
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0316AL044_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_4-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    E     289      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    A     290      T     304          3.337
LGA    S     291      L     305           -
LGA    Q     292      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    V     293      K     325          4.644
LGA    H     294      G     326          1.710
LGA    -       -      E     327           -
LGA    F     295      K     328          4.986
LGA    T     296      T     329          3.863
LGA    R     297      E     330          4.609
LGA    E     298      V     331          3.385
LGA    M     299      I     332          1.912
LGA    P     300      F     333          1.481
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    E     301      Q     337          4.745
LGA    -       -      R     338           -
LGA    E     302      A     339           #
LGA    F     303      I     340          3.355
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    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    T     304      N     362          1.815
LGA    L     305      A     363          2.532
LGA    C     307      Y     364          3.333
LGA    T     308      R     365          1.773
LGA    A     309      D     366          2.179
LGA    K     310      G     367          1.648
LGA    F     311      Q     368          3.868
LGA    K     319      V     369          4.245
LGA    V     320      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   90    5.0     19    3.34     5.26     11.626     0.552

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.129930 * X  +   0.588783 * Y  +  -0.797780 * Z  +  78.665359
  Y_new =  -0.118089 * X  +   0.789685 * Y  +   0.602041 * Z  + -47.397385
  Z_new =   0.984466 * X  +   0.172432 * Y  +  -0.033075 * Z  +  50.483955 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.760309   -1.381284  [ DEG:   100.8583    -79.1417 ]
  Theta =  -1.394306   -1.747287  [ DEG:   -79.8878   -100.1122 ]
  Phi   =  -2.403900    0.737692  [ DEG:  -137.7334     42.2667 ]
 
# 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: T0316AL044_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_4-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   90   5.0   19   3.34    5.26  11.626
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_4-D3
REMARK Aligment from pdb entry: 1wy5_A
ATOM    789  N   GLU   289      18.445  -5.242   0.742  1.00  0.00              
ATOM    790  CA  GLU   289      18.342  -4.874   2.161  1.00  0.00              
ATOM    791  C   GLU   289      19.503  -3.997   2.636  1.00  0.00              
ATOM    792  O   GLU   289      20.653  -4.212   2.250  1.00  0.00              
ATOM    793  N   ALA   290      19.199  -3.021   3.485  1.00  0.00              
ATOM    794  CA  ALA   290      20.215  -2.106   4.003  1.00  0.00              
ATOM    795  C   ALA   290      21.456  -2.837   4.523  1.00  0.00              
ATOM    796  O   ALA   290      22.590  -2.460   4.211  1.00  0.00              
ATOM    797  N   SER   291      21.234  -3.881   5.319  1.00  0.00              
ATOM    798  CA  SER   291      22.327  -4.652   5.902  1.00  0.00              
ATOM    799  C   SER   291      23.293  -5.179   4.853  1.00  0.00              
ATOM    800  O   SER   291      24.507  -5.037   4.995  1.00  0.00              
ATOM    801  N   GLN   292      22.759  -5.785   3.799  1.00  0.00              
ATOM    802  CA  GLN   292      23.614  -6.330   2.752  1.00  0.00              
ATOM    803  C   GLN   292      24.266  -5.236   1.904  1.00  0.00              
ATOM    804  O   GLN   292      25.363  -5.427   1.377  1.00  0.00              
ATOM    805  N   VAL   293      35.803  -0.557   7.259  1.00  0.00              
ATOM    806  CA  VAL   293      34.721  -0.830   8.201  1.00  0.00              
ATOM    807  C   VAL   293      34.104   0.439   8.793  1.00  0.00              
ATOM    808  O   VAL   293      33.002   0.394   9.340  1.00  0.00              
ATOM    809  N   HIS   294      34.806   1.563   8.675  1.00  0.00              
ATOM    810  CA  HIS   294      34.330   2.846   9.203  1.00  0.00              
ATOM    811  C   HIS   294      32.883   3.151   8.835  1.00  0.00              
ATOM    812  O   HIS   294      32.551   3.323   7.661  1.00  0.00              
ATOM    813  N   PHE   295      29.802   6.341   0.994  1.00  0.00              
ATOM    814  CA  PHE   295      29.915   5.636  -0.271  1.00  0.00              
ATOM    815  C   PHE   295      28.542   5.077  -0.651  1.00  0.00              
ATOM    816  O   PHE   295      28.147   5.101  -1.815  1.00  0.00              
ATOM    817  N   THR   296      27.801   4.593   0.337  1.00  0.00              
ATOM    818  CA  THR   296      26.482   4.031   0.077  1.00  0.00              
ATOM    819  C   THR   296      25.545   5.036  -0.592  1.00  0.00              
ATOM    820  O   THR   296      24.720   4.662  -1.428  1.00  0.00              
ATOM    821  N   ARG   297      25.675   6.309  -0.228  1.00  0.00              
ATOM    822  CA  ARG   297      24.822   7.352  -0.788  1.00  0.00              
ATOM    823  C   ARG   297      24.948   7.497  -2.301  1.00  0.00              
ATOM    824  O   ARG   297      24.019   7.969  -2.959  1.00  0.00              
ATOM    825  N   GLU   298      26.084   7.090  -2.859  1.00  0.00              
ATOM    826  CA  GLU   298      26.277   7.193  -4.302  1.00  0.00              
ATOM    827  C   GLU   298      25.420   6.173  -5.038  1.00  0.00              
ATOM    828  O   GLU   298      25.469   6.067  -6.264  1.00  0.00              
ATOM    829  N   MET   299      24.628   5.425  -4.279  1.00  0.00              
ATOM    830  CA  MET   299      23.740   4.428  -4.856  1.00  0.00              
ATOM    831  C   MET   299      22.415   5.090  -5.240  1.00  0.00              
ATOM    832  O   MET   299      21.598   4.500  -5.952  1.00  0.00              
ATOM    833  N   PRO   300      22.209   6.321  -4.772  1.00  0.00              
ATOM    834  CA  PRO   300      20.971   7.036  -5.061  1.00  0.00              
ATOM    835  C   PRO   300      21.179   8.354  -5.807  1.00  0.00              
ATOM    836  O   PRO   300      20.229   8.907  -6.366  1.00  0.00              
ATOM    837  N   GLU   301      22.413   8.857  -5.809  1.00  0.00              
ATOM    838  CA  GLU   301      22.734  10.107  -6.495  1.00  0.00              
ATOM    839  C   GLU   301      24.181  10.110  -6.987  1.00  0.00              
ATOM    840  O   GLU   301      25.107   9.888  -6.209  1.00  0.00              
ATOM    841  N   GLU   302      24.368  10.363  -8.280  1.00  0.00              
ATOM    842  CA  GLU   302      25.706  10.391  -8.849  1.00  0.00              
ATOM    843  C   GLU   302      26.686  11.259  -8.077  1.00  0.00              
ATOM    844  O   GLU   302      26.282  12.104  -7.275  1.00  0.00              
ATOM    845  N   PHE   303      27.977  11.053  -8.316  1.00  0.00              
ATOM    846  CA  PHE   303      28.990  11.834  -7.626  1.00  0.00              
ATOM    847  C   PHE   303      30.297  11.085  -7.449  1.00  0.00              
ATOM    848  O   PHE   303      30.537  10.076  -8.111  1.00  0.00              
ATOM    849  N   THR   304      31.146  11.581  -6.554  1.00  0.00              
ATOM    850  CA  THR   304      32.435  10.952  -6.290  1.00  0.00              
ATOM    851  C   THR   304      32.763  10.979  -4.797  1.00  0.00              
ATOM    852  O   THR   304      32.250  11.818  -4.057  1.00  0.00              
ATOM    853  N   LEU   305      30.271   7.434  -9.740  1.00  0.00              
ATOM    854  CA  LEU   305      29.012   6.820 -10.149  1.00  0.00              
ATOM    855  C   LEU   305      28.848   7.105 -11.640  1.00  0.00              
ATOM    856  O   LEU   305      28.536   8.227 -12.042  1.00  0.00              
ATOM    857  N   CYS   307      29.082   6.084 -12.456  1.00  0.00              
ATOM    858  CA  CYS   307      28.968   6.210 -13.901  1.00  0.00              
ATOM    859  C   CYS   307      27.691   5.519 -14.365  1.00  0.00              
ATOM    860  O   CYS   307      27.745   4.429 -14.931  1.00  0.00              
ATOM    861  N   THR   308      26.551   6.160 -14.115  1.00  0.00              
ATOM    862  CA  THR   308      25.244   5.624 -14.497  1.00  0.00              
ATOM    863  C   THR   308      25.131   4.104 -14.349  1.00  0.00              
ATOM    864  O   THR   308      25.545   3.352 -15.228  1.00  0.00              
ATOM    865  N   ALA   309      24.570   3.660 -13.229  1.00  0.00              
ATOM    866  CA  ALA   309      24.382   2.236 -12.965  1.00  0.00              
ATOM    867  C   ALA   309      25.624   1.495 -12.470  1.00  0.00              
ATOM    868  O   ALA   309      25.502   0.506 -11.750  1.00  0.00              
ATOM    869  N   LYS   310      26.812   1.957 -12.850  1.00  0.00              
ATOM    870  CA  LYS   310      28.042   1.297 -12.414  1.00  0.00              
ATOM    871  C   LYS   310      28.755   2.141 -11.358  1.00  0.00              
ATOM    872  O   LYS   310      28.259   3.196 -10.965  1.00  0.00              
ATOM    873  N   PHE   311      29.916   1.675 -10.900  1.00  0.00              
ATOM    874  CA  PHE   311      30.682   2.391  -9.880  1.00  0.00              
ATOM    875  C   PHE   311      32.089   1.811  -9.669  1.00  0.00              
ATOM    876  O   PHE   311      32.224   0.643  -9.316  1.00  0.00              
ATOM    877  N   LYS   319      33.124   2.635  -9.849  1.00  0.00              
ATOM    878  CA  LYS   319      34.512   2.176  -9.710  1.00  0.00              
ATOM    879  C   LYS   319      35.230   2.406  -8.380  1.00  0.00              
ATOM    880  O   LYS   319      34.848   3.259  -7.582  1.00  0.00              
ATOM    881  N   VAL   320      36.294   1.621  -8.202  1.00  0.00              
ATOM    882  CA  VAL   320      37.219   1.609  -7.067  1.00  0.00              
ATOM    883  C   VAL   320      37.475   0.177  -6.631  1.00  0.00              
ATOM    884  O   VAL   320      36.894  -0.249  -5.611  1.00  0.00              
END
