
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0316AL316_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL316_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    -       -      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     298      E     301          3.937
LGA    M     299      E     302          2.912
LGA    P     300      F     303          3.538
LGA    E     301      T     304          2.101
LGA    E     302      L     305          3.127
LGA    F     303      E     306           #
LGA    T     304      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    L     305      T     321          1.848
LGA    E     306      V     322          1.399
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    C     307      V     331          2.220
LGA    T     308      I     332          0.560
LGA    A     309      F     333          3.904
LGA    K     310      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    F     311      Q     337           #
LGA    R     312      R     338           #
LGA    Y     313      A     339           #
LGA    R     314      I     340          3.191
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    Q     315      G     343           #
LGA    P     316      Q     344          3.515
LGA    D     317      A     345          3.477
LGA    S     318      V     346          3.971
LGA    K     319      V     347          1.882
LGA    V     320      F     348          5.076
LGA    F     348      Y     349          5.360
LGA    Y     349      D     350           #
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    D     350      C     354          1.671
LGA    G     351      L     355          1.796
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   90    5.0     19    3.17     5.26     13.199     0.581

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.201928 * X  +   0.459566 * Y  +  -0.864884 * Z  +  80.182060
  Y_new =  -0.050409 * X  +   0.877028 * Y  +   0.477788 * Z  + -93.059006
  Z_new =   0.978102 * X  +   0.140076 * Y  +  -0.153931 * Z  +   4.077734 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.403282   -0.738311  [ DEG:   137.6979    -42.3021 ]
  Theta =  -1.361139   -1.780454  [ DEG:   -77.9875   -102.0125 ]
  Phi   =  -2.896956    0.244636  [ DEG:  -165.9834     14.0166 ]
 
# 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: T0316AL316_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_4-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   90   5.0   19   3.17    5.26  13.199
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_4-D3
REMARK Aligment from pdb entry: 1ct9_A
ATOM    965  N   GLU   298      26.287   2.645   9.751  1.00  0.00              
ATOM    966  CA  GLU   298      26.681   1.720  10.827  1.00  0.00              
ATOM    967  C   GLU   298      26.113   0.292  10.687  1.00  0.00              
ATOM    968  O   GLU   298      26.362  -0.595  11.506  1.00  0.00              
ATOM    969  N   MET   299      25.299   0.086   9.666  1.00  0.00              
ATOM    970  CA  MET   299      24.668  -1.192   9.414  1.00  0.00              
ATOM    971  C   MET   299      24.633  -1.377   7.924  1.00  0.00              
ATOM    972  O   MET   299      24.759  -0.397   7.152  1.00  0.00              
ATOM    973  N   PRO   300      24.462  -2.652   7.566  1.00  0.00              
ATOM    974  CA  PRO   300      24.419  -3.092   6.185  1.00  0.00              
ATOM    975  C   PRO   300      23.273  -2.467   5.393  1.00  0.00              
ATOM    976  O   PRO   300      23.488  -2.118   4.216  1.00  0.00              
ATOM    977  N   GLU   301      22.096  -2.316   6.065  1.00  0.00              
ATOM    978  CA  GLU   301      20.910  -1.693   5.495  1.00  0.00              
ATOM    979  C   GLU   301      21.193  -0.220   5.239  1.00  0.00              
ATOM    980  O   GLU   301      20.996   0.234   4.129  1.00  0.00              
ATOM    981  N   GLU   302      21.735   0.468   6.256  1.00  0.00              
ATOM    982  CA  GLU   302      22.119   1.875   6.130  1.00  0.00              
ATOM    983  C   GLU   302      23.059   2.061   4.988  1.00  0.00              
ATOM    984  O   GLU   302      22.932   2.977   4.178  1.00  0.00              
ATOM    985  N   PHE   303      24.010   1.145   4.916  1.00  0.00              
ATOM    986  CA  PHE   303      24.992   1.176   3.869  1.00  0.00              
ATOM    987  C   PHE   303      24.385   1.020   2.477  1.00  0.00              
ATOM    988  O   PHE   303      24.767   1.711   1.522  1.00  0.00              
ATOM    989  N   THR   304      23.455   0.080   2.362  1.00  0.00              
ATOM    990  CA  THR   304      22.743  -0.209   1.114  1.00  0.00              
ATOM    991  C   THR   304      22.063   1.056   0.564  1.00  0.00              
ATOM    992  O   THR   304      22.219   1.464  -0.586  1.00  0.00              
ATOM    993  N   LEU   305      21.260   1.659   1.438  1.00  0.00              
ATOM    994  CA  LEU   305      20.524   2.853   1.134  1.00  0.00              
ATOM    995  C   LEU   305      21.461   4.015   0.865  1.00  0.00              
ATOM    996  O   LEU   305      21.254   4.796  -0.069  1.00  0.00              
ATOM    997  N   GLU   306      22.489   4.162   1.679  1.00  0.00              
ATOM    998  CA  GLU   306      23.435   5.257   1.477  1.00  0.00              
ATOM    999  C   GLU   306      24.112   5.151   0.104  1.00  0.00              
ATOM   1000  O   GLU   306      24.341   6.129  -0.631  1.00  0.00              
ATOM   1001  N   CYS   307      24.476   3.931  -0.252  1.00  0.00              
ATOM   1002  CA  CYS   307      25.145   3.700  -1.516  1.00  0.00              
ATOM   1003  C   CYS   307      24.275   4.146  -2.690  1.00  0.00              
ATOM   1004  O   CYS   307      24.733   4.738  -3.670  1.00  0.00              
ATOM   1005  N   THR   308      22.980   3.838  -2.648  1.00  0.00              
ATOM   1006  CA  THR   308      22.097   4.265  -3.743  1.00  0.00              
ATOM   1007  C   THR   308      21.950   5.775  -3.771  1.00  0.00              
ATOM   1008  O   THR   308      22.063   6.408  -4.819  1.00  0.00              
ATOM   1009  N   ALA   309      21.741   6.293  -2.569  1.00  0.00              
ATOM   1010  CA  ALA   309      21.594   7.705  -2.370  1.00  0.00              
ATOM   1011  C   ALA   309      22.728   8.454  -3.037  1.00  0.00              
ATOM   1012  O   ALA   309      22.517   9.316  -3.909  1.00  0.00              
ATOM   1013  N   LYS   310      23.940   8.129  -2.582  1.00  0.00              
ATOM   1014  CA  LYS   310      25.140   8.816  -3.081  1.00  0.00              
ATOM   1015  C   LYS   310      25.208   8.659  -4.555  1.00  0.00              
ATOM   1016  O   LYS   310      25.520   9.565  -5.329  1.00  0.00              
ATOM   1017  N   PHE   311      24.845   7.495  -4.944  1.00  0.00              
ATOM   1018  CA  PHE   311      24.871   7.237  -6.339  1.00  0.00              
ATOM   1019  C   PHE   311      23.945   8.155  -7.112  1.00  0.00              
ATOM   1020  O   PHE   311      24.203   8.528  -8.247  1.00  0.00              
ATOM   1021  N   ARG   312      22.850   8.525  -6.488  1.00  0.00              
ATOM   1022  CA  ARG   312      21.875   9.360  -7.163  1.00  0.00              
ATOM   1023  C   ARG   312      22.133  10.829  -6.998  1.00  0.00              
ATOM   1024  O   ARG   312      21.771  11.624  -7.863  1.00  0.00              
ATOM   1025  N   TYR   313      22.708  11.185  -5.853  1.00  0.00              
ATOM   1026  CA  TYR   313      22.959  12.577  -5.534  1.00  0.00              
ATOM   1027  C   TYR   313      24.401  12.748  -5.126  1.00  0.00              
ATOM   1028  O   TYR   313      24.724  12.893  -3.941  1.00  0.00              
ATOM   1029  N   ARG   314      25.253  12.640  -6.134  1.00  0.00              
ATOM   1030  CA  ARG   314      26.699  12.693  -6.018  1.00  0.00              
ATOM   1031  C   ARG   314      27.301  13.947  -5.359  1.00  0.00              
ATOM   1032  O   ARG   314      28.480  14.240  -5.491  1.00  0.00              
ATOM   1033  N   GLN   315      26.514  14.729  -4.665  1.00  0.00              
ATOM   1034  CA  GLN   315      27.065  15.941  -4.112  1.00  0.00              
ATOM   1035  C   GLN   315      27.146  15.927  -2.615  1.00  0.00              
ATOM   1036  O   GLN   315      26.172  15.652  -1.928  1.00  0.00              
ATOM   1037  N   PRO   316      28.334  16.221  -2.107  1.00  0.00              
ATOM   1038  CA  PRO   316      28.555  16.214  -0.681  1.00  0.00              
ATOM   1039  C   PRO   316      27.506  16.896   0.179  1.00  0.00              
ATOM   1040  O   PRO   316      27.057  16.313   1.166  1.00  0.00              
ATOM   1041  N   ASP   317      27.115  18.140  -0.133  1.00  0.00              
ATOM   1042  CA  ASP   317      26.157  18.787   0.720  1.00  0.00              
ATOM   1043  C   ASP   317      24.786  18.040   0.709  1.00  0.00              
ATOM   1044  O   ASP   317      23.955  18.205   1.589  1.00  0.00              
ATOM   1045  N   SER   318      24.515  17.244  -0.342  1.00  0.00              
ATOM   1046  CA  SER   318      23.248  16.508  -0.379  1.00  0.00              
ATOM   1047  C   SER   318      23.154  15.623   0.836  1.00  0.00              
ATOM   1048  O   SER   318      22.165  15.637   1.561  1.00  0.00              
ATOM   1049  N   LYS   319      24.223  14.840   1.047  1.00  0.00              
ATOM   1050  CA  LYS   319      24.309  13.894   2.145  1.00  0.00              
ATOM   1051  C   LYS   319      24.147  14.598   3.455  1.00  0.00              
ATOM   1052  O   LYS   319      23.663  14.050   4.451  1.00  0.00              
ATOM   1053  N   VAL   320      24.561  15.859   3.432  1.00  0.00              
ATOM   1054  CA  VAL   320      24.531  16.685   4.632  1.00  0.00              
ATOM   1055  C   VAL   320      23.195  17.254   5.012  1.00  0.00              
ATOM   1056  O   VAL   320      23.034  17.728   6.144  1.00  0.00              
ATOM   1057  N   PHE   348      22.260  17.219   4.067  1.00  0.00              
ATOM   1058  CA  PHE   348      20.914  17.690   4.330  1.00  0.00              
ATOM   1059  C   PHE   348      20.197  16.656   5.172  1.00  0.00              
ATOM   1060  O   PHE   348      19.208  16.959   5.845  1.00  0.00              
ATOM   1061  N   TYR   349      20.682  15.404   5.030  1.00  0.00              
ATOM   1062  CA  TYR   349      20.161  14.227   5.729  1.00  0.00              
ATOM   1063  C   TYR   349      20.706  14.231   7.148  1.00  0.00              
ATOM   1064  O   TYR   349      21.902  14.081   7.340  1.00  0.00              
ATOM   1065  N   ASP   350      19.804  14.445   8.120  1.00  0.00              
ATOM   1066  CA  ASP   350      20.117  14.519   9.546  1.00  0.00              
ATOM   1067  C   ASP   350      20.864  13.316  10.144  1.00  0.00              
ATOM   1068  O   ASP   350      20.347  12.185  10.138  1.00  0.00              
ATOM   1069  N   GLY   351      22.073  13.598  10.687  1.00  0.00              
ATOM   1070  CA  GLY   351      22.946  12.609  11.312  1.00  0.00              
ATOM   1071  C   GLY   351      22.472  12.230  12.715  1.00  0.00              
ATOM   1072  O   GLY   351      22.948  12.757  13.719  1.00  0.00              
END
