
#######################################################
#                                                     #
#                        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_3_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_3_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    D     314      G      20          2.014
LGA    A     315      E      21          3.493
LGA    I     316      L      22          1.328
LGA    Y     317      K      23          2.231
LGA    H     318      R      24          2.561
LGA    S     319      I      25          3.225
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    T     320      E      53          1.756
LGA    Y     321      N      54          2.996
LGA    -       -      P      55           -
LGA    T     322      K      56          1.867
LGA    G     323      G      57          1.428
LGA    R     324      Y      58          0.355
LGA    P     325      S      59          1.964
LGA    P     326      M      60          1.463
LGA    D     327      P      61          1.447
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    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  124    5.0     14    2.17     7.14      9.344     0.618

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.823542 * X  +  -0.213253 * Y  +   0.525644 * Z  +  96.956673
  Y_new =  -0.517625 * X  +  -0.096537 * Y  +  -0.850144 * Z  +  86.113503
  Z_new =   0.232039 * X  +  -0.972216 * Y  +  -0.030883 * Z  + 183.259521 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.602551    1.539041  [ DEG:   -91.8194     88.1806 ]
  Theta =  -0.234174   -2.907419  [ DEG:   -13.4172   -166.5828 ]
  Phi   =  -2.580455    0.561138  [ DEG:  -147.8492     32.1508 ]
 
# 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_3_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_3_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   2.17    7.14   9.344
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_3_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1g5h_A
ATOM    417  N   ASP   314      59.272  84.600  87.239  1.00  9.99
ATOM    418  CA  ASP   314      59.098  83.217  86.895  1.00  9.99
ATOM    419  CB  ASP   314      60.326  82.532  86.257  1.00  9.99
ATOM    420  CG  ASP   314      61.496  82.450  87.230  1.00  9.99
ATOM    421  OD1 ASP   314      61.492  83.173  88.258  1.00  9.99
ATOM    422  OD2 ASP   314      62.430  81.653  86.940  1.00  9.99
ATOM    423  C   ASP   314      58.784  82.536  88.189  1.00  9.99
ATOM    424  O   ASP   314      59.170  83.009  89.245  1.00  9.99
ATOM    425  N   ALA   315      58.080  81.399  88.128  1.00  9.99
ATOM    426  CA  ALA   315      57.565  80.676  89.260  1.00  9.99
ATOM    427  CB  ALA   315      56.674  79.492  88.842  1.00  9.99
ATOM    428  C   ALA   315      58.619  80.125  90.175  1.00  9.99
ATOM    429  O   ALA   315      58.322  79.848  91.333  1.00  9.99
ATOM    430  N   ILE   316      59.846  79.873  89.690  1.00  9.99
ATOM    431  CA  ILE   316      60.798  79.140  90.479  1.00  9.99
ATOM    432  CB  ILE   316      61.913  78.616  89.630  1.00  9.99
ATOM    433  CG2 ILE   316      62.917  77.885  90.537  1.00  9.99
ATOM    434  CG1 ILE   316      61.336  77.742  88.507  1.00  9.99
ATOM    435  CD1 ILE   316      62.331  77.468  87.384  1.00  9.99
ATOM    436  C   ILE   316      61.424  79.939  91.574  1.00  9.99
ATOM    437  O   ILE   316      62.189  80.873  91.351  1.00  9.99
ATOM    438  N   TYR   317      61.210  79.446  92.804  1.00  9.99
ATOM    439  CA  TYR   317      61.687  79.989  94.035  1.00  9.99
ATOM    440  CB  TYR   317      60.701  79.782  95.203  1.00  9.99
ATOM    441  CG  TYR   317      59.491  80.628  95.045  1.00  9.99
ATOM    442  CD1 TYR   317      58.521  80.352  94.112  1.00  9.99
ATOM    443  CD2 TYR   317      59.305  81.683  95.894  1.00  9.99
ATOM    444  CE1 TYR   317      57.411  81.155  93.992  1.00  9.99
ATOM    445  CE2 TYR   317      58.202  82.495  95.771  1.00  9.99
ATOM    446  CZ  TYR   317      57.246  82.235  94.823  1.00  9.99
ATOM    447  OH  TYR   317      56.112  83.067  94.703  1.00  9.99
ATOM    448  C   TYR   317      62.792  79.046  94.371  1.00  9.99
ATOM    449  O   TYR   317      63.137  78.196  93.554  1.00  9.99
ATOM    450  N   HIS   318      63.423  79.200  95.545  1.00  9.99
ATOM    451  CA  HIS   318      64.448  78.270  95.897  1.00  9.99
ATOM    452  ND1 HIS   318      67.105  79.891  94.899  1.00  9.99
ATOM    453  CG  HIS   318      66.194  80.045  95.921  1.00  9.99
ATOM    454  CB  HIS   318      65.588  78.913  96.693  1.00  9.99
ATOM    455  NE2 HIS   318      66.733  82.075  95.096  1.00  9.99
ATOM    456  CD2 HIS   318      65.979  81.386  96.026  1.00  9.99
ATOM    457  CE1 HIS   318      67.394  81.136  94.442  1.00  9.99
ATOM    458  C   HIS   318      63.789  77.226  96.742  1.00  9.99
ATOM    459  O   HIS   318      63.108  77.534  97.719  1.00  9.99
ATOM    460  N   SER   319      63.963  75.952  96.358  1.00  9.99
ATOM    461  CA  SER   319      63.326  74.890  97.073  1.00  9.99
ATOM    462  CB  SER   319      62.637  73.869  96.152  1.00  9.99
ATOM    463  OG  SER   319      62.023  72.844  96.917  1.00  9.99
ATOM    464  C   SER   319      64.378  74.152  97.831  1.00  9.99
ATOM    465  O   SER   319      65.470  73.896  97.330  1.00  9.99
ATOM    466  N   THR   320      64.065  73.795  99.092  1.00  9.99
ATOM    467  CA  THR   320      65.024  73.068  99.864  1.00  9.99
ATOM    468  CB  THR   320      65.348  73.659 101.196  1.00  9.99
ATOM    469  OG1 THR   320      64.169  73.726 101.977  1.00  9.99
ATOM    470  CG2 THR   320      65.952  75.053 101.010  1.00  9.99
ATOM    471  C   THR   320      64.449  71.724 100.161  1.00  9.99
ATOM    472  O   THR   320      63.265  71.578 100.466  1.00  9.99
ATOM    473  N   TYR   321      65.329  70.712 100.100  1.00  9.99
ATOM    474  CA  TYR   321      65.000  69.334 100.294  1.00  9.99
ATOM    475  CB  TYR   321      65.557  68.408  99.196  1.00  9.99
ATOM    476  CG  TYR   321      64.915  68.784  97.902  1.00  9.99
ATOM    477  CD1 TYR   321      65.470  69.755  97.099  1.00  9.99
ATOM    478  CD2 TYR   321      63.755  68.169  97.491  1.00  9.99
ATOM    479  CE1 TYR   321      64.883  70.104  95.906  1.00  9.99
ATOM    480  CE2 TYR   321      63.161  68.512  96.301  1.00  9.99
ATOM    481  CZ  TYR   321      63.725  69.481  95.505  1.00  9.99
ATOM    482  OH  TYR   321      63.116  69.835  94.282  1.00  9.99
ATOM    483  C   TYR   321      65.610  68.901 101.596  1.00  9.99
ATOM    484  O   TYR   321      66.644  69.415 102.019  1.00  9.99
ATOM    485  N   THR   322      64.905  67.975 102.278  1.00  9.99
ATOM    486  CA  THR   322      65.169  67.473 103.609  1.00  9.99
ATOM    487  CB  THR   322      64.128  66.492 104.065  1.00  9.99
ATOM    488  OG1 THR   322      62.818  67.020 103.969  1.00  9.99
ATOM    489  CG2 THR   322      64.444  66.126 105.526  1.00  9.99
ATOM    490  C   THR   322      66.402  66.653 103.871  1.00  9.99
ATOM    491  O   THR   322      67.216  67.012 104.724  1.00  9.99
ATOM    492  N   GLY   323      66.539  65.497 103.186  1.00  9.99
ATOM    493  CA  GLY   323      67.548  64.543 103.567  1.00  9.99
ATOM    494  C   GLY   323      68.906  65.111 103.367  1.00  9.99
ATOM    495  O   GLY   323      69.761  65.048 104.252  1.00  9.99
ATOM    496  N   ARG   324      69.133  65.685 102.178  1.00  9.99
ATOM    497  CA  ARG   324      70.390  66.289 101.889  1.00  9.99
ATOM    498  CB  ARG   324      71.012  65.784 100.568  1.00  9.99
ATOM    499  CG  ARG   324      70.114  65.940  99.337  1.00  9.99
ATOM    500  CD  ARG   324      70.702  65.314  98.066  1.00  9.99
ATOM    501  NE  ARG   324      69.689  65.436  96.976  1.00  9.99
ATOM    502  CZ  ARG   324      68.817  64.415  96.728  1.00  9.99
ATOM    503  NH1 ARG   324      68.874  63.269  97.470  1.00  9.99
ATOM    504  NH2 ARG   324      67.885  64.533  95.737  1.00  9.99
ATOM    505  C   ARG   324      70.095  67.748 101.783  1.00  9.99
ATOM    506  O   ARG   324      69.144  68.160 101.127  1.00  9.99
ATOM    507  N   PRO   325      70.909  68.526 102.428  1.00  9.99
ATOM    508  CA  PRO   325      70.745  69.956 102.444  1.00  9.99
ATOM    509  CD  PRO   325      71.570  68.043 103.631  1.00  9.99
ATOM    510  CB  PRO   325      71.681  70.463 103.541  1.00  9.99
ATOM    511  CG  PRO   325      71.773  69.280 104.518  1.00  9.99
ATOM    512  C   PRO   325      70.947  70.658 101.124  1.00  9.99
ATOM    513  O   PRO   325      70.843  71.883 101.159  1.00  9.99
ATOM    514  N   PRO   326      71.246  70.065  99.994  1.00  9.99
ATOM    515  CA  PRO   326      71.414  70.888  98.829  1.00  9.99
ATOM    516  CD  PRO   326      72.166  68.937  99.928  1.00  9.99
ATOM    517  CB  PRO   326      72.217  70.070  97.813  1.00  9.99
ATOM    518  CG  PRO   326      72.325  68.670  98.430  1.00  9.99
ATOM    519  C   PRO   326      70.176  71.483  98.244  1.00  9.99
ATOM    520  O   PRO   326      69.059  71.118  98.620  1.00  9.99
ATOM    521  N   ASP   327      70.385  72.456  97.338  1.00  9.99
ATOM    522  CA  ASP   327      69.317  73.098  96.643  1.00  9.99
ATOM    523  CB  ASP   327      69.623  74.563  96.284  1.00  9.99
ATOM    524  CG  ASP   327      68.381  75.179  95.653  1.00  9.99
ATOM    525  OD1 ASP   327      67.378  74.439  95.467  1.00  9.99
ATOM    526  OD2 ASP   327      68.421  76.400  95.343  1.00  9.99
ATOM    527  C   ASP   327      69.137  72.339  95.336  1.00  9.99
ATOM    528  O   ASP   327      70.076  72.382  94.494  1.00  9.99
ATOM    529  OXT ASP   327      68.059  71.714  95.158  1.00  9.99
TER
END
