
#######################################################
#                                                     #
#                        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 (   44),  selected   11 , name T0316AL333_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL333_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    Q     344      Q     337          0.655
LGA    A     345      R     338          0.712
LGA    V     346      A     339          1.939
LGA    V     347      I     340          2.224
LGA    F     348      T     341          1.915
LGA    Y     349      P     342          2.274
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    D     350      N     362          3.467
LGA    G     351      A     363          2.590
LGA    Q     371      Y     364          1.844
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    Y     372      C     370          1.459
LGA    I     373      Q     371          1.774
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11   90    5.0     11    2.04     9.09      9.531     0.513

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.586057 * X  +   0.035797 * Y  +  -0.809479 * Z  +  33.067345
  Y_new =  -0.603793 * X  +  -0.646925 * Y  +  -0.465749 * Z  +  76.198311
  Z_new =  -0.540344 * X  +   0.761713 * Y  +  -0.357521 * Z  + -44.922535 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.009637   -1.131956  [ DEG:   115.1437    -64.8563 ]
  Theta =   0.570846    2.570746  [ DEG:    32.7071    147.2929 ]
  Phi   =  -0.800303    2.341290  [ DEG:   -45.8540    134.1460 ]
 
# 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: T0316AL333_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   90   5.0   11   2.04    9.09   9.531
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_5-D3
REMARK Aligment from pdb entry: 1kqp_A
ATOM    861  N   GLN   344      20.876  10.777 -10.179  1.00  0.00              
ATOM    862  CA  GLN   344      20.626  12.203  -9.922  1.00  0.00              
ATOM    863  C   GLN   344      21.709  13.020 -10.582  1.00  0.00              
ATOM    864  O   GLN   344      22.732  12.485 -11.025  1.00  0.00              
ATOM    865  N   ALA   345      21.514  14.328 -10.768  1.00  0.00              
ATOM    866  CA  ALA   345      22.527  15.137 -11.490  1.00  0.00              
ATOM    867  C   ALA   345      23.920  14.937 -10.897  1.00  0.00              
ATOM    868  O   ALA   345      24.119  14.821  -9.702  1.00  0.00              
ATOM    869  N   VAL   346      24.902  14.870 -11.788  1.00  0.00              
ATOM    870  CA  VAL   346      26.257  14.575 -11.384  1.00  0.00              
ATOM    871  C   VAL   346      26.920  15.701 -10.612  1.00  0.00              
ATOM    872  O   VAL   346      26.804  16.864 -10.958  1.00  0.00              
ATOM    873  N   VAL   347      27.660  15.334  -9.580  1.00  0.00              
ATOM    874  CA  VAL   347      28.577  16.214  -8.915  1.00  0.00              
ATOM    875  C   VAL   347      29.982  15.641  -8.837  1.00  0.00              
ATOM    876  O   VAL   347      30.221  14.484  -9.202  1.00  0.00              
ATOM    877  N   PHE   348      30.904  16.456  -8.373  1.00  0.00              
ATOM    878  CA  PHE   348      32.309  16.053  -8.287  1.00  0.00              
ATOM    879  C   PHE   348      32.520  14.977  -7.250  1.00  0.00              
ATOM    880  O   PHE   348      33.571  14.340  -7.205  1.00  0.00              
ATOM    881  N   TYR   349      31.607  14.742  -6.392  1.00  0.00              
ATOM    882  CA  TYR   349      31.589  13.706  -5.344  1.00  0.00              
ATOM    883  C   TYR   349      31.105  12.374  -5.843  1.00  0.00              
ATOM    884  O   TYR   349      31.235  11.375  -5.110  1.00  0.00              
ATOM    885  N   ASP   350      30.534  12.317  -7.031  1.00  0.00              
ATOM    886  CA  ASP   350      30.065  11.047  -7.600  1.00  0.00              
ATOM    887  C   ASP   350      31.220  10.407  -8.361  1.00  0.00              
ATOM    888  O   ASP   350      32.056  11.154  -8.894  1.00  0.00              
ATOM    889  N   GLY   351      31.287   9.085  -8.371  1.00  0.00              
ATOM    890  CA  GLY   351      32.320   8.400  -9.138  1.00  0.00              
ATOM    891  C   GLY   351      31.739   7.757 -10.372  1.00  0.00              
ATOM    892  O   GLY   351      32.538   7.389 -11.240  1.00  0.00              
ATOM    893  N   GLN   371      30.444   7.558 -10.506  1.00  0.00              
ATOM    894  CA  GLN   371      29.922   6.688 -11.563  1.00  0.00              
ATOM    895  C   GLN   371      30.295   7.183 -12.954  1.00  0.00              
ATOM    896  O   GLN   371      30.357   6.356 -13.874  1.00  0.00              
ATOM    897  N   TYR   372      30.478   8.481 -13.116  1.00  0.00              
ATOM    898  CA  TYR   372      30.639   9.109 -14.429  1.00  0.00              
ATOM    899  C   TYR   372      32.072   9.135 -14.920  1.00  0.00              
ATOM    900  O   TYR   372      32.349   9.492 -16.082  1.00  0.00              
ATOM    901  N   ILE   373      33.022   8.803 -14.060  1.00  0.00              
ATOM    902  CA  ILE   373      34.434   8.986 -14.399  1.00  0.00              
ATOM    903  C   ILE   373      34.989   7.982 -15.399  1.00  0.00              
ATOM    904  O   ILE   373      36.046   8.304 -16.021  1.00  0.00              
END
