
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0295AL044_3-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL044_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    D     184      N     182          1.081
LGA    N     188      F     183          0.739
LGA    L     189      D     184          0.504
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    L     190      N     188          0.348
LGA    R     191      L     189          1.129
LGA    T     200      L     190          1.204
LGA    H     202      R     191          0.875
LGA    A     203      I     192          0.977
LGA    I     204      C     193          1.205
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    F     205      R     196          3.387
LGA    R     207      K     197          2.183
LGA    N     208      R     198          1.601
LGA    -       -      K     199           -
LGA    -       -      T     200           -
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    -       -      V     210           -
LGA    -       -      L     211           -
LGA    -       -      N     212           -
LGA    -       -      M     213           -
LGA    -       -      L     214           -
LGA    -       -      E     215           -
LGA    -       -      H     216           -
LGA    -       -      N     217           -
LGA    -       -      Y     218           -
LGA    -       -      K     219           -
LGA    -       -      N     220           -
LGA    -       -      W     221           -
LGA    -       -      C     222           -
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      N     225           -
LGA    -       -      K     226           -
LGA    -       -      Q     227           -
LGA    -       -      V     228           -
LGA    -       -      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    A     209      S     252          1.460
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)   13   95    5.0     13    1.49     0.00     12.982     0.817

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.362689 * X  +  -0.660355 * Y  +   0.657562 * Z  + -16.544060
  Y_new =   0.929877 * X  +   0.303024 * Y  +  -0.208578 * Z  +  -6.823270
  Z_new =  -0.061522 * X  +   0.687101 * Y  +   0.723952 * Z  + -103.326553 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.759288   -2.382305  [ DEG:    43.5040   -136.4960 ]
  Theta =   0.061560    3.080032  [ DEG:     3.5272    176.4729 ]
  Phi   =   1.198905   -1.942687  [ DEG:    68.6922   -111.3078 ]
 
# 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: T0295AL044_3-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL044_3-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   95   5.0   13   1.49    0.00  12.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL044_3-D2
REMARK Aligment from pdb entry: 1xxl_A
ATOM    641  N   ASP   184      20.236  18.218  10.516  1.00  0.00              
ATOM    642  CA  ASP   184      20.557  17.226   9.474  1.00  0.00              
ATOM    643  C   ASP   184      19.297  16.680   8.807  1.00  0.00              
ATOM    644  O   ASP   184      19.227  16.605   7.576  1.00  0.00              
ATOM    645  N   ASN   188      18.301  16.320   9.614  1.00  0.00              
ATOM    646  CA  ASN   188      17.048  15.833   9.068  1.00  0.00              
ATOM    647  C   ASN   188      16.344  16.881   8.232  1.00  0.00              
ATOM    648  O   ASN   188      15.795  16.544   7.190  1.00  0.00              
ATOM    649  N   LEU   189      16.345  18.142   8.662  1.00  0.00              
ATOM    650  CA  LEU   189      15.698  19.180   7.868  1.00  0.00              
ATOM    651  C   LEU   189      16.331  19.239   6.473  1.00  0.00              
ATOM    652  O   LEU   189      15.625  19.457   5.491  1.00  0.00              
ATOM    653  N   LEU   190      14.332  18.665   2.888  1.00  0.00              
ATOM    654  CA  LEU   190      14.473  19.599   1.749  1.00  0.00              
ATOM    655  C   LEU   190      14.950  18.876   0.473  1.00  0.00              
ATOM    656  O   LEU   190      14.436  19.117  -0.609  1.00  0.00              
ATOM    657  N   ARG   191      15.939  17.999   0.624  1.00  0.00              
ATOM    658  CA  ARG   191      16.495  17.223  -0.492  1.00  0.00              
ATOM    659  C   ARG   191      15.415  16.390  -1.175  1.00  0.00              
ATOM    660  O   ARG   191      15.291  16.400  -2.395  1.00  0.00              
ATOM    661  N   THR   200      14.626  15.681  -0.371  1.00  0.00              
ATOM    662  CA  THR   200      13.528  14.837  -0.881  1.00  0.00              
ATOM    663  C   THR   200      12.395  15.661  -1.486  1.00  0.00              
ATOM    664  O   THR   200      11.854  15.307  -2.522  1.00  0.00              
ATOM    665  N   HIS   202      12.041  16.766  -0.834  1.00  0.00              
ATOM    666  CA  HIS   202      10.965  17.633  -1.309  1.00  0.00              
ATOM    667  C   HIS   202      11.295  18.386  -2.576  1.00  0.00              
ATOM    668  O   HIS   202      10.397  18.727  -3.327  1.00  0.00              
ATOM    669  N   ALA   203      12.579  18.664  -2.805  1.00  0.00              
ATOM    670  CA  ALA   203      13.010  19.363  -4.010  1.00  0.00              
ATOM    671  C   ALA   203      13.557  18.429  -5.101  1.00  0.00              
ATOM    672  O   ALA   203      14.122  18.885  -6.082  1.00  0.00              
ATOM    673  N   ILE   204      13.380  17.124  -4.938  1.00  0.00              
ATOM    674  CA  ILE   204      13.766  16.150  -5.972  1.00  0.00              
ATOM    675  C   ILE   204      13.157  16.446  -7.368  1.00  0.00              
ATOM    676  O   ILE   204      11.985  16.781  -7.480  1.00  0.00              
ATOM    677  N   PHE   205      13.952  16.311  -8.429  1.00  0.00              
ATOM    678  CA  PHE   205      13.425  16.390  -9.798  1.00  0.00              
ATOM    679  C   PHE   205      12.380  15.302 -10.037  1.00  0.00              
ATOM    680  O   PHE   205      12.274  14.345  -9.265  1.00  0.00              
ATOM    681  N   ARG   207      11.623  15.441 -11.111  1.00  0.00              
ATOM    682  CA  ARG   207      10.671  14.426 -11.501  1.00  0.00              
ATOM    683  C   ARG   207      11.351  13.085 -11.717  1.00  0.00              
ATOM    684  O   ARG   207      10.825  12.060 -11.322  1.00  0.00              
ATOM    685  N   ASN   208      12.532  13.104 -12.325  1.00  0.00              
ATOM    686  CA  ASN   208      13.272  11.880 -12.602  1.00  0.00              
ATOM    687  C   ASN   208      13.715  11.193 -11.286  1.00  0.00              
ATOM    688  O   ASN   208      13.643   9.977 -11.190  1.00  0.00              
ATOM    689  N   ALA   209      14.171  11.967 -10.299  1.00  0.00              
ATOM    690  CA  ALA   209      14.566  11.424  -8.995  1.00  0.00              
ATOM    691  C   ALA   209      13.363  10.849  -8.220  1.00  0.00              
ATOM    692  O   ALA   209      13.443   9.780  -7.584  1.00  0.00              
END
