
#######################################################
#                                                     #
#                        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   19 (   80),  selected   19 , name T0386AL242_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL242_1-D2.T0386_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     219      N     219          4.331
LGA    P     220      P     220          2.996
LGA    E     221      E     221          4.500
LGA    K     222      K     222          3.491
LGA    I     223      I     223          4.234
LGA    R     224      R     224          2.926
LGA    L     225      L     225          4.064
LGA    L     226      -       -           -
LGA    K     227      L     226           #
LGA    E     228      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    F     229      G     265          4.331
LGA    M     230      F     266          2.646
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    H     231      I     279          1.928
LGA    T     232      D     280          1.942
LGA    -       -      H     281           -
LGA    M     233      L     282          2.202
LGA    K     234      P     283           #
LGA    N     235      P     284          2.535
LGA    T     236      E     285          2.966
LGA    G     237      Q     286          0.857
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   81    5.0     15    3.24    46.67     11.995     0.449

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.266195 * X  +   0.963817 * Y  +  -0.014039 * Z  + -48.548649
  Y_new =   0.377825 * X  +  -0.117728 * Y  +  -0.918362 * Z  +  65.975807
  Z_new =  -0.886786 * X  +   0.239159 * Y  +  -0.395493 * Z  +  59.961891 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.597717   -0.543876  [ DEG:   148.8382    -31.1618 ]
  Theta =   1.090343    2.051250  [ DEG:    62.4721    117.5279 ]
  Phi   =   0.957026   -2.184566  [ DEG:    54.8336   -125.1664 ]
 
# 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: T0386AL242_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL242_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   81   5.0   15   3.24   46.67  11.995
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL242_1-D2
REMARK Aligment from pdb entry: 2g03_A
ATOM    649  N   ASN   219      -0.543  57.423  77.271  1.00  0.00              
ATOM    650  CA  ASN   219       0.329  56.491  77.998  1.00  0.00              
ATOM    651  C   ASN   219       1.733  56.365  77.387  1.00  0.00              
ATOM    652  O   ASN   219       2.650  55.831  78.040  1.00  0.00              
ATOM    653  N   PRO   220       1.892  56.852  76.157  1.00  0.00              
ATOM    654  CA  PRO   220       3.138  56.696  75.414  1.00  0.00              
ATOM    655  C   PRO   220       3.773  58.034  75.060  1.00  0.00              
ATOM    656  O   PRO   220       4.683  58.099  74.249  1.00  0.00              
ATOM    657  N   GLU   221       3.282  59.093  75.673  1.00  0.00              
ATOM    658  CA  GLU   221       3.796  60.424  75.431  1.00  0.00              
ATOM    659  C   GLU   221       5.215  60.585  76.006  1.00  0.00              
ATOM    660  O   GLU   221       5.458  60.298  77.178  1.00  0.00              
ATOM    661  N   LYS   222       6.158  61.008  75.167  1.00  0.00              
ATOM    662  CA  LYS   222       7.552  61.155  75.585  1.00  0.00              
ATOM    663  C   LYS   222       7.732  62.058  76.824  1.00  0.00              
ATOM    664  O   LYS   222       8.515  61.734  77.712  1.00  0.00              
ATOM    665  N   ILE   223       6.995  63.161  76.897  1.00  0.00              
ATOM    666  CA  ILE   223       7.141  64.096  78.000  1.00  0.00              
ATOM    667  C   ILE   223       6.628  63.514  79.325  1.00  0.00              
ATOM    668  O   ILE   223       7.273  63.658  80.378  1.00  0.00              
ATOM    669  N   ARG   224       5.476  62.846  79.274  1.00  0.00              
ATOM    670  CA  ARG   224       4.920  62.166  80.436  1.00  0.00              
ATOM    671  C   ARG   224       5.853  61.052  80.888  1.00  0.00              
ATOM    672  O   ARG   224       6.121  60.920  82.084  1.00  0.00              
ATOM    673  N   LEU   225       6.358  60.251  79.952  1.00  0.00              
ATOM    674  CA  LEU   225       7.285  59.177  80.323  1.00  0.00              
ATOM    675  C   LEU   225       8.571  59.759  80.973  1.00  0.00              
ATOM    676  O   LEU   225       8.902  59.443  82.111  1.00  0.00              
ATOM    677  N   LEU   226       9.262  60.643  80.277  1.00  0.00              
ATOM    678  CA  LEU   226      10.556  61.108  80.760  1.00  0.00              
ATOM    679  C   LEU   226      10.541  62.071  81.962  1.00  0.00              
ATOM    680  O   LEU   226      11.382  61.934  82.837  1.00  0.00              
ATOM    681  N   LYS   227       9.602  63.016  82.006  1.00  0.00              
ATOM    682  CA  LYS   227       9.434  63.863  83.188  1.00  0.00              
ATOM    683  C   LYS   227       8.959  63.033  84.373  1.00  0.00              
ATOM    684  O   LYS   227       9.271  63.355  85.522  1.00  0.00              
ATOM    685  N   GLU   228       8.213  61.961  84.088  1.00  0.00              
ATOM    686  CA  GLU   228       7.761  61.021  85.094  1.00  0.00              
ATOM    687  C   GLU   228       8.884  60.215  85.715  1.00  0.00              
ATOM    688  O   GLU   228       8.931  60.052  86.929  1.00  0.00              
ATOM    689  N   PHE   229       9.767  59.667  84.883  1.00  0.00              
ATOM    690  CA  PHE   229      10.980  58.989  85.337  1.00  0.00              
ATOM    691  C   PHE   229      11.833  59.928  86.199  1.00  0.00              
ATOM    692  O   PHE   229      12.314  59.532  87.251  1.00  0.00              
ATOM    693  N   MET   230      12.034  61.160  85.750  1.00  0.00              
ATOM    694  CA  MET   230      12.742  62.134  86.574  1.00  0.00              
ATOM    695  C   MET   230      12.092  62.375  87.940  1.00  0.00              
ATOM    696  O   MET   230      12.796  62.508  88.931  1.00  0.00              
ATOM    697  N   HIS   231      10.765  62.446  87.987  1.00  0.00              
ATOM    698  CA  HIS   231      10.072  62.692  89.245  1.00  0.00              
ATOM    699  C   HIS   231      10.178  61.463  90.145  1.00  0.00              
ATOM    700  O   HIS   231      10.471  61.583  91.319  1.00  0.00              
ATOM    701  N   THR   232       9.955  60.279  89.578  1.00  0.00              
ATOM    702  CA  THR   232      10.105  59.016  90.279  1.00  0.00              
ATOM    703  C   THR   232      11.459  58.873  90.982  1.00  0.00              
ATOM    704  O   THR   232      11.528  58.429  92.140  1.00  0.00              
ATOM    705  N  AMET   233      12.529  59.226  90.274  1.00  0.00              
ATOM    706  N  BMET   233      12.511  59.221  90.264  1.00  0.00              
ATOM    707  CA AMET   233      13.898  59.153  90.804  1.00  0.00              
ATOM    708  CA BMET   233      13.861  59.148  90.772  1.00  0.00              
ATOM    709  C  AMET   233      14.170  60.216  91.872  1.00  0.00              
ATOM    710  C  BMET   233      14.078  60.156  91.908  1.00  0.00              
ATOM    711  O  AMET   233      15.046  60.042  92.738  1.00  0.00              
ATOM    712  O  BMET   233      14.846  59.891  92.843  1.00  0.00              
ATOM    713  N   LYS   234      13.419  61.312  91.802  1.00  0.00              
ATOM    714  CA  LYS   234      13.477  62.373  92.813  1.00  0.00              
ATOM    715  C   LYS   234      12.839  61.948  94.169  1.00  0.00              
ATOM    716  O   LYS   234      13.301  62.359  95.233  1.00  0.00              
ATOM    717  N   ASN   235      11.817  61.096  94.124  1.00  0.00              
ATOM    718  CA  ASN   235      11.089  60.686  95.317  1.00  0.00              
ATOM    719  C   ASN   235      12.019  60.051  96.323  1.00  0.00              
ATOM    720  O   ASN   235      11.817  60.181  97.532  1.00  0.00              
ATOM    721  N   THR   236      13.059  59.374  95.851  1.00  0.00              
ATOM    722  CA  THR   236      13.932  58.719  96.829  1.00  0.00              
ATOM    723  C   THR   236      15.360  59.214  96.783  1.00  0.00              
ATOM    724  O   THR   236      16.255  58.502  97.199  1.00  0.00              
ATOM    725  N   GLY   237      15.564  60.454  96.342  1.00  0.00              
ATOM    726  CA  GLY   237      16.915  61.027  96.230  1.00  0.00              
ATOM    727  C   GLY   237      16.906  62.521  95.961  1.00  0.00              
ATOM    728  O   GLY   237      17.866  63.085  95.407  1.00  0.00              
END
