
#######################################################
#                                                     #
#                        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   37 (  185),  selected   37 , name T0295TS239_5_2-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295TS239_5_2-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     181           -
LGA    -       -      N     182           -
LGA    -       -      F     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      L     190           -
LGA    -       -      R     191           -
LGA    T     181      I     192          3.790
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    -       -      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    -       -      T     200           -
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    -       -      I     204           -
LGA    -       -      F     205           -
LGA    -       -      K     206           -
LGA    -       -      R     207           -
LGA    -       -      N     208           -
LGA    -       -      A     209           -
LGA    -       -      V     210           -
LGA    -       -      L     211           -
LGA    -       -      N     212           -
LGA    N     182      M     213          2.454
LGA    F     183      L     214          2.674
LGA    -       -      E     215           -
LGA    D     184      H     216          1.052
LGA    E     185      N     217          1.391
LGA    W     186      Y     218          1.548
LGA    D     187      K     219          1.505
LGA    N     188      N     220          2.215
LGA    L     189      W     221          2.740
LGA    -       -      C     222           -
LGA    -       -      T     223           -
LGA    L     190      L     224          1.748
LGA    R     191      N     225          1.572
LGA    I     192      K     226          2.042
LGA    C     193      Q     227          2.244
LGA    F     194      V     228          4.405
LGA    S     195      P     229           #
LGA    R     196      -       -           -
LGA    K     197      V     230          4.999
LGA    R     198      N     231           -
LGA    -       -      F     232           -
LGA    -       -      P     233           -
LGA    K     199      F     234          1.339
LGA    -       -      K     235           -
LGA    T     200      K     236           #
LGA    L     201      Y     237          4.424
LGA    H     202      C     238          1.121
LGA    A     203      L     239          2.903
LGA    I     204      D     240          2.266
LGA    F     205      V     241          2.502
LGA    -       -      L     242           -
LGA    K     206      E     243          2.844
LGA    R     207      H     244          4.614
LGA    N     208      L     245           -
LGA    A     209      -       -           -
LGA    V     210      D     246          4.902
LGA    L     211      M     247           #
LGA    N     212      C     248           -
LGA    M     213      -       -           -
LGA    L     214      -       -           -
LGA    E     215      -       -           -
LGA    H     216      E     249          4.908
LGA    N     217      K     250           -
LGA    -       -      R     251           -
LGA    -       -      S     252           -
LGA    -       -      I     253           -
LGA    -       -      N     254           -
LGA    -       -      L     255           -
LGA    -       -      D     256           -
LGA    -       -      E     257           -
LGA    -       -      N     258           -
LGA    -       -      D     259           -
LGA    -       -      F     260           -
LGA    -       -      L     261           -
LGA    -       -      K     262           -
LGA    -       -      L     263           -
LGA    -       -      L     264           -
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)   37   95    5.0     25    3.01     8.00     17.824     0.804

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.027817 * X  +   0.996528 * Y  +   0.078476 * Z  +  39.742809
  Y_new =   0.326068 * X  +  -0.065166 * Y  +   0.943098 * Z  + -26.179752
  Z_new =   0.944937 * X  +   0.051822 * Y  +  -0.323123 * Z  + -28.796810 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.982567   -0.159025  [ DEG:   170.8885     -9.1115 ]
  Theta =  -1.237402   -1.904190  [ DEG:   -70.8979   -109.1021 ]
  Phi   =   1.655900   -1.485693  [ DEG:    94.8761    -85.1239 ]
 
# 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: T0295TS239_5_2-D2                             
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS239_5_2-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   95   5.0   25   3.01    8.00  17.824
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS239_5_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT 1jq3_C
ATOM    859  N   THR   181      16.292  21.980  -4.159  1.00  9.99
ATOM    860  CA  THR   181      15.977  22.514  -2.848  1.00  9.99
ATOM    861  C   THR   181      17.045  23.417  -2.241  1.00  9.99
ATOM    862  O   THR   181      17.004  23.697  -1.041  1.00  9.99
ATOM    863  CB  THR   181      15.633  21.381  -1.897  1.00  9.99
ATOM    864  N   ASN   182      18.736  26.853  -1.495  1.00  9.99
ATOM    865  CA  ASN   182      18.368  28.262  -1.371  1.00  9.99
ATOM    866  C   ASN   182      19.672  29.046  -1.171  1.00  9.99
ATOM    867  O   ASN   182      20.229  29.066  -0.076  1.00  9.99
ATOM    868  CB  ASN   182      17.456  28.445  -0.157  1.00  9.99
ATOM    869  N   PHE   183      20.150  29.727  -2.224  1.00  9.99
ATOM    870  CA  PHE   183      21.390  30.509  -2.181  1.00  9.99
ATOM    871  C   PHE   183      21.393  31.601  -1.122  1.00  9.99
ATOM    872  O   PHE   183      22.450  32.007  -0.637  1.00  9.99
ATOM    873  CB  PHE   183      21.470  31.109  -3.582  1.00  9.99
ATOM    874  N   ASP   184      20.208  32.093  -0.784  1.00  9.99
ATOM    875  CA  ASP   184      20.094  33.137   0.220  1.00  9.99
ATOM    876  C   ASP   184      20.634  32.723   1.584  1.00  9.99
ATOM    877  O   ASP   184      21.207  33.550   2.295  1.00  9.99
ATOM    878  CB  ASP   184      18.646  33.607   0.330  1.00  9.99
ATOM    879  N   GLU   185      20.473  31.449   1.946  1.00  9.99
ATOM    880  CA  GLU   185      20.974  30.965   3.232  1.00  9.99
ATOM    881  C   GLU   185      22.489  31.119   3.300  1.00  9.99
ATOM    882  O   GLU   185      23.049  31.461   4.342  1.00  9.99
ATOM    883  CB  GLU   185      20.593  29.491   3.452  1.00  9.99
ATOM    884  N   TRP   186      23.155  30.842   2.187  1.00  9.99
ATOM    885  CA  TRP   186      24.610  30.954   2.127  1.00  9.99
ATOM    886  C   TRP   186      25.038  32.425   2.069  1.00  9.99
ATOM    887  O   TRP   186      25.975  32.833   2.759  1.00  9.99
ATOM    888  CB  TRP   186      25.163  30.184   0.907  1.00  9.99
ATOM    889  N   ASP   187      24.345  33.221   1.258  1.00  9.99
ATOM    890  CA  ASP   187      24.664  34.645   1.144  1.00  9.99
ATOM    891  C   ASP   187      24.544  35.389   2.464  1.00  9.99
ATOM    892  O   ASP   187      25.339  36.282   2.749  1.00  9.99
ATOM    893  CB  ASP   187      23.775  35.334   0.104  1.00  9.99
ATOM    894  N   ASN   188      23.577  34.981   3.279  1.00  9.99
ATOM    895  CA  ASN   188      23.314  35.604   4.575  1.00  9.99
ATOM    896  C   ASN   188      24.020  34.941   5.760  1.00  9.99
ATOM    897  O   ASN   188      23.921  35.414   6.899  1.00  9.99
ATOM    898  CB  ASN   188      21.800  35.650   4.820  1.00  9.99
ATOM    899  N   LEU   189      24.761  33.869   5.487  1.00  9.99
ATOM    900  CA  LEU   189      25.481  33.144   6.534  1.00  9.99
ATOM    901  C   LEU   189      26.367  34.110   7.314  1.00  9.99
ATOM    902  O   LEU   189      27.102  34.907   6.727  1.00  9.99
ATOM    903  CB  LEU   189      26.336  32.047   5.912  1.00  9.99
ATOM    904  N   LEU   190      26.306  34.026   8.636  1.00  9.99
ATOM    905  CA  LEU   190      27.075  34.934   9.491  1.00  9.99
ATOM    906  C   LEU   190      28.452  34.439   9.937  1.00  9.99
ATOM    907  O   LEU   190      29.048  35.024  10.847  1.00  9.99
ATOM    908  CB  LEU   190      26.237  35.330  10.723  1.00  9.99
ATOM    909  N   ARG   191      28.966  33.395   9.284  1.00  9.99
ATOM    910  CA  ARG   191      30.267  32.831   9.645  1.00  9.99
ATOM    911  C   ARG   191      31.246  32.829   8.469  1.00  9.99
ATOM    912  O   ARG   191      30.839  32.904   7.314  1.00  9.99
ATOM    913  CB  ARG   191      30.082  31.408  10.178  1.00  9.99
ATOM    914  N   ILE   192      32.540  32.735   8.765  1.00  9.99
ATOM    915  CA  ILE   192      33.552  32.734   7.717  1.00  9.99
ATOM    916  C   ILE   192      33.567  31.435   6.916  1.00  9.99
ATOM    917  O   ILE   192      33.403  30.352   7.480  1.00  9.99
ATOM    918  CB  ILE   192      34.948  32.963   8.315  1.00  9.99
ATOM    919  N   CYS   193      33.699  31.564   5.598  1.00  9.99
ATOM    920  CA  CYS   193      33.796  30.411   4.687  1.00  9.99
ATOM    921  C   CYS   193      34.942  30.737   3.729  1.00  9.99
ATOM    922  O   CYS   193      34.943  31.794   3.095  1.00  9.99
ATOM    923  CB  CYS   193      32.493  30.212   3.897  1.00  9.99
ATOM    924  N   PHE   194      35.939  29.859   3.659  1.00  9.99
ATOM    925  CA  PHE   194      37.088  30.084   2.794  1.00  9.99
ATOM    926  C   PHE   194      37.002  29.389   1.428  1.00  9.99
ATOM    927  O   PHE   194      37.787  29.683   0.512  1.00  9.99
ATOM    928  CB  PHE   194      38.361  29.656   3.520  1.00  9.99
ATOM    929  N   SER   195      36.043  28.481   1.281  1.00  9.99
ATOM    930  CA  SER   195      35.887  27.767   0.013  1.00  9.99
ATOM    931  C   SER   195      34.465  27.833  -0.504  1.00  9.99
ATOM    932  O   SER   195      34.192  28.374  -1.573  1.00  9.99
ATOM    933  CB  SER   195      36.316  26.302   0.203  1.00  9.99
ATOM    934  N   ARG   196      33.567  27.254   0.266  1.00  9.99
ATOM    935  CA  ARG   196      32.171  27.168  -0.078  1.00  9.99
ATOM    936  C   ARG   196      31.427  28.494  -0.248  1.00  9.99
ATOM    937  O   ARG   196      31.575  29.412   0.556  1.00  9.99
ATOM    938  CB  ARG   196      31.468  26.322   0.993  1.00  9.99
ATOM    939  N   LYS   197      30.592  28.535  -1.284  1.00  9.99
ATOM    940  CA  LYS   197      29.720  29.682  -1.587  1.00  9.99
ATOM    941  C   LYS   197      28.583  29.186  -2.493  1.00  9.99
ATOM    942  O   LYS   197      28.586  28.024  -2.911  1.00  9.99
ATOM    943  CB  LYS   197      30.494  30.873  -2.192  1.00  9.99
ATOM    944  N   ARG   198      27.591  30.035  -2.755  1.00  9.99
ATOM    945  CA  ARG   198      26.433  29.638  -3.570  1.00  9.99
ATOM    946  C   ARG   198      26.753  29.084  -4.960  1.00  9.99
ATOM    947  O   ARG   198      26.119  28.117  -5.388  1.00  9.99
ATOM    948  CB  ARG   198      25.421  30.792  -3.749  1.00  9.99
ATOM    949  N   LYS   199      27.673  29.724  -5.689  1.00  9.99
ATOM    950  CA  LYS   199      28.029  29.275  -7.048  1.00  9.99
ATOM    951  C   LYS   199      28.743  27.934  -6.986  1.00  9.99
ATOM    952  O   LYS   199      28.582  27.086  -7.858  1.00  9.99
ATOM    953  CB  LYS   199      28.982  30.246  -7.763  1.00  9.99
ATOM    954  N   THR   200      29.612  27.797  -5.998  1.00  9.99
ATOM    955  CA  THR   200      30.371  26.558  -5.833  1.00  9.99
ATOM    956  C   THR   200      29.454  25.394  -5.455  1.00  9.99
ATOM    957  O   THR   200      29.668  24.255  -5.904  1.00  9.99
ATOM    958  CB  THR   200      31.517  26.767  -4.824  1.00  9.99
ATOM    959  N   LEU   201      28.427  25.681  -4.660  1.00  9.99
ATOM    960  CA  LEU   201      27.473  24.631  -4.264  1.00  9.99
ATOM    961  C   LEU   201      26.897  23.984  -5.520  1.00  9.99
ATOM    962  O   LEU   201      26.963  22.772  -5.710  1.00  9.99
ATOM    963  CB  LEU   201      26.311  25.194  -3.433  1.00  9.99
ATOM    964  N   HIS   202      26.308  24.813  -6.374  1.00  9.99
ATOM    965  CA  HIS   202      25.698  24.339  -7.608  1.00  9.99
ATOM    966  C   HIS   202      26.713  23.709  -8.567  1.00  9.99
ATOM    967  O   HIS   202      26.485  22.626  -9.107  1.00  9.99
ATOM    968  CB  HIS   202      24.941  25.490  -8.286  1.00  9.99
ATOM    969  N   ALA   203      27.849  24.376  -8.726  1.00  9.99
ATOM    970  CA  ALA   203      28.912  23.933  -9.615  1.00  9.99
ATOM    971  C   ALA   203      29.520  22.579  -9.261  1.00  9.99
ATOM    972  O   ALA   203      29.889  21.804 -10.162  1.00  9.99
ATOM    973  CB  ALA   203      29.993  24.975  -9.661  1.00  9.99
ATOM    974  N   ILE   204      29.608  22.290  -7.965  1.00  9.99
ATOM    975  CA  ILE   204      30.216  21.033  -7.515  1.00  9.99
ATOM    976  C   ILE   204      29.455  19.805  -7.998  1.00  9.99
ATOM    977  O   ILE   204      30.027  18.707  -8.052  1.00  9.99
ATOM    978  CB  ILE   204      30.381  21.008  -5.987  1.00  9.99
ATOM    979  N   PHE   205      28.195  19.985  -8.395  1.00  9.99
ATOM    980  CA  PHE   205      27.399  18.863  -8.901  1.00  9.99
ATOM    981  C   PHE   205      27.568  18.600 -10.404  1.00  9.99
ATOM    982  O   PHE   205      27.048  17.609 -10.921  1.00  9.99
ATOM    983  CB  PHE   205      25.922  19.013  -8.509  1.00  9.99
ATOM    984  N   LYS   206      28.302  19.465 -11.098  1.00  9.99
ATOM    985  CA  LYS   206      28.568  19.280 -12.532  1.00  9.99
ATOM    986  C   LYS   206      29.721  18.284 -12.635  1.00  9.99
ATOM    987  O   LYS   206      30.847  18.571 -12.218  1.00  9.99
ATOM    988  CB  LYS   206      28.964  20.617 -13.186  1.00  9.99
ATOM    989  N   ARG   207      29.433  17.110 -13.183  1.00  9.99
ATOM    990  CA  ARG   207      30.434  16.052 -13.307  1.00  9.99
ATOM    991  C   ARG   207      31.065  15.943 -14.684  1.00  9.99
ATOM    992  O   ARG   207      30.357  15.914 -15.676  1.00  9.99
ATOM    993  CB  ARG   207      29.770  14.712 -12.990  1.00  9.99
ATOM    994  N   ASN   208      32.407  15.828 -14.756  1.00  9.99
ATOM    995  CA  ASN   208      33.093  15.704 -16.047  1.00  9.99
ATOM    996  C   ASN   208      32.615  14.402 -16.708  1.00  9.99
ATOM    997  O   ASN   208      32.193  13.467 -16.014  1.00  9.99
ATOM    998  CB  ASN   208      34.574  15.596 -15.642  1.00  9.99
ATOM    999  N   ALA   209      34.077  11.674 -17.870  1.00  9.99
ATOM   1000  CA  ALA   209      34.645  10.404 -17.409  1.00  9.99
ATOM   1001  C   ALA   209      34.015   9.913 -16.105  1.00  9.99
ATOM   1002  O   ALA   209      33.811   8.704 -15.921  1.00  9.99
ATOM   1003  CB  ALA   209      36.184  10.460 -17.352  1.00  9.99
ATOM   1004  N   VAL   210      33.629  10.859 -15.245  1.00  9.99
ATOM   1005  CA  VAL   210      32.980  10.532 -13.979  1.00  9.99
ATOM   1006  C   VAL   210      31.550  10.062 -14.246  1.00  9.99
ATOM   1007  O   VAL   210      31.091   9.078 -13.654  1.00  9.99
ATOM   1008  CB  VAL   210      32.971  11.746 -13.025  1.00  9.99
ATOM   1009  N   LEU   211      30.849  10.759 -15.140  1.00  9.99
ATOM   1010  CA  LEU   211      29.490  10.377 -15.503  1.00  9.99
ATOM   1011  C   LEU   211      29.458   8.961 -16.085  1.00  9.99
ATOM   1012  O   LEU   211      28.573   8.164 -15.757  1.00  9.99
ATOM   1013  CB  LEU   211      28.899  11.367 -16.515  1.00  9.99
ATOM   1014  N   ASN   212      30.441   8.647 -16.929  1.00  9.99
ATOM   1015  CA  ASN   212      30.492   7.329 -17.555  1.00  9.99
ATOM   1016  C   ASN   212      30.735   6.255 -16.501  1.00  9.99
ATOM   1017  O   ASN   212      30.131   5.188 -16.535  1.00  9.99
ATOM   1018  CB  ASN   212      31.597   7.284 -18.612  1.00  9.99
ATOM   1019  N   MET   213      31.603   6.557 -15.547  1.00  9.99
ATOM   1020  CA  MET   213      31.916   5.614 -14.489  1.00  9.99
ATOM   1021  C   MET   213      30.702   5.284 -13.615  1.00  9.99
ATOM   1022  O   MET   213      30.587   4.160 -13.112  1.00  9.99
ATOM   1023  CB  MET   213      33.051   6.159 -13.626  1.00  9.99
ATOM   1024  N   LEU   214      29.818   6.268 -13.423  1.00  9.99
ATOM   1025  CA  LEU   214      28.609   6.101 -12.607  1.00  9.99
ATOM   1026  C   LEU   214      27.394   5.663 -13.420  1.00  9.99
ATOM   1027  O   LEU   214      26.321   5.434 -12.857  1.00  9.99
ATOM   1028  CB  LEU   214      28.257   7.410 -11.891  1.00  9.99
ATOM   1029  N   GLU   215      27.557   5.585 -14.739  1.00  9.99
ATOM   1030  CA  GLU   215      26.460   5.193 -15.611  1.00  9.99
ATOM   1031  C   GLU   215      25.439   6.300 -15.808  1.00  9.99
ATOM   1032  O   GLU   215      24.244   6.023 -15.973  1.00  9.99
ATOM   1033  CB  GLU   215      25.793   3.934 -15.032  1.00  9.99
ATOM   1034  N   HIS   216      25.912   7.546 -15.834  1.00  9.99
ATOM   1035  CA  HIS   216      25.061   8.720 -16.003  1.00  9.99
ATOM   1036  C   HIS   216      25.190   9.429 -17.359  1.00  9.99
ATOM   1037  O   HIS   216      24.609  10.502 -17.542  1.00  9.99
ATOM   1038  CB  HIS   216      25.345   9.740 -14.895  1.00  9.99
ATOM   1039  N   ASN   217      25.956   8.872 -18.298  1.00  9.99
ATOM   1040  CA  ASN   217      26.099   9.525 -19.614  1.00  9.99
ATOM   1041  C   ASN   217      24.811   9.426 -20.441  1.00  9.99
ATOM   1042  O   ASN   217      24.293  10.487 -20.862  1.00  9.99
ATOM   1043  CB  ASN   217      27.280   8.943 -20.410  1.00  9.99
TER
END
