
#######################################################
#                                                     #
#                        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    6 (   40),  selected    6 , name T0301TS186_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301TS186_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    D     187      A     315          1.132
LGA    G     188      M     316          1.073
LGA    G     189      M     317          0.602
LGA    A     190      G     318          1.745
LGA    I     191      T     319          1.226
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    F     192      V     322          2.326
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)    6  191    5.0      6    1.46     0.00      3.024     0.385

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.253879 * X  +   0.927779 * Y  +   0.273443 * Z  + 106.911308
  Y_new =  -0.447695 * X  +  -0.363316 * Y  +   0.817050 * Z  +  62.946701
  Z_new =   0.857388 * X  +   0.085012 * Y  +   0.507600 * Z  + -88.463699 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.165939   -2.975653  [ DEG:     9.5076   -170.4924 ]
  Theta =  -1.030174   -2.111419  [ DEG:   -59.0246   -120.9754 ]
  Phi   =  -2.086658    1.054935  [ DEG:  -119.5567     60.4433 ]
 
# 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: T0301TS186_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS186_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  191   5.0    6   1.46    0.00   3.024
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS186_2-D2
PFRMAT TS
TARGET T0301
MODEL  2
PARENT 1fcf_A
ATOM   1394  N   ASP   187      94.239  15.498  22.833  1.00  0.00
ATOM   1395  CA  ASP   187      93.828  16.529  21.900  1.00  0.00
ATOM   1396  C   ASP   187      94.019  16.107  20.420  1.00  0.00
ATOM   1397  O   ASP   187      93.981  16.916  19.511  1.00  0.00
ATOM   1398  CB  ASP   187      94.643  17.805  22.118  1.00  0.00
ATOM   1399  CG  ASP   187      96.121  17.605  21.845  1.00  0.00
ATOM   1400  OD1 ASP   187      96.515  16.470  21.506  1.00  0.00
ATOM   1401  OD2 ASP   187      96.885  18.586  21.970  1.00  0.00
ATOM   1402  N   GLY   188      94.240  14.825  20.142  1.00  0.00
ATOM   1403  CA  GLY   188      94.470  14.368  18.778  1.00  0.00
ATOM   1404  C   GLY   188      93.429  14.878  17.835  1.00  0.00
ATOM   1405  O   GLY   188      92.297  15.020  18.244  1.00  0.00
ATOM   1406  N   GLY   189      93.792  15.106  16.586  1.00  0.00
ATOM   1407  CA  GLY   189      92.853  15.585  15.593  1.00  0.00
ATOM   1408  C   GLY   189      91.942  14.515  15.101  1.00  0.00
ATOM   1409  O   GLY   189      92.301  13.347  15.022  1.00  0.00
ATOM   1410  N   ALA   190      90.752  14.977  14.821  1.00  0.00
ATOM   1411  CA  ALA   190      89.649  14.185  14.379  1.00  0.00
ATOM   1412  C   ALA   190      89.781  14.065  12.884  1.00  0.00
ATOM   1413  O   ALA   190      89.051  14.689  12.107  1.00  0.00
ATOM   1414  CB  ALA   190      88.334  14.856  14.746  1.00  0.00
ATOM   1415  N   ILE   191      90.745  13.244  12.542  1.00  0.00
ATOM   1416  CA  ILE   191      91.180  12.961  11.178  1.00  0.00
ATOM   1417  C   ILE   191      90.096  12.551  10.169  1.00  0.00
ATOM   1418  O   ILE   191      90.090  13.002   9.010  1.00  0.00
ATOM   1419  CB  ILE   191      92.195  11.804  11.138  1.00  0.00
ATOM   1420  CG1 ILE   191      93.481  12.197  11.869  1.00  0.00
ATOM   1421  CG2 ILE   191      92.546  11.453   9.700  1.00  0.00
ATOM   1422  CD1 ILE   191      94.221  13.348  11.226  1.00  0.00
ATOM   1423  N   PHE   192      89.207  11.643  10.581  1.00  0.00
ATOM   1424  CA  PHE   192      88.150  11.051   9.796  1.00  0.00
ATOM   1425  C   PHE   192      86.742  11.585  10.058  1.00  0.00
ATOM   1426  O   PHE   192      86.488  12.798  10.020  1.00  0.00
ATOM   1427  CB  PHE   192      88.140   9.582  10.137  1.00  0.00
ATOM   1428  CG  PHE   192      89.431   8.906   9.757  1.00  0.00
ATOM   1429  CD1 PHE   192      90.564   8.998  10.561  1.00  0.00
ATOM   1430  CD2 PHE   192      89.507   8.137   8.601  1.00  0.00
ATOM   1431  CE1 PHE   192      91.729   8.329  10.186  1.00  0.00
ATOM   1432  CE2 PHE   192      90.671   7.488   8.203  1.00  0.00
ATOM   1433  CZ  PHE   192      91.808   7.601   8.997  1.00  0.00
TER
END
