
#######################################################
#                                                     #
#                        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   14 (  113),  selected   14 , name T0356TS249_4_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_4_3-D1.T0356_D1.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    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    D     314      Y     321          1.127
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    A     315      D     327          3.826
LGA    I     316      E     328          1.932
LGA    Y     317      P     329          3.556
LGA    H     318      A     330          3.018
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    S     319      V     334          1.221
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    T     320      N     337          2.004
LGA    Y     321      E     338          1.299
LGA    T     322      V     339          2.486
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    G     323      P     342          1.884
LGA    R     324      I     343          0.985
LGA    P     325      L     344          1.532
LGA    P     326      Q     345          2.060
LGA    D     327      K     346          2.542
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  124    5.0     14    2.27     0.00      8.532     0.590

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.630897 * X  +  -0.773537 * Y  +  -0.060072 * Z  +  54.530972
  Y_new =  -0.477116 * X  +  -0.447858 * Y  +   0.756164 * Z  +  73.683418
  Z_new =  -0.611824 * X  +  -0.448400 * Y  +  -0.651619 * Z  +  80.597404 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.538876    0.602717  [ DEG:  -145.4669     34.5331 ]
  Theta =   0.658365    2.483228  [ DEG:    37.7215    142.2785 ]
  Phi   =  -0.647489    2.494104  [ DEG:   -37.0984    142.9016 ]
 
# 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: T0356TS249_4_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_4_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14  124   5.0   14   2.27    0.00   8.532
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_4_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 2gm2_A
ATOM    417  N   ASP   314      61.592  62.030  86.406  1.00  9.99
ATOM    418  CA  ASP   314      60.729  63.167  86.527  1.00  9.99
ATOM    419  CB  ASP   314      61.324  64.497  86.017  1.00  9.99
ATOM    420  CG  ASP   314      62.307  65.071  87.013  1.00  9.99
ATOM    421  OD1 ASP   314      62.098  64.859  88.235  1.00  9.99
ATOM    422  OD2 ASP   314      63.278  65.735  86.563  1.00  9.99
ATOM    423  C   ASP   314      59.556  62.998  85.630  1.00  9.99
ATOM    424  O   ASP   314      59.401  62.006  84.918  1.00  9.99
ATOM    425  N   ALA   315      58.662  64.001  85.697  1.00  9.99
ATOM    426  CA  ALA   315      57.624  64.101  84.732  1.00  9.99
ATOM    427  CB  ALA   315      56.350  64.786  85.253  1.00  9.99
ATOM    428  C   ALA   315      58.274  65.008  83.743  1.00  9.99
ATOM    429  O   ALA   315      58.645  66.137  84.061  1.00  9.99
ATOM    430  N   ILE   316      58.476  64.525  82.512  1.00  9.99
ATOM    431  CA  ILE   316      59.178  65.366  81.602  1.00  9.99
ATOM    432  CB  ILE   316      60.482  64.777  81.150  1.00  9.99
ATOM    433  CG2 ILE   316      61.118  65.739  80.134  1.00  9.99
ATOM    434  CG1 ILE   316      61.381  64.516  82.370  1.00  9.99
ATOM    435  CD1 ILE   316      62.609  63.664  82.059  1.00  9.99
ATOM    436  C   ILE   316      58.296  65.560  80.421  1.00  9.99
ATOM    437  O   ILE   316      57.630  64.641  79.950  1.00  9.99
ATOM    438  N   TYR   317      58.206  66.801  79.934  1.00  9.99
ATOM    439  CA  TYR   317      57.400  66.921  78.771  1.00  9.99
ATOM    440  CB  TYR   317      56.111  67.714  79.002  1.00  9.99
ATOM    441  CG  TYR   317      55.252  66.737  79.728  1.00  9.99
ATOM    442  CD1 TYR   317      55.380  66.513  81.079  1.00  9.99
ATOM    443  CD2 TYR   317      54.321  66.014  79.023  1.00  9.99
ATOM    444  CE1 TYR   317      54.574  65.594  81.714  1.00  9.99
ATOM    445  CE2 TYR   317      53.514  65.097  79.651  1.00  9.99
ATOM    446  CZ  TYR   317      53.638  64.884  81.001  1.00  9.99
ATOM    447  OH  TYR   317      52.810  63.942  81.647  1.00  9.99
ATOM    448  C   TYR   317      58.241  67.523  77.727  1.00  9.99
ATOM    449  O   TYR   317      58.789  68.596  77.931  1.00  9.99
ATOM    450  N   HIS   318      58.400  66.836  76.585  1.00  9.99
ATOM    451  CA  HIS   318      59.279  67.395  75.605  1.00  9.99
ATOM    452  ND1 HIS   318      62.123  68.267  74.445  1.00  9.99
ATOM    453  CG  HIS   318      61.446  67.077  74.295  1.00  9.99
ATOM    454  CB  HIS   318      60.504  66.504  75.313  1.00  9.99
ATOM    455  NE2 HIS   318      62.700  67.456  72.457  1.00  9.99
ATOM    456  CD2 HIS   318      61.812  66.593  73.075  1.00  9.99
ATOM    457  CE1 HIS   318      62.856  68.446  73.318  1.00  9.99
ATOM    458  C   HIS   318      58.539  67.590  74.334  1.00  9.99
ATOM    459  O   HIS   318      58.088  66.626  73.740  1.00  9.99
ATOM    460  N   SER   319      58.386  68.835  73.851  1.00  9.99
ATOM    461  CA  SER   319      57.705  68.947  72.587  1.00  9.99
ATOM    462  CB  SER   319      56.497  69.897  72.616  1.00  9.99
ATOM    463  OG  SER   319      55.500  69.375  73.481  1.00  9.99
ATOM    464  C   SER   319      58.692  69.494  71.618  1.00  9.99
ATOM    465  O   SER   319      59.400  70.435  71.938  1.00  9.99
ATOM    466  N   THR   320      58.793  68.946  70.395  1.00  9.99
ATOM    467  CA  THR   320      59.826  69.496  69.563  1.00  9.99
ATOM    468  CB  THR   320      60.746  68.434  69.040  1.00  9.99
ATOM    469  OG1 THR   320      61.310  67.719  70.130  1.00  9.99
ATOM    470  CG2 THR   320      61.862  69.087  68.207  1.00  9.99
ATOM    471  C   THR   320      59.195  70.173  68.397  1.00  9.99
ATOM    472  O   THR   320      58.314  69.611  67.767  1.00  9.99
ATOM    473  N   TYR   321      59.591  71.414  68.061  1.00  9.99
ATOM    474  CA  TYR   321      58.973  71.961  66.885  1.00  9.99
ATOM    475  CB  TYR   321      58.189  73.265  67.137  1.00  9.99
ATOM    476  CG  TYR   321      57.322  73.501  65.942  1.00  9.99
ATOM    477  CD1 TYR   321      56.144  72.800  65.804  1.00  9.99
ATOM    478  CD2 TYR   321      57.662  74.417  64.972  1.00  9.99
ATOM    479  CE1 TYR   321      55.328  72.996  64.715  1.00  9.99
ATOM    480  CE2 TYR   321      56.849  74.618  63.879  1.00  9.99
ATOM    481  CZ  TYR   321      55.680  73.905  63.749  1.00  9.99
ATOM    482  OH  TYR   321      54.846  74.110  62.629  1.00  9.99
ATOM    483  C   TYR   321      60.096  72.254  65.933  1.00  9.99
ATOM    484  O   TYR   321      61.019  72.998  66.264  1.00  9.99
ATOM    485  N   THR   322      60.055  71.670  64.715  1.00  9.99
ATOM    486  CA  THR   322      61.147  71.872  63.802  1.00  9.99
ATOM    487  CB  THR   322      61.778  70.591  63.335  1.00  9.99
ATOM    488  OG1 THR   322      62.239  69.836  64.446  1.00  9.99
ATOM    489  CG2 THR   322      62.960  70.934  62.412  1.00  9.99
ATOM    490  C   THR   322      60.657  72.607  62.585  1.00  9.99
ATOM    491  O   THR   322      59.629  72.267  62.001  1.00  9.99
ATOM    492  N   GLY   323      61.410  73.667  62.219  1.00  9.99
ATOM    493  CA  GLY   323      61.244  74.587  61.122  1.00  9.99
ATOM    494  C   GLY   323      61.545  73.974  59.784  1.00  9.99
ATOM    495  O   GLY   323      61.047  74.440  58.762  1.00  9.99
ATOM    496  N   ARG   324      62.393  72.934  59.764  1.00  9.99
ATOM    497  CA  ARG   324      62.965  72.315  58.594  1.00  9.99
ATOM    498  CB  ARG   324      63.893  71.134  58.931  1.00  9.99
ATOM    499  CG  ARG   324      65.115  71.521  59.768  1.00  9.99
ATOM    500  CD  ARG   324      66.209  70.448  59.789  1.00  9.99
ATOM    501  NE  ARG   324      67.220  70.834  60.818  1.00  9.99
ATOM    502  CZ  ARG   324      68.436  70.217  60.843  1.00  9.99
ATOM    503  NH1 ARG   324      68.793  69.361  59.842  1.00  9.99
ATOM    504  NH2 ARG   324      69.287  70.431  61.890  1.00  9.99
ATOM    505  C   ARG   324      61.969  71.786  57.597  1.00  9.99
ATOM    506  O   ARG   324      62.354  71.699  56.432  1.00  9.99
ATOM    507  N   PRO   325      60.750  71.416  57.889  1.00  9.99
ATOM    508  CA  PRO   325      59.941  70.790  56.880  1.00  9.99
ATOM    509  CD  PRO   325      60.332  71.006  59.224  1.00  9.99
ATOM    510  CB  PRO   325      58.637  70.424  57.579  1.00  9.99
ATOM    511  CG  PRO   325      59.081  70.138  59.024  1.00  9.99
ATOM    512  C   PRO   325      59.764  71.501  55.572  1.00  9.99
ATOM    513  O   PRO   325      59.433  70.802  54.615  1.00  9.99
ATOM    514  N   PRO   326      59.928  72.783  55.433  1.00  9.99
ATOM    515  CA  PRO   326      59.786  73.336  54.118  1.00  9.99
ATOM    516  CD  PRO   326      59.545  73.728  56.469  1.00  9.99
ATOM    517  CB  PRO   326      59.756  74.847  54.313  1.00  9.99
ATOM    518  CG  PRO   326      59.140  75.008  55.716  1.00  9.99
ATOM    519  C   PRO   326      60.909  72.832  53.276  1.00  9.99
ATOM    520  O   PRO   326      62.008  72.649  53.799  1.00  9.99
ATOM    521  N   ASP   327      60.662  72.587  51.976  1.00  9.99
ATOM    522  CA  ASP   327      61.718  72.069  51.162  1.00  9.99
ATOM    523  CB  ASP   327      61.418  70.659  50.629  1.00  9.99
ATOM    524  CG  ASP   327      62.719  70.067  50.114  1.00  9.99
ATOM    525  OD1 ASP   327      63.775  70.727  50.299  1.00  9.99
ATOM    526  OD2 ASP   327      62.677  68.946  49.541  1.00  9.99
ATOM    527  C   ASP   327      61.876  72.982  49.952  1.00  9.99
ATOM    528  O   ASP   327      61.899  72.447  48.811  1.00  9.99
ATOM    529  OXT ASP   327      61.977  74.222  50.150  1.00  9.99
TER
END
