
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0356TS245_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS245_1-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      -       -           -
LGA    P     349      -       -           -
LGA    E     350      F     348          5.005
LGA    I     351      P     349          3.276
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    V     352      V     352          4.473
LGA    D     353      D     353          3.277
LGA    F     354      F     354          1.815
LGA    Y     355      Y     355          0.375
LGA    L     356      L     356          1.362
LGA    E     359      P     357          1.510
LGA    G     360      P     358          2.196
LGA    -       -      E     359           -
LGA    -       -      G     360           -
LGA    C     361      C     361          1.507
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    S     362      R     364          1.635
LGA    Y     363      L     365          0.903
LGA    R     364      A     366          1.073
LGA    L     365      V     367          0.395
LGA    A     366      V     368          0.605
LGA    V     367      T     369          1.902
LGA    V     368      I     370          1.443
LGA    -       -      K     371           -
LGA    -       -      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    -       -      V     381           -
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    -       -      W     386           -
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    T     369      D     402          1.052
LGA    I     370      D     403          1.738
LGA    K     371      D     404          2.283
LGA    K     372      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
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)   23  120    5.0     20    2.25    30.00     14.150     0.851

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.737028 * X  +   0.177648 * Y  +   0.652098 * Z  +  56.034523
  Y_new =  -0.671425 * X  +  -0.082070 * Y  +  -0.736514 * Z  + 118.566505
  Z_new =  -0.077322 * X  +  -0.980666 * Y  +   0.179765 * Z  + 102.621689 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.389500    1.752093  [ DEG:   -79.6125    100.3875 ]
  Theta =   0.077399    3.064193  [ DEG:     4.4347    175.5653 ]
  Phi   =  -2.402739    0.738854  [ DEG:  -137.6668     42.3332 ]
 
# 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: T0356TS245_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS245_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  120   5.0   20   2.25   30.00  14.150
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS245_1-D3
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    806  N   PHE   348      51.929  76.009  54.865  1.00  0.00
ATOM    807  CA  PHE   348      51.708  74.725  55.519  1.00  0.00
ATOM    808  C   PHE   348      51.376  73.639  54.510  1.00  0.00
ATOM    809  O   PHE   348      51.655  72.460  54.819  1.00  0.00
ATOM    810  CB  PHE   348      50.557  74.888  56.514  1.00  0.00
ATOM    811  N   PRO   349      50.760  73.947  53.441  1.00  0.00
ATOM    812  CA  PRO   349      50.297  72.996  52.440  1.00  0.00
ATOM    813  C   PRO   349      51.540  72.421  51.781  1.00  0.00
ATOM    814  O   PRO   349      51.486  71.214  51.457  1.00  0.00
ATOM    815  CB  PRO   349      49.424  73.695  51.397  1.00  0.00
ATOM    816  N   GLU   350      52.559  73.119  51.627  1.00  0.00
ATOM    817  CA  GLU   350      53.830  72.740  51.082  1.00  0.00
ATOM    818  C   GLU   350      54.723  72.324  52.189  1.00  0.00
ATOM    819  O   GLU   350      54.869  71.142  51.808  1.00  0.00
ATOM    820  CB  GLU   350      54.438  73.928  50.334  1.00  0.00
ATOM    821  N   ILE   351      55.101  72.683  53.104  1.00  0.00
ATOM    822  CA  ILE   351      55.802  72.478  54.318  1.00  0.00
ATOM    823  C   ILE   351      54.903  71.799  55.246  1.00  0.00
ATOM    824  O   ILE   351      55.283  72.200  56.367  1.00  0.00
ATOM    825  CB  ILE   351      56.241  73.824  54.900  1.00  0.00
ATOM    826  N   VAL   352      53.994  70.878  55.093  1.00  0.00
ATOM    827  CA  VAL   352      53.330  70.221  56.153  1.00  0.00
ATOM    828  C   VAL   352      53.722  70.260  57.558  1.00  0.00
ATOM    829  O   VAL   352      54.247  69.129  57.653  1.00  0.00
ATOM    830  CB  VAL   352      53.350  68.779  55.641  1.00  0.00
ATOM    831  N   ASP   353      53.846  71.109  58.395  1.00  0.00
ATOM    832  CA  ASP   353      54.542  71.187  59.672  1.00  0.00
ATOM    833  C   ASP   353      54.115  70.064  60.599  1.00  0.00
ATOM    834  O   ASP   353      52.953  69.619  60.486  1.00  0.00
ATOM    835  CB  ASP   353      54.226  72.543  60.307  1.00  0.00
ATOM    836  N   PHE   354      54.987  69.557  61.406  1.00  0.00
ATOM    837  CA  PHE   354      54.704  68.416  62.263  1.00  0.00
ATOM    838  C   PHE   354      54.182  68.941  63.589  1.00  0.00
ATOM    839  O   PHE   354      54.878  69.778  64.205  1.00  0.00
ATOM    840  CB  PHE   354      55.981  67.602  62.486  1.00  0.00
ATOM    841  N   TYR   355      53.041  68.506  64.033  1.00  0.00
ATOM    842  CA  TYR   355      52.436  68.929  65.286  1.00  0.00
ATOM    843  C   TYR   355      52.401  67.732  66.220  1.00  0.00
ATOM    844  O   TYR   355      53.033  66.804  65.671  1.00  0.00
ATOM    845  CB  TYR   355      51.016  69.439  65.032  1.00  0.00
ATOM    846  N   LEU   356      52.249  67.819  67.505  1.00  0.00
ATOM    847  CA  LEU   356      52.755  66.909  68.493  1.00  0.00
ATOM    848  C   LEU   356      51.477  66.765  69.257  1.00  0.00
ATOM    849  O   LEU   356      51.850  67.400  70.267  1.00  0.00
ATOM    850  CB  LEU   356      53.850  67.470  69.402  1.00  0.00
ATOM    851  N   GLU   359      50.673  66.049  69.280  1.00  0.00
ATOM    852  CA  GLU   359      49.652  65.354  70.030  1.00  0.00
ATOM    853  C   GLU   359      49.979  64.690  71.339  1.00  0.00
ATOM    854  O   GLU   359      49.220  65.151  72.218  1.00  0.00
ATOM    855  CB  GLU   359      49.129  64.320  69.032  1.00  0.00
ATOM    856  N   GLY   360      50.894  63.994  71.582  1.00  0.00
ATOM    857  CA  GLY   360      51.497  63.432  72.720  1.00  0.00
ATOM    858  C   GLY   360      52.430  62.357  72.511  1.00  0.00
ATOM    859  O   GLY   360      52.873  63.244  71.751  1.00  0.00
ATOM    861  N   CYS   361      52.957  61.540  72.764  1.00  0.00
ATOM    862  CA  CYS   361      53.888  60.500  72.958  1.00  0.00
ATOM    863  C   CYS   361      54.087  60.097  71.607  1.00  0.00
ATOM    864  O   CYS   361      53.496  61.095  71.141  1.00  0.00
ATOM    865  CB  CYS   361      53.345  59.330  73.782  1.00  0.00
ATOM    866  N   SER   362      54.625  59.231  70.889  1.00  0.00
ATOM    867  CA  SER   362      54.643  59.257  69.434  1.00  0.00
ATOM    868  C   SER   362      53.590  59.655  68.429  1.00  0.00
ATOM    869  O   SER   362      53.811  59.186  67.292  1.00  0.00
ATOM    870  CB  SER   362      55.045  57.796  69.223  1.00  0.00
ATOM    871  N   TYR   363      52.588  60.241  68.706  1.00  0.00
ATOM    872  CA  TYR   363      51.419  60.569  67.903  1.00  0.00
ATOM    873  C   TYR   363      51.585  62.004  67.438  1.00  0.00
ATOM    874  O   TYR   363      51.997  62.894  68.214  1.00  0.00
ATOM    875  CB  TYR   363      50.145  60.432  68.738  1.00  0.00
ATOM    876  N   ARG   364      51.332  62.230  66.120  1.00  0.00
ATOM    877  CA  ARG   364      51.553  63.572  65.600  1.00  0.00
ATOM    878  C   ARG   364      50.536  63.863  64.515  1.00  0.00
ATOM    879  O   ARG   364      49.782  62.985  64.044  1.00  0.00
ATOM    880  CB  ARG   364      52.970  63.665  65.031  1.00  0.00
ATOM    881  N   LEU   365      50.443  65.142  64.193  1.00  0.00
ATOM    882  CA  LEU   365      49.444  65.622  63.255  1.00  0.00
ATOM    883  C   LEU   365      50.295  66.348  62.233  1.00  0.00
ATOM    884  O   LEU   365      51.252  67.049  62.626  1.00  0.00
ATOM    885  CB  LEU   365      48.447  66.591  63.894  1.00  0.00
ATOM    886  N   ALA   366      49.977  66.230  60.993  1.00  0.00
ATOM    887  CA  ALA   366      50.638  66.857  59.877  1.00  0.00
ATOM    888  C   ALA   366      49.741  68.029  59.587  1.00  0.00
ATOM    889  O   ALA   366      48.536  67.726  59.451  1.00  0.00
ATOM    890  CB  ALA   366      50.721  65.943  58.653  1.00  0.00
ATOM    891  N   VAL   367      50.141  69.200  59.644  1.00  0.00
ATOM    892  CA  VAL   367      49.288  70.383  59.563  1.00  0.00
ATOM    893  C   VAL   367      48.925  70.930  58.201  1.00  0.00
ATOM    894  O   VAL   367      48.225  71.965  58.177  1.00  0.00
ATOM    895  CB  VAL   367      50.039  71.444  60.372  1.00  0.00
ATOM    896  N   VAL   368      49.190  70.179  57.079  1.00  0.00
ATOM    897  CA  VAL   368      48.621  70.622  55.821  1.00  0.00
ATOM    898  C   VAL   368      47.190  70.976  55.511  1.00  0.00
ATOM    899  O   VAL   368      46.989  71.451  54.374  1.00  0.00
ATOM    900  CB  VAL   368      49.079  69.462  54.934  1.00  0.00
ATOM    901  N   THR   369      46.231  70.797  56.393  1.00  0.00
ATOM    902  CA  THR   369      44.851  71.142  56.105  1.00  0.00
ATOM    903  C   THR   369      44.674  72.643  56.238  1.00  0.00
ATOM    904  O   THR   369      45.051  73.169  57.307  1.00  0.00
ATOM    905  CB  THR   369      43.932  70.415  57.089  1.00  0.00
ATOM    906  N   ILE   370      44.242  73.306  55.267  1.00  0.00
ATOM    907  CA  ILE   370      44.113  74.749  55.228  1.00  0.00
ATOM    908  C   ILE   370      42.633  75.002  55.094  1.00  0.00
ATOM    909  O   ILE   370      42.199  74.357  54.116  1.00  0.00
ATOM    910  CB  ILE   370      44.857  75.346  54.031  1.00  0.00
ATOM    911  N   LYS   371      41.953  75.600  55.801  1.00  0.00
ATOM    912  CA  LYS   371      40.617  75.961  56.054  1.00  0.00
ATOM    913  C   LYS   371      40.489  77.405  56.113  1.00  0.00
ATOM    914  O   LYS   371      41.173  77.371  57.159  1.00  0.00
ATOM    915  CB  LYS   371      40.184  75.339  57.384  1.00  0.00
ATOM    916  N   LYS   372      40.050  78.274  55.752  1.00  0.00
ATOM    917  CA  LYS   372      39.725  79.642  55.743  1.00  0.00
ATOM    918  C   LYS   372      38.823  79.938  54.646  1.00  0.00
ATOM    919  O   LYS   372      39.775  79.694  53.873  1.00  0.00
ATOM    920  CB  LYS   372      41.014  80.453  55.596  1.00  0.00
TER
END
