
#######################################################
#                                                     #
#                        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_1_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_1_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    D     314      S     319          1.436
LGA    A     315      T     320          0.513
LGA    I     316      Y     321          1.404
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    Y     317      E     328          1.782
LGA    H     318      P     329          0.885
LGA    S     319      A     330          1.610
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    T     320      G     333          1.107
LGA    Y     321      V     334          2.604
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    T     322      N     337          2.023
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    G     323      F     340          2.969
LGA    R     324      V     341          1.425
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    P     325      L     344          0.586
LGA    P     326      Q     345          3.152
LGA    D     327      K     346          2.005
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  124    5.0     14    1.85     0.00     10.095     0.717

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.048018 * X  +   0.180831 * Y  +  -0.982341 * Z  + 120.664497
  Y_new =  -0.934870 * X  +   0.338178 * Y  +   0.107950 * Z  + 103.863403
  Z_new =   0.351727 * X  +   0.923545 * Y  +   0.152815 * Z  +   8.010898 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.406816   -1.734776  [ DEG:    80.6046    -99.3954 ]
  Theta =  -0.359415   -2.782177  [ DEG:   -20.5930   -159.4070 ]
  Phi   =  -1.622115    1.519478  [ DEG:   -92.9403     87.0597 ]
 
# 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_1_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_1_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   1.85    0.00  10.095
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1tqy_B
ATOM    417  N   ASP   314      67.579  64.403  88.700  1.00  9.99
ATOM    418  CA  ASP   314      66.675  65.315  89.327  1.00  9.99
ATOM    419  CB  ASP   314      67.242  66.746  89.366  1.00  9.99
ATOM    420  CG  ASP   314      68.471  66.733  90.258  1.00  9.99
ATOM    421  OD1 ASP   314      68.728  65.669  90.881  1.00  9.99
ATOM    422  OD2 ASP   314      69.167  67.781  90.332  1.00  9.99
ATOM    423  C   ASP   314      65.341  65.421  88.643  1.00  9.99
ATOM    424  O   ASP   314      64.317  65.441  89.325  1.00  9.99
ATOM    425  N   ALA   315      65.280  65.469  87.294  1.00  9.99
ATOM    426  CA  ALA   315      63.992  65.858  86.770  1.00  9.99
ATOM    427  CB  ALA   315      64.040  67.175  85.975  1.00  9.99
ATOM    428  C   ALA   315      63.336  64.840  85.869  1.00  9.99
ATOM    429  O   ALA   315      63.940  64.304  84.943  1.00  9.99
ATOM    430  N   ILE   316      62.048  64.568  86.182  1.00  9.99
ATOM    431  CA  ILE   316      61.075  63.686  85.583  1.00  9.99
ATOM    432  CB  ILE   316      60.066  63.250  86.620  1.00  9.99
ATOM    433  CG2 ILE   316      59.371  64.507  87.146  1.00  9.99
ATOM    434  CG1 ILE   316      59.130  62.126  86.136  1.00  9.99
ATOM    435  CD1 ILE   316      58.070  62.537  85.114  1.00  9.99
ATOM    436  C   ILE   316      60.391  64.154  84.304  1.00  9.99
ATOM    437  O   ILE   316      60.097  63.323  83.448  1.00  9.99
ATOM    438  N   TYR   317      60.072  65.457  84.107  1.00  9.99
ATOM    439  CA  TYR   317      59.220  65.750  82.968  1.00  9.99
ATOM    440  CB  TYR   317      58.049  66.690  83.305  1.00  9.99
ATOM    441  CG  TYR   317      57.190  66.011  84.314  1.00  9.99
ATOM    442  CD1 TYR   317      57.438  66.163  85.657  1.00  9.99
ATOM    443  CD2 TYR   317      56.136  65.219  83.919  1.00  9.99
ATOM    444  CE1 TYR   317      56.649  65.540  86.595  1.00  9.99
ATOM    445  CE2 TYR   317      55.344  64.591  84.850  1.00  9.99
ATOM    446  CZ  TYR   317      55.598  64.751  86.191  1.00  9.99
ATOM    447  OH  TYR   317      54.786  64.106  87.147  1.00  9.99
ATOM    448  C   TYR   317      59.973  66.399  81.840  1.00  9.99
ATOM    449  O   TYR   317      60.516  67.495  81.972  1.00  9.99
ATOM    450  N   HIS   318      59.942  65.757  80.652  1.00  9.99
ATOM    451  CA  HIS   318      60.719  66.226  79.537  1.00  9.99
ATOM    452  ND1 HIS   318      63.703  66.167  78.036  1.00  9.99
ATOM    453  CG  HIS   318      62.399  65.797  77.811  1.00  9.99
ATOM    454  CB  HIS   318      61.545  65.141  78.843  1.00  9.99
ATOM    455  NE2 HIS   318      63.180  66.882  76.001  1.00  9.99
ATOM    456  CD2 HIS   318      62.095  66.234  76.559  1.00  9.99
ATOM    457  CE1 HIS   318      64.121  66.814  76.921  1.00  9.99
ATOM    458  C   HIS   318      59.855  66.782  78.450  1.00  9.99
ATOM    459  O   HIS   318      59.569  67.970  78.436  1.00  9.99
ATOM    460  N   SER   319      59.407  65.924  77.510  1.00  9.99
ATOM    461  CA  SER   319      58.621  66.306  76.362  1.00  9.99
ATOM    462  CB  SER   319      57.182  66.728  76.719  1.00  9.99
ATOM    463  OG  SER   319      57.179  67.974  77.400  1.00  9.99
ATOM    464  C   SER   319      59.225  67.384  75.484  1.00  9.99
ATOM    465  O   SER   319      58.985  68.579  75.665  1.00  9.99
ATOM    466  N   THR   320      60.077  66.956  74.518  1.00  9.99
ATOM    467  CA  THR   320      60.763  67.799  73.566  1.00  9.99
ATOM    468  CB  THR   320      61.594  67.001  72.583  1.00  9.99
ATOM    469  OG1 THR   320      60.812  65.994  71.956  1.00  9.99
ATOM    470  CG2 THR   320      62.781  66.345  73.278  1.00  9.99
ATOM    471  C   THR   320      59.911  68.654  72.671  1.00  9.99
ATOM    472  O   THR   320      59.630  69.786  73.044  1.00  9.99
ATOM    473  N   TYR   321      59.369  68.143  71.525  1.00  9.99
ATOM    474  CA  TYR   321      59.000  69.195  70.606  1.00  9.99
ATOM    475  CB  TYR   321      60.191  69.863  69.872  1.00  9.99
ATOM    476  CG  TYR   321      60.948  70.697  70.838  1.00  9.99
ATOM    477  CD1 TYR   321      60.493  71.952  71.162  1.00  9.99
ATOM    478  CD2 TYR   321      62.079  70.206  71.448  1.00  9.99
ATOM    479  CE1 TYR   321      61.175  72.720  72.072  1.00  9.99
ATOM    480  CE2 TYR   321      62.762  70.968  72.360  1.00  9.99
ATOM    481  CZ  TYR   321      62.310  72.226  72.670  1.00  9.99
ATOM    482  OH  TYR   321      63.012  73.010  73.607  1.00  9.99
ATOM    483  C   TYR   321      58.072  68.919  69.485  1.00  9.99
ATOM    484  O   TYR   321      57.321  67.951  69.441  1.00  9.99
ATOM    485  N   THR   322      58.113  69.899  68.545  1.00  9.99
ATOM    486  CA  THR   322      57.384  69.890  67.310  1.00  9.99
ATOM    487  CB  THR   322      56.454  71.057  67.144  1.00  9.99
ATOM    488  OG1 THR   322      55.544  71.118  68.232  1.00  9.99
ATOM    489  CG2 THR   322      55.669  70.855  65.839  1.00  9.99
ATOM    490  C   THR   322      58.400  69.938  66.204  1.00  9.99
ATOM    491  O   THR   322      59.456  70.541  66.360  1.00  9.99
ATOM    492  N   GLY   323      58.136  69.290  65.050  1.00  9.99
ATOM    493  CA  GLY   323      59.149  69.332  64.029  1.00  9.99
ATOM    494  C   GLY   323      58.521  69.641  62.708  1.00  9.99
ATOM    495  O   GLY   323      57.494  69.077  62.332  1.00  9.99
ATOM    496  N   ARG   324      59.150  70.558  61.950  1.00  9.99
ATOM    497  CA  ARG   324      58.627  70.881  60.659  1.00  9.99
ATOM    498  CB  ARG   324      58.068  72.310  60.555  1.00  9.99
ATOM    499  CG  ARG   324      57.511  72.657  59.171  1.00  9.99
ATOM    500  CD  ARG   324      57.002  74.097  59.056  1.00  9.99
ATOM    501  NE  ARG   324      56.566  74.313  57.648  1.00  9.99
ATOM    502  CZ  ARG   324      55.295  73.999  57.265  1.00  9.99
ATOM    503  NH1 ARG   324      54.414  73.481  58.169  1.00  9.99
ATOM    504  NH2 ARG   324      54.907  74.209  55.973  1.00  9.99
ATOM    505  C   ARG   324      59.737  70.764  59.672  1.00  9.99
ATOM    506  O   ARG   324      60.830  71.290  59.874  1.00  9.99
ATOM    507  N   PRO   325      59.470  70.046  58.618  1.00  9.99
ATOM    508  CA  PRO   325      60.413  69.983  57.547  1.00  9.99
ATOM    509  CD  PRO   325      58.768  68.788  58.776  1.00  9.99
ATOM    510  CB  PRO   325      59.904  68.886  56.620  1.00  9.99
ATOM    511  CG  PRO   325      59.219  67.910  57.597  1.00  9.99
ATOM    512  C   PRO   325      60.414  71.358  56.989  1.00  9.99
ATOM    513  O   PRO   325      59.343  71.959  56.935  1.00  9.99
ATOM    514  N   PRO   326      61.553  71.852  56.606  1.00  9.99
ATOM    515  CA  PRO   326      61.665  73.220  56.178  1.00  9.99
ATOM    516  CD  PRO   326      62.799  71.351  57.162  1.00  9.99
ATOM    517  CB  PRO   326      63.164  73.495  56.071  1.00  9.99
ATOM    518  CG  PRO   326      63.780  72.535  57.104  1.00  9.99
ATOM    519  C   PRO   326      60.886  73.615  54.967  1.00  9.99
ATOM    520  O   PRO   326      60.402  74.745  54.926  1.00  9.99
ATOM    521  N   ASP   327      60.749  72.730  53.967  1.00  9.99
ATOM    522  CA  ASP   327      60.009  73.111  52.803  1.00  9.99
ATOM    523  CB  ASP   327      60.330  72.233  51.579  1.00  9.99
ATOM    524  CG  ASP   327      59.610  72.791  50.357  1.00  9.99
ATOM    525  OD1 ASP   327      58.702  73.646  50.536  1.00  9.99
ATOM    526  OD2 ASP   327      59.960  72.362  49.224  1.00  9.99
ATOM    527  C   ASP   327      58.547  72.889  53.168  1.00  9.99
ATOM    528  O   ASP   327      58.188  71.722  53.487  1.00  9.99
ATOM    529  OXT ASP   327      57.771  73.882  53.143  1.00  9.99
TER
END
