
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0316AL333_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL333_2-D3.T0316_D3.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    -       -      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    M     284      H     294          2.515
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     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
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    S     285      L     355          4.759
LGA    T     286      G     356          4.502
LGA    S     287      G     357          3.291
LGA    D     361      G     358          3.363
LGA    N     362      -       -           -
LGA    A     363      L     359          1.709
LGA    Y     364      I     360          3.182
LGA    R     365      -       -           -
LGA    D     366      -       -           -
LGA    G     367      D     361          1.857
LGA    Q     368      N     362          1.852
LGA    V     369      A     363          1.593
LGA    C     370      Y     364           #
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    Q     371      V     369          4.449
LGA    Y     372      C     370          2.055
LGA    I     373      Q     371          2.792
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17   90    5.0     13    3.11     0.00      9.443     0.405

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.021023 * X  +  -0.004480 * Y  +   0.999769 * Z  +  31.741913
  Y_new =   0.963206 * X  +  -0.267905 * Y  +  -0.021455 * Z  +   1.870695
  Z_new =   0.267939 * X  +   0.963435 * Y  +  -0.001317 * Z  + -62.070217 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.572163   -1.569429  [ DEG:    90.0783    -89.9217 ]
  Theta =  -0.271253   -2.870339  [ DEG:   -15.5417   -164.4583 ]
  Phi   =   1.548974   -1.592619  [ DEG:    88.7497    -91.2503 ]
 
# 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_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_2-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17   90   5.0   13   3.11    0.00   9.443
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_2-D3
REMARK Aligment from pdb entry: 1ni5_A
ATOM    805  N   MET   284      27.391  12.508  10.320  1.00  0.00              
ATOM    806  CA  MET   284      27.577  11.262   9.578  1.00  0.00              
ATOM    807  C   MET   284      26.849  11.443   8.258  1.00  0.00              
ATOM    808  O   MET   284      27.277  10.945   7.217  1.00  0.00              
ATOM    809  N   SER   285      25.741  12.171   8.321  1.00  0.00              
ATOM    810  CA  SER   285      24.942  12.453   7.146  1.00  0.00              
ATOM    811  C   SER   285      25.804  13.238   6.169  1.00  0.00              
ATOM    812  O   SER   285      25.867  12.903   4.985  1.00  0.00              
ATOM    813  N   THR   286      26.477  14.277   6.656  1.00  0.00              
ATOM    814  CA  THR   286      27.340  15.060   5.780  1.00  0.00              
ATOM    815  C   THR   286      28.477  14.189   5.256  1.00  0.00              
ATOM    816  O   THR   286      28.789  14.210   4.064  1.00  0.00              
ATOM    817  N   SER   287      29.107  13.427   6.141  1.00  0.00              
ATOM    818  CA  SER   287      30.196  12.572   5.708  1.00  0.00              
ATOM    819  C   SER   287      29.691  11.723   4.557  1.00  0.00              
ATOM    820  O   SER   287      30.316  11.655   3.501  1.00  0.00              
ATOM    821  N   ASP   361      28.536  11.098   4.759  1.00  0.00              
ATOM    822  CA  ASP   361      27.959  10.229   3.750  1.00  0.00              
ATOM    823  C   ASP   361      27.734  10.935   2.435  1.00  0.00              
ATOM    824  O   ASP   361      27.956  10.356   1.371  1.00  0.00              
ATOM    825  N   ASN   362      27.288  12.183   2.494  1.00  0.00              
ATOM    826  CA  ASN   362      27.031  12.934   1.270  1.00  0.00              
ATOM    827  C   ASN   362      28.323  13.280   0.532  1.00  0.00              
ATOM    828  O   ASN   362      28.357  13.297  -0.699  1.00  0.00              
ATOM    829  N   ALA   363      29.384  13.553   1.284  1.00  0.00              
ATOM    830  CA  ALA   363      30.655  13.863   0.670  1.00  0.00              
ATOM    831  C   ALA   363      31.106  12.627  -0.067  1.00  0.00              
ATOM    832  O   ALA   363      31.605  12.705  -1.191  1.00  0.00              
ATOM    833  N   TYR   364      30.927  11.478   0.571  1.00  0.00              
ATOM    834  CA  TYR   364      31.311  10.218  -0.038  1.00  0.00              
ATOM    835  C   TYR   364      30.514   9.988  -1.326  1.00  0.00              
ATOM    836  O   TYR   364      31.089   9.653  -2.358  1.00  0.00              
ATOM    837  N   ARG   365      29.200  10.181  -1.281  1.00  0.00              
ATOM    838  CA  ARG   365      28.399   9.983  -2.478  1.00  0.00              
ATOM    839  C   ARG   365      28.917  10.813  -3.639  1.00  0.00              
ATOM    840  O   ARG   365      28.938  10.359  -4.778  1.00  0.00              
ATOM    841  N   ASP   366      29.337  12.035  -3.353  1.00  0.00              
ATOM    842  CA  ASP   366      29.838  12.909  -4.404  1.00  0.00              
ATOM    843  C   ASP   366      31.177  12.430  -4.955  1.00  0.00              
ATOM    844  O   ASP   366      31.413  12.488  -6.160  1.00  0.00              
ATOM    845  N   GLY   367      32.060  11.960  -4.076  1.00  0.00              
ATOM    846  CA  GLY   367      33.362  11.484  -4.535  1.00  0.00              
ATOM    847  C   GLY   367      33.162  10.270  -5.426  1.00  0.00              
ATOM    848  O   GLY   367      33.904  10.066  -6.381  1.00  0.00              
ATOM    849  N   GLN   368      32.151   9.467  -5.126  1.00  0.00              
ATOM    850  CA  GLN   368      31.902   8.293  -5.939  1.00  0.00              
ATOM    851  C   GLN   368      31.260   8.743  -7.238  1.00  0.00              
ATOM    852  O   GLN   368      31.423   8.092  -8.266  1.00  0.00              
ATOM    853  N   VAL   369      30.531   9.858  -7.192  1.00  0.00              
ATOM    854  CA  VAL   369      29.903  10.382  -8.401  1.00  0.00              
ATOM    855  C   VAL   369      31.051  10.757  -9.327  1.00  0.00              
ATOM    856  O   VAL   369      31.033  10.428 -10.513  1.00  0.00              
ATOM    857  N   CYS   370      32.055  11.436  -8.783  1.00  0.00              
ATOM    858  CA  CYS   370      33.209  11.810  -9.582  1.00  0.00              
ATOM    859  C   CYS   370      33.908  10.559 -10.068  1.00  0.00              
ATOM    860  O   CYS   370      34.369  10.518 -11.205  1.00  0.00              
ATOM    861  N   GLN   371      33.997   9.544  -9.214  1.00  0.00              
ATOM    862  CA  GLN   371      34.638   8.294  -9.610  1.00  0.00              
ATOM    863  C   GLN   371      34.009   7.820 -10.920  1.00  0.00              
ATOM    864  O   GLN   371      34.698   7.463 -11.886  1.00  0.00              
ATOM    865  N   TYR   372      32.687   7.828 -10.943  1.00  0.00              
ATOM    866  CA  TYR   372      31.950   7.416 -12.114  1.00  0.00              
ATOM    867  C   TYR   372      32.328   8.355 -13.245  1.00  0.00              
ATOM    868  O   TYR   372      32.889   7.942 -14.250  1.00  0.00              
ATOM    869  N   ILE   373      32.055   9.634 -13.049  1.00  0.00              
ATOM    870  CA  ILE   373      32.327  10.652 -14.048  1.00  0.00              
ATOM    871  C   ILE   373      33.732  10.735 -14.599  1.00  0.00              
ATOM    872  O   ILE   373      33.917  11.183 -15.732  1.00  0.00              
END
