12.584  1.00  0.00              
ATOM    853  N   LEU   255      19.622   8.455 -10.940  1.00  0.00              
ATOM    854  CA  LEU   255      20.665   8.496  -9.921  1.00  0.00              
ATOM    855  C   LEU   255      20.398   7.498  -8.799  1.00  0.00              
ATOM    856  O   LEU   255      19.249   7.292  -8.391  1.00  0.00              
ATOM    857  N   ASP   256      21.465   6.882  -8.299  1.00  0.00              
ATOM    858  CA  ASP   256      21.330   5.920  -7.217  1.00  0.00              
ATOM    859  C   ASP   256      21.141   6.692  -5.924  1.00  0.00              
ATOM    860  O   ASP   256      21.345   7.906  -5.875  1.00  0.00              
ATOM    861  N   GLU   257      20.752   5.983  -4.873  1.00  0.00              
ATOM    862  CA  GLU   257      20.552   6.628  -3.597  1.00  0.00              
ATOM    863  C   GLU   257      21.895   7.120  -3.058  1.00  0.00              
ATOM    864  O   GLU   257      21.956   8.173  -2.432  1.00  0.00              
ATOM    865  N   ASN   258      22.967   6.364  -3.301  1.00  0.00              
ATOM    866  CA  ASN   258      24.294   6.776  -2.837  1.00  0.00              
ATOM    867  C   ASN   258      24.672   8.105  -3.467  1.00  0.00              
ATOM    868  O   ASN   258      25.271   8.966  -2.820  1.00  0.00              
ATOM    869  N   ASP   259      24.324   8.261  -4.738  1.00  0.00              
ATOM    870  CA  ASP   259      24.601   9.491  -5.452  1.00  0.00              
ATOM    871  C   ASP   259      23.778  10.628  -4.854  1.00  0.00              
ATOM    872  O   ASP   259      24.280  11.745  -4.684  1.00  0.00              
ATOM    873  N   PHE   260      22.521  10.348  -4.521  1.00  0.00              
ATOM    874  CA  PHE   260      21.694  11.376  -3.914  1.00  0.00              
ATOM    875  C   PHE   260      22.326  11.802  -2.579  1.00  0.00              
ATOM    876  O   PHE   260      22.430  12.996  -2.292  1.00  0.00              
ATOM    877  N   LEU   261      22.764  10.839  -1.770  1.00  0.00              
ATOM    878  CA  LEU   261      23.391  11.180  -0.486  1.00  0.00              
ATOM    879  C   LEU   261      24.636  12.032  -0.681  1.00  0.00              
ATOM    880  O   LEU   261      24.945  12.895   0.146  1.00  0.00              
ATOM    881  N   LYS   262      25.356  11.783  -1.769  1.00  0.00              
ATOM    882  CA  LYS   262      26.553  12.559  -2.081  1.00  0.00              
ATOM    883  C   LYS   262      26.115  14.016  -2.277  1.00  0.00              
ATOM    884  O   LYS   262      26.718  14.946  -1.735  1.00  0.00              
ATOM    885  N   LEU   263      25.049  14.198  -3.052  1.00  0.00              
ATOM    886  CA  LEU   263      24.504  15.521  -3.320  1.00  0.00              
ATOM    887  C   LEU   263      24.119  16.211  -2.023  1.00  0.00              
ATOM    888  O   LEU   263      24.413  17.390  -1.826  1.00  0.00              
ATOM    889  N   LEU   264      23.456  15.477  -1.135  1.00  0.00              
ATOM    890  CA  LEU   264      23.051  16.070   0.131  1.00  0.00              
ATOM    891  C   LEU   264      24.270  16.476   0.946  1.00  0.00              
ATOM    892  O   LEU   264      24.252  17.489   1.652  1.00  0.00              
END
