
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0301AL044_5-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_5-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    T     194      A     211          4.144
LGA    G     195      T     212          3.014
LGA    N     196      M     213          2.718
LGA    L     197      I     214          2.305
LGA    D     200      N     215          1.983
LGA    V     203      A     216          2.740
LGA    P     204      G     217          2.679
LGA    G     205      I     218          3.773
LGA    V     206      -       -           -
LGA    T     208      P     219           #
LGA    K     210      T     220          3.074
LGA    T     212      V     221          1.813
LGA    M     213      F     222          1.640
LGA    I     214      V     223          2.524
LGA    N     215      N     224          1.809
LGA    A     216      A     225          2.451
LGA    G     217      E     226          3.833
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    E     227      G     232          2.626
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    I     228      F     280          2.956
LGA    G     229      V     281          4.454
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    Y     230      A     306          4.521
LGA    R     231      L     307          4.347
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)   22  191    5.0     20    3.10    10.00      6.604     0.625

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.048251 * X  +  -0.552651 * Y  +   0.832015 * Z  +  61.032326
  Y_new =  -0.661084 * X  +  -0.606762 * Y  +  -0.441370 * Z  +  78.704376
  Z_new =   0.748759 * X  +  -0.571328 * Y  +  -0.336072 * Z  +  34.583317 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.102516    1.039077  [ DEG:  -120.4653     59.5347 ]
  Theta =  -0.846187   -2.295405  [ DEG:   -48.4830   -131.5170 ]
  Phi   =  -1.643655    1.497938  [ DEG:   -94.1745     85.8255 ]
 
# 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_5-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_5-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  191   5.0   20   3.10   10.00   6.604
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_5-D2
REMARK Aligment from pdb entry: 1t6k_A
ATOM    281  N   THR   194     103.104   1.548   8.403  1.00  0.00              
ATOM    282  CA  THR   194     102.136   2.496   7.874  1.00  0.00              
ATOM    283  C   THR   194     100.760   2.255   8.516  1.00  0.00              
ATOM    284  O   THR   194     100.366   1.105   8.738  1.00  0.00              
ATOM    285  N   GLY   195     100.020   3.324   8.774  1.00  0.00              
ATOM    286  CA  GLY   195      98.669   3.174   9.321  1.00  0.00              
ATOM    287  C   GLY   195      97.730   2.508   8.271  1.00  0.00              
ATOM    288  O   GLY   195      96.871   1.636   8.592  1.00  0.00              
ATOM    289  N   ASN   196      97.867   2.954   7.031  1.00  0.00              
ATOM    290  CA  ASN   196      97.019   2.423   5.956  1.00  0.00              
ATOM    291  C   ASN   196      95.532   2.796   5.983  1.00  0.00              
ATOM    292  O   ASN   196      94.714   2.085   5.357  1.00  0.00              
ATOM    293  N   LEU   197      95.172   3.885   6.677  1.00  0.00              
ATOM    294  CA  LEU   197      93.849   4.463   6.670  1.00  0.00              
ATOM    295  C   LEU   197      94.008   5.959   6.489  1.00  0.00              
ATOM    296  O   LEU   197      93.362   6.724   7.179  1.00  0.00              
ATOM    297  N   ASP   200      94.816   6.373   5.525  1.00  0.00              
ATOM    298  CA  ASP   200      95.117   7.790   5.377  1.00  0.00              
ATOM    299  C   ASP   200      93.935   8.616   5.023  1.00  0.00              
ATOM    300  O   ASP   200      93.761   9.614   5.654  1.00  0.00              
ATOM    301  N   VAL   203      93.111   8.246   4.022  1.00  0.00              
ATOM    302  CA  VAL   203      92.070   9.167   3.642  1.00  0.00              
ATOM    303  C   VAL   203      91.045   9.342   4.794  1.00  0.00              
ATOM    304  O   VAL   203      90.545  10.424   5.000  1.00  0.00              
ATOM    305  N   PRO   204      90.785   8.275   5.528  1.00  0.00              
ATOM    306  CA  PRO   204      89.848   8.309   6.656  1.00  0.00              
ATOM    307  C   PRO   204      90.368   9.258   7.749  1.00  0.00              
ATOM    308  O   PRO   204      89.638  10.112   8.264  1.00  0.00              
ATOM    309  N   GLY   205      91.640   9.102   8.076  1.00  0.00              
ATOM    310  CA  GLY   205      92.235   9.886   9.171  1.00  0.00              
ATOM    311  C   GLY   205      92.310  11.345   8.769  1.00  0.00              
ATOM    312  O   GLY   205      91.870  12.196   9.494  1.00  0.00              
ATOM    313  N   VAL   206     104.740  14.198   6.106  1.00  0.00              
ATOM    314  CA  VAL   206     105.535  12.956   6.183  1.00  0.00              
ATOM    315  C   VAL   206     104.594  11.738   6.214  1.00  0.00              
ATOM    316  O   VAL   206     103.403  11.912   6.473  1.00  0.00              
ATOM    317  N   THR   208     105.088  10.520   5.936  1.00  0.00              
ATOM    318  CA  THR   208     104.240   9.316   5.915  1.00  0.00              
ATOM    319  C   THR   208     103.434   9.136   7.205  1.00  0.00              
ATOM    320  O   THR   208     103.960   9.362   8.276  1.00  0.00              
ATOM    321  N   LYS   210     102.169   8.721   7.079  1.00  0.00              
ATOM    322  CA  LYS   210     101.341   8.550   8.285  1.00  0.00              
ATOM    323  C   LYS   210     101.637   7.163   8.839  1.00  0.00              
ATOM    324  O   LYS   210     101.212   6.143   8.264  1.00  0.00              
ATOM    325  N   THR   212     102.366   7.115   9.940  1.00  0.00              
ATOM    326  CA  THR   212     102.826   5.842  10.457  1.00  0.00              
ATOM    327  C   THR   212     102.364   5.725  11.881  1.00  0.00              
ATOM    328  O   THR   212     102.250   6.726  12.576  1.00  0.00              
ATOM    329  N   MET   213     102.117   4.490  12.286  1.00  0.00              
ATOM    330  CA  MET   213     101.645   4.226  13.641  1.00  0.00              
ATOM    331  C   MET   213     102.714   3.470  14.399  1.00  0.00              
ATOM    332  O   MET   213     103.213   2.451  13.922  1.00  0.00              
ATOM    333  N   ILE   214     103.054   3.983  15.604  1.00  0.00              
ATOM    334  CA  ILE   214     104.126   3.441  16.433  1.00  0.00              
ATOM    335  C   ILE   214     103.566   2.757  17.639  1.00  0.00              
ATOM    336  O   ILE   214     102.550   3.225  18.192  1.00  0.00              
ATOM    337  N   ASN   215     104.232   1.680  18.053  1.00  0.00              
ATOM    338  CA  ASN   215     103.800   0.933  19.231  1.00  0.00              
ATOM    339  C   ASN   215     104.904   0.850  20.234  1.00  0.00              
ATOM    340  O   ASN   215     105.980   0.385  19.912  1.00  0.00              
ATOM    341  N   ALA   216     104.636   1.310  21.468  1.00  0.00              
ATOM    342  CA  ALA   216     105.534   1.050  22.588  1.00  0.00              
ATOM    343  C   ALA   216     104.770   0.736  23.897  1.00  0.00              
ATOM    344  O   ALA   216     105.251   1.050  24.972  1.00  0.00              
ATOM    345  N   GLY   217     103.621   0.084  23.768  1.00  0.00              
ATOM    346  CA  GLY   217     102.654   0.000  24.868  1.00  0.00              
ATOM    347  C   GLY   217     101.382   0.554  24.299  1.00  0.00              
ATOM    348  O   GLY   217     100.581  -0.218  23.683  1.00  0.00              
ATOM    349  N   GLU   227     101.201   1.882  24.422  1.00  0.00              
ATOM    350  CA  GLU   227     100.192   2.561  23.642  1.00  0.00              
ATOM    351  C   GLU   227     100.620   2.559  22.154  1.00  0.00              
ATOM    352  O   GLU   227     101.732   2.126  21.843  1.00  0.00              
ATOM    353  N   ILE   228      99.712   2.981  21.284  1.00  0.00              
ATOM    354  CA  ILE   228     100.023   3.198  19.851  1.00  0.00              
ATOM    355  C   ILE   228      99.803   4.696  19.530  1.00  0.00              
ATOM    356  O   ILE   228      98.854   5.336  19.993  1.00  0.00              
ATOM    357  N   GLY   229     100.713   5.272  18.742  1.00  0.00              
ATOM    358  CA  GLY   229     100.633   6.689  18.380  1.00  0.00              
ATOM    359  C   GLY   229     100.876   6.831  16.877  1.00  0.00              
ATOM    360  O   GLY   229     101.876   6.279  16.383  1.00  0.00              
ATOM    361  N   TYR   230      99.947   7.509  16.207  1.00  0.00              
ATOM    362  CA  TYR   230     100.034   7.780  14.775  1.00  0.00              
ATOM    363  C   TYR   230     100.464   9.192  14.612  1.00  0.00              
ATOM    364  O   TYR   230     100.023  10.033  15.370  1.00  0.00              
ATOM    365  N   ARG   231     101.351   9.462  13.641  1.00  0.00              
ATOM    366  CA  ARG   231     101.860  10.811  13.413  1.00  0.00              
ATOM    367  C   ARG   231     101.460  11.388  12.102  1.00  0.00              
ATOM    368  O   ARG   231     101.653  10.742  11.059  1.00  0.00              
END
