
#######################################################
#                                                     #
#                        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 T0301AL333_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL333_2-D2.T0301_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    -       -      D     187           -
LGA    -       -      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      V     198           -
LGA    -       -      D     199           -
LGA    -       -      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    -       -      F     209           -
LGA    -       -      K     210           -
LGA    -       -      A     211           -
LGA    -       -      T     212           -
LGA    -       -      M     213           -
LGA    -       -      I     214           -
LGA    -       -      N     215           -
LGA    -       -      A     216           -
LGA    -       -      G     217           -
LGA    -       -      I     218           -
LGA    -       -      P     219           -
LGA    -       -      T     220           -
LGA    -       -      V     221           -
LGA    -       -      F     222           -
LGA    -       -      V     223           -
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    -       -      A     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      L     303           -
LGA    -       -      V     304           -
LGA    -       -      R     305           -
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    -       -      A     315           -
LGA    -       -      M     316           -
LGA    -       -      M     317           -
LGA    A     257      G     318          3.028
LGA    L     258      T     319          2.700
LGA    R     259      A     320          3.146
LGA    -       -      A     321           -
LGA    M     260      V     322          0.949
LGA    -       -      A     323           -
LGA    -       -      I     324           -
LGA    G     261      G     325          2.308
LGA    L     262      T     326          2.314
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    I     263      I     330          2.772
LGA    P     331      P     331          2.902
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    -       -      V     335           -
LGA    -       -      N     336           -
LGA    -       -      L     337           -
LGA    -       -      A     338           -
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    G     332      E     343          0.721
LGA    L     356      R     344          4.474
LGA    R     357      S     345          1.358
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    -       -      R     357           -
LGA    -       -      V     358           -
LGA    V     358      G     359          2.910
LGA    G     359      A     360          4.555
LGA    -       -      E     361           -
LGA    -       -      A     362           -
LGA    -       -      S     363           -
LGA    -       -      Q     364           -
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    -       -      E     368           -
LGA    -       -      W     369           -
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    -       -      A     374           -
LGA    -       -      I     375           -
LGA    A     374      M     376          4.323
LGA    I     375      S     377           #
LGA    M     376      -       -           -
LGA    S     377      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  191    5.0     14    2.98    21.43      4.890     0.455

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.151715 * X  +  -0.552647 * Y  +  -0.819490 * Z  + 123.770172
  Y_new =  -0.855811 * X  +   0.341372 * Y  +  -0.388654 * Z  +  26.341429
  Z_new =   0.494540 * X  +   0.760294 * Y  +  -0.421170 * Z  +  -7.797870 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.076673   -1.064920  [ DEG:   118.9846    -61.0154 ]
  Theta =  -0.517305   -2.624288  [ DEG:   -29.6394   -150.3606 ]
  Phi   =  -1.395343    1.746250  [ DEG:   -79.9473    100.0527 ]
 
# 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: T0301AL333_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL333_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  191   5.0   14   2.98   21.43   4.890
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL333_2-D2
REMARK Aligment from pdb entry: 1hnj_A
ATOM    405  N   ALA   257      90.122  19.541  12.522  1.00  0.00              
ATOM    406  CA  ALA   257      90.755  18.269  12.199  1.00  0.00              
ATOM    407  C   ALA   257      89.760  17.124  12.425  1.00  0.00              
ATOM    408  O   ALA   257      89.102  17.049  13.462  1.00  0.00              
ATOM    409  N   LEU   258      89.658  16.237  11.444  1.00  0.00              
ATOM    410  CA  LEU   258      88.764  15.090  11.553  1.00  0.00              
ATOM    411  C   LEU   258      89.576  13.802  11.646  1.00  0.00              
ATOM    412  O   LEU   258      90.362  13.508  10.742  1.00  0.00              
ATOM    413  N   ARG   259      89.405  13.079  12.750  1.00  0.00              
ATOM    414  CA  ARG   259      90.099  11.807  12.958  1.00  0.00              
ATOM    415  C   ARG   259      89.099  10.707  12.657  1.00  0.00              
ATOM    416  O   ARG   259      87.924  10.843  13.020  1.00  0.00              
ATOM    417  N   MET   260      89.498   9.658  11.951  1.00  0.00              
ATOM    418  CA  MET   260      88.562   8.540  11.719  1.00  0.00              
ATOM    419  C   MET   260      89.320   7.242  11.619  1.00  0.00              
ATOM    420  O   MET   260      90.540   7.233  11.368  1.00  0.00              
ATOM    421  N   GLY   261      88.610   6.134  11.846  1.00  0.00              
ATOM    422  CA  GLY   261      89.229   4.819  11.804  1.00  0.00              
ATOM    423  C   GLY   261      88.181   3.738  11.645  1.00  0.00              
ATOM    424  O   GLY   261      87.037   3.926  12.032  1.00  0.00              
ATOM    425  N   LEU   262      88.589   2.602  11.090  1.00  0.00              
ATOM    426  CA  LEU   262      87.696   1.462  10.824  1.00  0.00              
ATOM    427  C   LEU   262      88.535   0.229  11.150  1.00  0.00              
ATOM    428  O   LEU   262      89.705   0.144  10.778  1.00  0.00              
ATOM    429  N   ILE   263      87.940  -0.739  11.824  1.00  0.00              
ATOM    430  CA  ILE   263      88.683  -1.925  12.203  1.00  0.00              
ATOM    431  C   ILE   263      87.840  -3.157  12.417  1.00  0.00              
ATOM    432  O   ILE   263      86.633  -3.149  12.217  1.00  0.00              
ATOM    433  N   PRO   331      88.526  -4.214  12.823  1.00  0.00              
ATOM    434  CA  PRO   331      87.912  -5.499  13.104  1.00  0.00              
ATOM    435  C   PRO   331      86.753  -5.386  14.077  1.00  0.00              
ATOM    436  O   PRO   331      86.791  -4.617  15.034  1.00  0.00              
ATOM    437  N   GLY   332      85.714  -6.161  13.816  1.00  0.00              
ATOM    438  CA  GLY   332      84.522  -6.123  14.641  1.00  0.00              
ATOM    439  C   GLY   332      83.277  -6.438  13.807  1.00  0.00              
ATOM    440  O   GLY   332      82.622  -7.459  14.091  1.00  0.00              
ATOM    441  N   LEU   356      82.930  -5.607  12.807  1.00  0.00              
ATOM    442  CA  LEU   356      83.601  -4.361  12.493  1.00  0.00              
ATOM    443  C   LEU   356      83.247  -3.206  13.455  1.00  0.00              
ATOM    444  O   LEU   356      82.152  -3.130  14.020  1.00  0.00              
ATOM    445  N   ARG   357      84.207  -2.295  13.590  1.00  0.00              
ATOM    446  CA  ARG   357      84.025  -1.094  14.402  1.00  0.00              
ATOM    447  C   ARG   357      84.539   0.108  13.630  1.00  0.00              
ATOM    448  O   ARG   357      85.406  -0.034  12.773  1.00  0.00              
ATOM    449  N   VAL   358      83.984   1.284  13.892  1.00  0.00              
ATOM    450  CA  VAL   358      84.506   2.465  13.218  1.00  0.00              
ATOM    451  C   VAL   358      84.138   3.676  14.030  1.00  0.00              
ATOM    452  O   VAL   358      83.196   3.645  14.825  1.00  0.00              
ATOM    453  N   GLY   359      84.893   4.752  13.842  1.00  0.00              
ATOM    454  CA  GLY   359      84.608   5.914  14.647  1.00  0.00              
ATOM    455  C   GLY   359      85.268   7.160  14.130  1.00  0.00              
ATOM    456  O   GLY   359      86.137   7.133  13.290  1.00  0.00              
ATOM    457  N   ALA   374      84.872   8.276  14.698  1.00  0.00              
ATOM    458  CA  ALA   374      85.440   9.548  14.309  1.00  0.00              
ATOM    459  C   ALA   374      85.445  10.513  15.484  1.00  0.00              
ATOM    460  O   ALA   374      84.768  10.312  16.489  1.00  0.00              
ATOM    461  N   ILE   375      86.219  11.582  15.312  1.00  0.00              
ATOM    462  CA  ILE   375      86.277  12.693  16.252  1.00  0.00              
ATOM    463  C   ILE   375      86.543  13.982  15.459  1.00  0.00              
ATOM    464  O   ILE   375      87.414  14.015  14.574  1.00  0.00              
ATOM    465  N   MET   376      85.772  15.028  15.745  1.00  0.00              
ATOM    466  CA  MET   376      85.995  16.331  15.090  1.00  0.00              
ATOM    467  C   MET   376      86.645  17.216  16.156  1.00  0.00              
ATOM    468  O   MET   376      86.073  17.414  17.234  1.00  0.00              
ATOM    469  N   SER   377      87.825  17.750  15.866  1.00  0.00              
ATOM    470  CA  SER   377      88.564  18.514  16.862  1.00  0.00              
ATOM    471  C   SER   377      89.017  19.862  16.353  1.00  0.00              
ATOM    472  O   SER   377      89.541  19.956  15.236  1.00  0.00              
END
