
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0316AL044_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    M     284      S     318          1.737
LGA    S     285      K     319          1.181
LGA    T     286      V     320          2.396
LGA    S     287      T     321          3.569
LGA    L     288      V     322          3.802
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    E     289      E     327          3.985
LGA    A     290      K     328          1.939
LGA    S     291      T     329          0.965
LGA    Q     292      E     330          0.852
LGA    V     293      V     331          4.641
LGA    T     296      I     332          4.067
LGA    R     297      -       -           -
LGA    E     298      -       -           -
LGA    M     299      -       -           -
LGA    P     300      -       -           -
LGA    E     301      -       -           -
LGA    E     302      F     333          4.347
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    F     303      I     340           #
LGA    L     305      T     341           -
LGA    C     307      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    T     308      L     359          3.721
LGA    A     309      I     360          1.473
LGA    E     327      D     361           #
LGA    T     329      N     362           -
LGA    E     330      A     363           -
LGA    V     331      Y     364           -
LGA    I     332      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   90    5.0     14    3.07    14.29     10.324     0.442

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.609079 * X  +   0.687664 * Y  +   0.395147 * Z  +  28.545527
  Y_new =  -0.117007 * X  +  -0.570684 * Y  +   0.812791 * Z  +   3.711714
  Z_new =   0.784431 * X  +   0.448819 * Y  +   0.428053 * Z  + -151.036636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.809076   -2.332517  [ DEG:    46.3566   -133.6434 ]
  Theta =  -0.901778   -2.239815  [ DEG:   -51.6681   -128.3319 ]
  Phi   =  -2.951800    0.189793  [ DEG:  -169.1257     10.8743 ]
 
# 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: T0316AL044_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   90   5.0   14   3.07   14.29  10.324
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_5-D3
REMARK Aligment from pdb entry: 1gpm_A
ATOM    821  N   MET   284      13.679  14.962  -1.051  1.00  0.00              
ATOM    822  CA  MET   284      14.682  14.085  -1.633  1.00  0.00              
ATOM    823  C   MET   284      14.710  12.789  -0.866  1.00  0.00              
ATOM    824  O   MET   284      14.613  12.781   0.362  1.00  0.00              
ATOM    825  N   SER   285      14.714  11.692  -1.609  1.00  0.00              
ATOM    826  CA  SER   285      14.801  10.370  -1.019  1.00  0.00              
ATOM    827  C   SER   285      16.293  10.128  -0.823  1.00  0.00              
ATOM    828  O   SER   285      17.120  10.591  -1.619  1.00  0.00              
ATOM    829  N   THR   286      16.646   9.410   0.233  1.00  0.00              
ATOM    830  CA  THR   286      18.052   9.142   0.518  1.00  0.00              
ATOM    831  C   THR   286      18.174   7.721   1.032  1.00  0.00              
ATOM    832  O   THR   286      17.427   7.311   1.916  1.00  0.00              
ATOM    833  N   SER   287      21.396   4.616   1.512  1.00  0.00              
ATOM    834  CA  SER   287      22.799   4.239   1.372  1.00  0.00              
ATOM    835  C   SER   287      23.138   2.878   1.952  1.00  0.00              
ATOM    836  O   SER   287      22.445   2.365   2.837  1.00  0.00              
ATOM    837  N   LEU   288      24.246   2.333   1.462  1.00  0.00              
ATOM    838  CA  LEU   288      24.801   1.073   1.930  1.00  0.00              
ATOM    839  C   LEU   288      26.118   1.493   2.565  1.00  0.00              
ATOM    840  O   LEU   288      27.064   1.884   1.877  1.00  0.00              
ATOM    841  N   GLU   289      33.141   5.814   7.190  1.00  0.00              
ATOM    842  CA  GLU   289      33.698   6.874   6.367  1.00  0.00              
ATOM    843  C   GLU   289      33.329   6.655   4.897  1.00  0.00              
ATOM    844  O   GLU   289      33.538   7.533   4.058  1.00  0.00              
ATOM    845  N   ALA   290      32.699   5.521   4.608  1.00  0.00              
ATOM    846  CA  ALA   290      32.305   5.199   3.245  1.00  0.00              
ATOM    847  C   ALA   290      30.923   4.553   3.179  1.00  0.00              
ATOM    848  O   ALA   290      30.635   3.599   3.904  1.00  0.00              
ATOM    849  N   SER   291      30.065   5.100   2.322  1.00  0.00              
ATOM    850  CA  SER   291      28.705   4.594   2.123  1.00  0.00              
ATOM    851  C   SER   291      28.307   4.885   0.684  1.00  0.00              
ATOM    852  O   SER   291      28.580   5.963   0.174  1.00  0.00              
ATOM    853  N   GLN   292      27.688   3.926   0.017  1.00  0.00              
ATOM    854  CA  GLN   292      27.294   4.124  -1.373  1.00  0.00              
ATOM    855  C   GLN   292      25.803   4.398  -1.506  1.00  0.00              
ATOM    856  O   GLN   292      25.010   3.860  -0.737  1.00  0.00              
ATOM    857  N   VAL   293      22.319   3.741  -2.668  1.00  0.00              
ATOM    858  CA  VAL   293      21.621   2.537  -3.116  1.00  0.00              
ATOM    859  C   VAL   293      21.047   2.621  -4.532  1.00  0.00              
ATOM    860  O   VAL   293      20.340   3.568  -4.885  1.00  0.00              
ATOM    861  N   THR   296      21.309   1.595  -5.329  1.00  0.00              
ATOM    862  CA  THR   296      20.808   1.560  -6.693  1.00  0.00              
ATOM    863  C   THR   296      19.395   0.998  -6.681  1.00  0.00              
ATOM    864  O   THR   296      19.158  -0.098  -7.193  1.00  0.00              
ATOM    865  N   ARG   297      18.457   1.734  -6.096  1.00  0.00              
ATOM    866  CA  ARG   297      17.080   1.252  -6.021  1.00  0.00              
ATOM    867  C   ARG   297      16.430   1.126  -7.402  1.00  0.00              
ATOM    868  O   ARG   297      16.585   2.003  -8.258  1.00  0.00              
ATOM    869  N   GLU   298       3.967   9.762  -3.421  1.00  0.00              
ATOM    870  CA  GLU   298       4.248  10.980  -2.664  1.00  0.00              
ATOM    871  C   GLU   298       3.621  12.220  -3.295  1.00  0.00              
ATOM    872  O   GLU   298       2.955  12.988  -2.602  1.00  0.00              
ATOM    873  N   MET   299       3.814  12.415  -4.595  1.00  0.00              
ATOM    874  CA  MET   299       3.248  13.597  -5.234  1.00  0.00              
ATOM    875  C   MET   299       1.719  13.578  -5.248  1.00  0.00              
ATOM    876  O   MET   299       1.085  14.611  -5.041  1.00  0.00              
ATOM    877  N   PRO   300       0.535  13.290  -0.858  1.00  0.00              
ATOM    878  CA  PRO   300       0.882  14.339   0.092  1.00  0.00              
ATOM    879  C   PRO   300       0.623  15.709  -0.508  1.00  0.00              
ATOM    880  O   PRO   300       1.403  16.196  -1.320  1.00  0.00              
ATOM    881  N   GLU   301      18.777  11.204  -4.053  1.00  0.00              
ATOM    882  CA  GLU   301      20.172  11.540  -3.786  1.00  0.00              
ATOM    883  C   GLU   301      21.108  10.509  -4.407  1.00  0.00              
ATOM    884  O   GLU   301      21.054   9.319  -4.072  1.00  0.00              
ATOM    885  N   GLU   302      21.955  10.966  -5.323  1.00  0.00              
ATOM    886  CA  GLU   302      22.884  10.077  -5.995  1.00  0.00              
ATOM    887  C   GLU   302      24.312  10.459  -5.663  1.00  0.00              
ATOM    888  O   GLU   302      25.226  10.262  -6.462  1.00  0.00              
ATOM    889  N   PHE   303      24.494  11.010  -4.470  1.00  0.00              
ATOM    890  CA  PHE   303      25.810  11.414  -3.998  1.00  0.00              
ATOM    891  C   PHE   303      26.254  10.387  -2.965  1.00  0.00              
ATOM    892  O   PHE   303      25.515  10.081  -2.028  1.00  0.00              
ATOM    893  N   LEU   305      27.443   9.833  -3.150  1.00  0.00              
ATOM    894  CA  LEU   305      27.949   8.842  -2.224  1.00  0.00              
ATOM    895  C   LEU   305      28.800   9.442  -1.126  1.00  0.00              
ATOM    896  O   LEU   305      28.962  10.662  -1.031  1.00  0.00              
ATOM    897  N   CYS   307      29.320   8.577  -0.269  1.00  0.00              
ATOM    898  CA  CYS   307      30.187   9.000   0.814  1.00  0.00              
ATOM    899  C   CYS   307      31.498   8.232   0.702  1.00  0.00              
ATOM    900  O   CYS   307      31.518   7.000   0.809  1.00  0.00              
ATOM    901  N   THR   308      32.579   8.929   0.333  1.00  0.00              
ATOM    902  CA  THR   308      32.587  10.362   0.028  1.00  0.00              
ATOM    903  C   THR   308      32.150  10.557  -1.434  1.00  0.00              
ATOM    904  O   THR   308      31.811   9.586  -2.118  1.00  0.00              
ATOM    905  N   ALA   309      32.151  11.804  -1.934  1.00  0.00              
ATOM    906  CA  ALA   309      32.521  13.060  -1.281  1.00  0.00              
ATOM    907  C   ALA   309      31.417  13.729  -0.469  1.00  0.00              
ATOM    908  O   ALA   309      31.638  14.791   0.120  1.00  0.00              
ATOM    909  N   GLU   327      30.230  13.134  -0.440  1.00  0.00              
ATOM    910  CA  GLU   327      29.140  13.717   0.332  1.00  0.00              
ATOM    911  C   GLU   327      28.942  12.902   1.606  1.00  0.00              
ATOM    912  O   GLU   327      29.533  11.836   1.761  1.00  0.00              
ATOM    913  N   THR   329      28.167  13.440   2.541  1.00  0.00              
ATOM    914  CA  THR   329      27.863  12.750   3.786  1.00  0.00              
ATOM    915  C   THR   329      26.505  12.079   3.611  1.00  0.00              
ATOM    916  O   THR   329      25.792  12.344   2.621  1.00  0.00              
ATOM    917  N   GLU   330      26.155  11.195   4.546  1.00  0.00              
ATOM    918  CA  GLU   330      24.871  10.492   4.497  1.00  0.00              
ATOM    919  C   GLU   330      23.733  11.471   4.747  1.00  0.00              
ATOM    920  O   GLU   330      22.785  11.539   3.959  1.00  0.00              
ATOM    921  N   VAL   331      23.844  12.243   5.823  1.00  0.00              
ATOM    922  CA  VAL   331      22.842  13.238   6.159  1.00  0.00              
ATOM    923  C   VAL   331      23.233  14.514   5.423  1.00  0.00              
ATOM    924  O   VAL   331      24.370  14.653   4.986  1.00  0.00              
ATOM    925  N   ILE   332      22.265  15.397   5.201  1.00  0.00              
ATOM    926  CA  ILE   332      22.497  16.651   4.500  1.00  0.00              
ATOM    927  C   ILE   332      22.922  17.793   5.412  1.00  0.00              
ATOM    928  O   ILE   332      23.430  18.810   4.924  1.00  0.00              
END
