
#######################################################
#                                                     #
#                        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   11 (   54),  selected   11 , name T0320TS102_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS102_5-D2.T0320_D2.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     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    H     246      S     273          0.448
LGA    F     247      V     274          0.647
LGA    E     248      V     275          0.808
LGA    W     249      D     276          0.822
LGA    E     250      K     277          0.908
LGA    I     251      E     278          0.670
LGA    I     252      R     279          0.573
LGA    H     253      F     280          1.486
LGA    A     254      S     281          1.862
LGA    F     255      K     282          2.637
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    G     256      D     285          2.903
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11   73    5.0     11    1.50     0.00     14.462     0.689

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.120178 * X  +   0.300325 * Y  +   0.946236 * Z  +  70.945641
  Y_new =   0.341883 * X  +   0.907361 * Y  +  -0.244565 * Z  +  43.047104
  Z_new =  -0.932026 * X  +   0.294111 * Y  +  -0.211721 * Z  +  43.842285 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.194732   -0.946861  [ DEG:   125.7489    -54.2511 ]
  Theta =   1.199965    1.941628  [ DEG:    68.7529    111.2471 ]
  Phi   =   1.908822   -1.232770  [ DEG:   109.3675    -70.6325 ]
 
# 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: T0320TS102_5-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS102_5-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   73   5.0   11   1.50    0.00  14.462
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS102_5-D2
PFRMAT TS
TARGET T0320
MODEL 5
PARENT 1ihg_A
ATOM    680  N   HIS   246      20.981  34.808   3.239  1.00  1.00
ATOM    681  CA  HIS   246      19.981  33.872   2.725  1.00  1.00
ATOM    682  C   HIS   246      20.262  33.413   1.306  1.00  1.00
ATOM    683  O   HIS   246      20.246  32.219   0.940  1.00  1.00
ATOM    684  CB  HIS   246      18.598  34.548   2.806  1.00  1.00
ATOM    685  N   PHE   247      20.537  34.363   0.413  1.00  1.00
ATOM    686  CA  PHE   247      20.806  34.006  -0.985  1.00  1.00
ATOM    687  C   PHE   247      22.063  33.149  -1.140  1.00  1.00
ATOM    688  O   PHE   247      22.138  32.227  -1.971  1.00  1.00
ATOM    689  CB  PHE   247      20.908  35.279  -1.806  1.00  1.00
ATOM    690  N   GLU   248      23.082  33.449  -0.338  1.00  1.00
ATOM    691  CA  GLU   248      24.360  32.728  -0.390  1.00  1.00
ATOM    692  C   GLU   248      24.200  31.297   0.115  1.00  1.00
ATOM    693  O   GLU   248      24.679  30.366  -0.546  1.00  1.00
ATOM    694  CB  GLU   248      25.412  33.487   0.418  1.00  1.00
ATOM    695  N   TRP   249      23.540  31.158   1.266  1.00  1.00
ATOM    696  CA  TRP   249      23.223  29.853   1.825  1.00  1.00
ATOM    697  C   TRP   249      22.318  29.049   0.892  1.00  1.00
ATOM    698  O   TRP   249      22.438  27.825   0.827  1.00  1.00
ATOM    699  CB  TRP   249      22.509  29.953   3.171  1.00  1.00
ATOM    700  N   GLU   250      21.411  29.731   0.187  1.00  1.00
ATOM    701  CA  GLU   250      20.518  28.999  -0.714  1.00  1.00
ATOM    702  C   GLU   250      21.299  28.429  -1.895  1.00  1.00
ATOM    703  O   GLU   250      21.049  27.281  -2.257  1.00  1.00
ATOM    704  CB  GLU   250      19.358  29.856  -1.219  1.00  1.00
ATOM    705  N   ILE   251      22.202  29.217  -2.454  1.00  1.00
ATOM    706  CA  ILE   251      23.040  28.812  -3.566  1.00  1.00
ATOM    707  C   ILE   251      23.945  27.649  -3.167  1.00  1.00
ATOM    708  O   ILE   251      24.220  26.749  -3.964  1.00  1.00
ATOM    709  CB  ILE   251      23.934  29.943  -4.065  1.00  1.00
ATOM    710  N   ILE   252      24.417  27.718  -1.921  1.00  1.00
ATOM    711  CA  ILE   252      25.338  26.656  -1.482  1.00  1.00
ATOM    712  C   ILE   252      24.594  25.354  -1.289  1.00  1.00
ATOM    713  O   ILE   252      25.144  24.281  -1.571  1.00  1.00
ATOM    714  CB  ILE   252      26.087  27.115  -0.211  1.00  1.00
ATOM    715  N   HIS   253      23.329  25.371  -0.852  1.00  1.00
ATOM    716  CA  HIS   253      22.664  24.082  -0.677  1.00  1.00
ATOM    717  C   HIS   253      21.775  23.640  -1.837  1.00  1.00
ATOM    718  O   HIS   253      21.340  22.482  -1.823  1.00  1.00
ATOM    719  CB  HIS   253      21.813  24.111   0.601  1.00  1.00
ATOM    720  N   ALA   254      21.482  24.482  -2.818  1.00  1.00
ATOM    721  CA  ALA   254      20.536  24.143  -3.885  1.00  1.00
ATOM    722  C   ALA   254      21.023  22.969  -4.709  1.00  1.00
ATOM    723  O   ALA   254      22.212  22.838  -4.993  1.00  1.00
ATOM    724  CB  ALA   254      20.288  25.356  -4.785  1.00  1.00
ATOM    725  N   PHE   255      20.079  22.111  -5.106  1.00  1.00
ATOM    726  CA  PHE   255      20.433  20.962  -5.924  1.00  1.00
ATOM    727  C   PHE   255      19.313  20.731  -6.937  1.00  1.00
ATOM    728  O   PHE   255      18.162  20.927  -6.570  1.00  1.00
ATOM    729  CB  PHE   255      20.678  19.725  -5.068  1.00  1.00
ATOM    730  N   GLY   256      19.647  20.349  -8.163  1.00  1.00
ATOM    731  CA  GLY   256      18.648  20.131  -9.194  1.00  1.00
ATOM    732  C   GLY   256      17.621  19.069  -8.799  1.00  1.00
ATOM    733  O   GLY   256      18.027  18.127  -8.099  1.00  1.00
TER
END
