
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0301AL044_3-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_3-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      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    G     189      Q     245          3.448
LGA    A     190      L     246          3.652
LGA    -       -      A     247           -
LGA    I     191      R     248          2.194
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    F     192      R     251          1.105
LGA    P     193      I     252          2.565
LGA    T     194      R     253          2.401
LGA    D     200      V     254          0.934
LGA    V     203      A     255          0.351
LGA    P     204      G     256          2.299
LGA    G     205      A     257          1.957
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    T     208      I     263          4.330
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    F     209      A     269          2.041
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    K     210      Q     273          3.024
LGA    A     211      H     274           #
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    T     212      K     277           #
LGA    M     213      I     278           #
LGA    I     214      A     279          6.292
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    E     227      L     303           #
LGA    I     228      V     304          1.656
LGA    G     229      R     305          3.120
LGA    Y     230      A     306          2.615
LGA    R     231      L     307          2.683
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    -       -      G     318           -
LGA    -       -      T     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      V     322           -
LGA    -       -      A     323           -
LGA    -       -      I     324           -
LGA    -       -      G     325           -
LGA    -       -      T     326           -
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
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    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
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    -       -      G     359           -
LGA    -       -      A     360           -
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    -       -      M     376           -
LGA    -       -      S     377           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  191    5.0     18    2.90     0.00      6.844     0.599

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.004472 * X  +  -0.352637 * Y  +  -0.935749 * Z  +  96.183144
  Y_new =  -0.586102 * X  +  -0.757258 * Y  +   0.288174 * Z  +  30.829220
  Z_new =  -0.810225 * X  +   0.549733 * Y  +  -0.203295 * Z  +  64.785027 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.925006   -1.216587  [ DEG:   110.2947    -69.7053 ]
  Theta =   0.944536    2.197057  [ DEG:    54.1179    125.8821 ]
  Phi   =  -1.578427    1.563166  [ DEG:   -90.4372     89.5628 ]
 
# 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: T0301AL044_3-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_3-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  191   5.0   18   2.90    0.00   6.844
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_3-D2
REMARK Aligment from pdb entry: 1s7j_A
ATOM    257  N   ASP   187     106.369  15.371  19.949  1.00  0.00              
ATOM    258  CA  ASP   187     107.124  14.140  19.976  1.00  0.00              
ATOM    259  C   ASP   187     108.279  14.286  18.986  1.00  0.00              
ATOM    260  O   ASP   187     108.241  15.166  18.108  1.00  0.00              
ATOM    261  N   GLY   189     109.388  13.539  19.198  1.00  0.00              
ATOM    262  CA  GLY   189     110.535  13.636  18.285  1.00  0.00              
ATOM    263  C   GLY   189     110.176  13.083  16.894  1.00  0.00              
ATOM    264  O   GLY   189     109.518  12.051  16.781  1.00  0.00              
ATOM    265  N   ALA   190     110.595  13.799  15.848  1.00  0.00              
ATOM    266  CA  ALA   190     110.327  13.371  14.470  1.00  0.00              
ATOM    267  C   ALA   190     111.372  12.336  14.006  1.00  0.00              
ATOM    268  O   ALA   190     112.425  12.701  13.459  1.00  0.00              
ATOM    269  N   ILE   191     111.084  11.067  14.245  1.00  0.00              
ATOM    270  CA  ILE   191     111.983   9.989  13.853  1.00  0.00              
ATOM    271  C   ILE   191     111.952   9.790  12.340  1.00  0.00              
ATOM    272  O   ILE   191     110.888   9.895  11.708  1.00  0.00              
ATOM    273  N   PHE   192     113.122   9.534  11.725  1.00  0.00              
ATOM    274  CA  PHE   192     113.193   9.330  10.276  1.00  0.00              
ATOM    275  C   PHE   192     112.461   8.066   9.826  1.00  0.00              
ATOM    276  O   PHE   192     112.084   7.942   8.660  1.00  0.00              
ATOM    277  N   PRO   193     112.282   7.118  10.746  1.00  0.00              
ATOM    278  CA  PRO   193     111.574   5.882  10.432  1.00  0.00              
ATOM    279  C   PRO   193     110.087   6.187  10.234  1.00  0.00              
ATOM    280  O   PRO   193     109.335   5.361   9.707  1.00  0.00              
ATOM    281  N   THR   194     109.663   7.356  10.736  1.00  0.00              
ATOM    282  CA  THR   194     108.287   7.812  10.614  1.00  0.00              
ATOM    283  C   THR   194     108.055   8.265   9.178  1.00  0.00              
ATOM    284  O   THR   194     107.097   7.835   8.520  1.00  0.00              
ATOM    285  N   ASP   200     108.933   9.150   8.704  1.00  0.00              
ATOM    286  CA  ASP   200     108.873   9.678   7.343  1.00  0.00              
ATOM    287  C   ASP   200     109.080   8.563   6.305  1.00  0.00              
ATOM    288  O   ASP   200     108.692   8.701   5.141  1.00  0.00              
ATOM    289  N   VAL   203     109.741   7.491   6.727  1.00  0.00              
ATOM    290  CA  VAL   203     110.003   6.352   5.863  1.00  0.00              
ATOM    291  C   VAL   203     108.708   5.604   5.547  1.00  0.00              
ATOM    292  O   VAL   203     108.399   5.350   4.383  1.00  0.00              
ATOM    293  N   PRO   204     105.643   6.640   5.935  1.00  0.00              
ATOM    294  CA  PRO   204     104.695   7.545   5.267  1.00  0.00              
ATOM    295  C   PRO   204     105.096   7.817   3.836  1.00  0.00              
ATOM    296  O   PRO   204     104.237   8.002   2.965  1.00  0.00              
ATOM    297  N   GLY   205     106.401   7.895   3.608  1.00  0.00              
ATOM    298  CA  GLY   205     106.910   8.177   2.289  1.00  0.00              
ATOM    299  C   GLY   205     106.816   9.661   1.989  1.00  0.00              
ATOM    300  O   GLY   205     106.576  10.061   0.842  1.00  0.00              
ATOM    301  N   THR   208     107.005  10.487   3.013  1.00  0.00              
ATOM    302  CA  THR   208     106.946  11.935   2.841  1.00  0.00              
ATOM    303  C   THR   208     107.563  12.642   4.038  1.00  0.00              
ATOM    304  O   THR   208     107.935  11.995   5.030  1.00  0.00              
ATOM    305  N   PHE   209     107.711  13.958   3.940  1.00  0.00              
ATOM    306  CA  PHE   209     108.274  14.753   5.012  1.00  0.00              
ATOM    307  C   PHE   209     107.236  15.124   6.076  1.00  0.00              
ATOM    308  O   PHE   209     106.158  15.640   5.770  1.00  0.00              
ATOM    309  N   LYS   210     106.530  17.529   8.975  1.00  0.00              
ATOM    310  CA  LYS   210     106.921  18.836   9.505  1.00  0.00              
ATOM    311  C   LYS   210     106.844  18.937  11.039  1.00  0.00              
ATOM    312  O   LYS   210     107.679  19.596  11.668  1.00  0.00              
ATOM    313  N   ALA   211     105.826  18.313  11.624  1.00  0.00              
ATOM    314  CA  ALA   211     105.629  18.337  13.069  1.00  0.00              
ATOM    315  C   ALA   211     105.147  16.967  13.543  1.00  0.00              
ATOM    316  O   ALA   211     104.519  16.227  12.781  1.00  0.00              
ATOM    317  N   THR   212     105.456  16.625  14.780  1.00  0.00              
ATOM    318  CA  THR   212     105.035  15.341  15.336  1.00  0.00              
ATOM    319  C   THR   212     104.493  15.531  16.749  1.00  0.00              
ATOM    320  O   THR   212     104.954  16.407  17.487  1.00  0.00              
ATOM    321  N   MET   213     103.470  14.745  17.096  1.00  0.00              
ATOM    322  CA  MET   213     102.832  14.809  18.409  1.00  0.00              
ATOM    323  C   MET   213     102.309  13.423  18.786  1.00  0.00              
ATOM    324  O   MET   213     102.269  12.517  17.948  1.00  0.00              
ATOM    325  N   ILE   214     101.932  13.247  20.050  1.00  0.00              
ATOM    326  CA  ILE   214     101.402  11.968  20.503  1.00  0.00              
ATOM    327  C   ILE   214     100.162  12.142  21.386  1.00  0.00              
ATOM    328  O   ILE   214     100.019  13.135  22.098  1.00  0.00              
ATOM    329  N   GLU   227      99.251  11.206  21.241  1.00  0.00              
ATOM    330  CA  GLU   227      98.021  11.178  21.999  1.00  0.00              
ATOM    331  C   GLU   227      97.704   9.709  22.017  1.00  0.00              
ATOM    332  O   GLU   227      98.573   8.889  22.383  1.00  0.00              
ATOM    333  N   ILE   228      96.498   9.331  21.645  1.00  0.00              
ATOM    334  CA  ILE   228      96.170   7.923  21.592  1.00  0.00              
ATOM    335  C   ILE   228      96.952   7.381  20.385  1.00  0.00              
ATOM    336  O   ILE   228      97.474   6.260  20.409  1.00  0.00              
ATOM    337  N   GLY   229      97.065   8.227  19.350  1.00  0.00              
ATOM    338  CA  GLY   229      97.769   7.894  18.111  1.00  0.00              
ATOM    339  C   GLY   229      98.867   8.880  17.807  1.00  0.00              
ATOM    340  O   GLY   229      98.858  10.017  18.286  1.00  0.00              
ATOM    341  N   TYR   230      99.803   8.464  16.959  1.00  0.00              
ATOM    342  CA  TYR   230     100.869   9.343  16.532  1.00  0.00              
ATOM    343  C   TYR   230     100.164  10.420  15.705  1.00  0.00              
ATOM    344  O   TYR   230      99.141  10.143  15.080  1.00  0.00              
ATOM    345  N   ARG   231     100.712  11.608  15.676  1.00  0.00              
ATOM    346  CA  ARG   231     100.069  12.716  14.997  1.00  0.00              
ATOM    347  C   ARG   231     101.093  13.503  14.186  1.00  0.00              
ATOM    348  O   ARG   231     101.845  14.300  14.737  1.00  0.00              
END
