
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0295AL333_3-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_3-D2.T0295_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    -       -      T     181           -
LGA    -       -      N     182           -
LGA    -       -      F     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      L     190           -
LGA    -       -      R     191           -
LGA    -       -      I     192           -
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    F     205      R     196          2.389
LGA    K     206      K     197           -
LGA    R     207      R     198          2.296
LGA    N     208      K     199          1.093
LGA    A     209      T     200          2.933
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    -       -      I     204           -
LGA    -       -      F     205           -
LGA    -       -      K     206           -
LGA    -       -      R     207           -
LGA    -       -      N     208           -
LGA    -       -      A     209           -
LGA    N     212      V     210          2.998
LGA    M     213      L     211          2.753
LGA    -       -      N     212           -
LGA    -       -      M     213           -
LGA    L     214      L     214          1.725
LGA    E     215      E     215          3.412
LGA    H     216      H     216          2.729
LGA    N     217      N     217          3.451
LGA    -       -      Y     218           -
LGA    -       -      K     219           -
LGA    -       -      N     220           -
LGA    -       -      W     221           -
LGA    Y     218      C     222          2.119
LGA    -       -      T     223           -
LGA    K     219      L     224          3.115
LGA    N     220      N     225          3.590
LGA    W     221      K     226          3.526
LGA    C     222      Q     227           -
LGA    T     223      V     228           -
LGA    L     224      P     229           -
LGA    -       -      V     230           -
LGA    -       -      N     231           -
LGA    -       -      F     232           -
LGA    -       -      P     233           -
LGA    -       -      F     234           -
LGA    -       -      K     235           -
LGA    -       -      K     236           -
LGA    -       -      Y     237           -
LGA    -       -      C     238           -
LGA    -       -      L     239           -
LGA    -       -      D     240           -
LGA    -       -      V     241           -
LGA    -       -      L     242           -
LGA    -       -      E     243           -
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    -       -      D     246           -
LGA    -       -      M     247           -
LGA    -       -      C     248           -
LGA    -       -      E     249           -
LGA    -       -      K     250           -
LGA    -       -      R     251           -
LGA    -       -      S     252           -
LGA    -       -      I     253           -
LGA    -       -      N     254           -
LGA    -       -      L     255           -
LGA    -       -      D     256           -
LGA    -       -      E     257           -
LGA    -       -      N     258           -
LGA    -       -      D     259           -
LGA    -       -      F     260           -
LGA    -       -      L     261           -
LGA    -       -      K     262           -
LGA    -       -      L     263           -
LGA    -       -      L     264           -
LGA    -       -      L     265           -
LGA    -       -      E     266           -
LGA    -       -      F     267           -
LGA    -       -      N     268           -
LGA    -       -      K     269           -
LGA    -       -      K     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   95    5.0     14    2.81    42.86      9.662     0.481

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.296421 * X  +  -0.141704 * Y  +   0.944486 * Z  + -26.573490
  Y_new =  -0.630845 * X  +  -0.713438 * Y  +  -0.305026 * Z  +  44.549976
  Z_new =   0.717056 * X  +  -0.686241 * Y  +   0.122085 * Z  +   9.700901 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.394734    1.746858  [ DEG:   -79.9124    100.0876 ]
  Theta =  -0.799569   -2.342023  [ DEG:   -45.8119   -134.1880 ]
  Phi   =  -2.010058    1.131534  [ DEG:  -115.1679     64.8321 ]
 
# 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: T0295AL333_3-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_3-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   95   5.0   14   2.81   42.86   9.662
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_3-D2
REMARK Aligment from pdb entry: 1l3i_A
ATOM    577  N   PHE   205      11.757  16.302 -12.053  1.00  0.00              
ATOM    578  CA  PHE   205      11.000  17.118 -13.020  1.00  0.00              
ATOM    579  C   PHE   205      11.068  16.536 -14.431  1.00  0.00              
ATOM    580  O   PHE   205      12.161  16.346 -14.966  1.00  0.00              
ATOM    581  N   LYS   206       9.906  16.306 -15.049  1.00  0.00              
ATOM    582  CA  LYS   206       9.819  15.748 -16.410  1.00  0.00              
ATOM    583  C   LYS   206      10.688  14.510 -16.579  1.00  0.00              
ATOM    584  O   LYS   206      11.519  14.419 -17.490  1.00  0.00              
ATOM    585  N   ARG   207      10.488  13.583 -15.651  1.00  0.00              
ATOM    586  CA  ARG   207      11.209  12.323 -15.613  1.00  0.00              
ATOM    587  C   ARG   207      12.719  12.459 -15.347  1.00  0.00              
ATOM    588  O   ARG   207      13.419  11.456 -15.207  1.00  0.00              
ATOM    589  N   ASN   208      13.198  13.696 -15.231  1.00  0.00              
ATOM    590  CA  ASN   208      14.600  13.936 -14.951  1.00  0.00              
ATOM    591  C   ASN   208      14.801  14.582 -13.590  1.00  0.00              
ATOM    592  O   ASN   208      13.865  14.621 -12.792  1.00  0.00              
ATOM    593  N   ALA   209      16.006  15.097 -13.323  1.00  0.00              
ATOM    594  CA  ALA   209      16.350  15.745 -12.043  1.00  0.00              
ATOM    595  C   ALA   209      16.839  17.173 -12.265  1.00  0.00              
ATOM    596  O   ALA   209      17.926  17.367 -12.799  1.00  0.00              
ATOM    597  N   ASN   212      17.696  22.648  -7.972  1.00  0.00              
ATOM    598  CA  ASN   212      17.036  23.803  -7.370  1.00  0.00              
ATOM    599  C   ASN   212      17.984  24.465  -6.374  1.00  0.00              
ATOM    600  O   ASN   212      18.393  23.837  -5.401  1.00  0.00              
ATOM    601  N   MET   213      18.337  25.722  -6.619  1.00  0.00              
ATOM    602  CA  MET   213      19.255  26.432  -5.736  1.00  0.00              
ATOM    603  C   MET   213      18.583  27.109  -4.543  1.00  0.00              
ATOM    604  O   MET   213      17.397  27.414  -4.557  1.00  0.00              
ATOM    605  N   LEU   214      19.362  27.313  -3.497  1.00  0.00              
ATOM    606  CA  LEU   214      18.886  27.993  -2.303  1.00  0.00              
ATOM    607  C   LEU   214      19.651  29.291  -2.324  1.00  0.00              
ATOM    608  O   LEU   214      20.745  29.353  -2.902  1.00  0.00              
ATOM    609  N   GLU   215      19.080  30.336  -1.739  1.00  0.00              
ATOM    610  CA  GLU   215      19.756  31.623  -1.700  1.00  0.00              
ATOM    611  C   GLU   215      21.087  31.456  -0.969  1.00  0.00              
ATOM    612  O   GLU   215      21.188  30.673  -0.027  1.00  0.00              
ATOM    613  N   HIS   216      22.138  32.131  -1.448  1.00  0.00              
ATOM    614  CA  HIS   216      23.418  31.994  -0.766  1.00  0.00              
ATOM    615  C   HIS   216      23.378  32.502   0.667  1.00  0.00              
ATOM    616  O   HIS   216      22.638  33.418   0.990  1.00  0.00              
ATOM    617  N   ASN   217      24.140  31.851   1.528  1.00  0.00              
ATOM    618  CA  ASN   217      24.228  32.237   2.915  1.00  0.00              
ATOM    619  C   ASN   217      25.709  32.233   3.283  1.00  0.00              
ATOM    620  O   ASN   217      26.457  31.326   2.883  1.00  0.00              
ATOM    621  N   TYR   218      26.152  33.273   3.977  1.00  0.00              
ATOM    622  CA  TYR   218      27.543  33.343   4.406  1.00  0.00              
ATOM    623  C   TYR   218      27.628  33.135   5.927  1.00  0.00              
ATOM    624  O   TYR   218      26.711  33.493   6.680  1.00  0.00              
ATOM    625  N   LYS   219      28.702  32.490   6.363  1.00  0.00              
ATOM    626  CA  LYS   219      28.927  32.262   7.779  1.00  0.00              
ATOM    627  C   LYS   219      30.216  32.988   8.134  1.00  0.00              
ATOM    628  O   LYS   219      31.273  32.699   7.557  1.00  0.00              
ATOM    629  N   ASN   220      30.094  34.023   8.968  1.00  0.00              
ATOM    630  CA  ASN   220      31.239  34.799   9.424  1.00  0.00              
ATOM    631  C   ASN   220      31.547  34.252  10.826  1.00  0.00              
ATOM    632  O   ASN   220      30.706  34.327  11.727  1.00  0.00              
ATOM    633  N   TRP   221      32.732  33.679  11.012  1.00  0.00              
ATOM    634  CA  TRP   221      33.073  33.091  12.298  1.00  0.00              
ATOM    635  C   TRP   221      34.449  33.490  12.823  1.00  0.00              
ATOM    636  O   TRP   221      35.363  33.798  12.049  1.00  0.00              
ATOM    637  N   CYS   222      34.581  33.452  14.151  1.00  0.00              
ATOM    638  CA  CYS   222      35.805  33.841  14.858  1.00  0.00              
ATOM    639  C   CYS   222      36.872  32.766  15.089  1.00  0.00              
ATOM    640  O   CYS   222      36.642  31.567  14.859  1.00  0.00              
ATOM    641  N   THR   223      38.025  33.233  15.596  1.00  0.00              
ATOM    642  CA  THR   223      39.198  32.404  15.880  1.00  0.00              
ATOM    643  C   THR   223      39.127  31.224  16.843  1.00  0.00              
ATOM    644  O   THR   223      38.048  30.833  17.309  1.00  0.00              
ATOM    645  N   LEU   224      40.316  30.718  17.205  1.00  0.00              
ATOM    646  CA  LEU   224      40.485  29.543  18.079  1.00  0.00              
ATOM    647  C   LEU   224      39.630  29.559  19.368  1.00  0.00              
ATOM    648  O   LEU   224      39.597  30.602  20.068  1.00  0.00              
END
