
#######################################################
#                                                     #
#                        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    5 (   42),  selected    5 , name T0386TS494_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS494_1-D2.T0386_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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    N     219      E     228          0.180
LGA    P     220      F     229          0.173
LGA    E     221      M     230          0.179
LGA    K     222      H     231          0.304
LGA    I     223      T     232          0.388
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   81    5.0      5    0.26     0.00      6.173     1.390

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.100991 * X  +   0.994833 * Y  +   0.010358 * Z  + -45.045574
  Y_new =  -0.993285 * X  +  -0.100232 * Y  +  -0.057783 * Z  +  71.736961
  Z_new =  -0.056446 * X  +  -0.016124 * Y  +   0.998275 * Z  +  81.738998 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.016151    3.125442  [ DEG:    -0.9254    179.0746 ]
  Theta =   0.056476    3.085116  [ DEG:     3.2359    176.7641 ]
  Phi   =  -1.672122    1.469471  [ DEG:   -95.8055     84.1945 ]
 
# 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: T0386TS494_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS494_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   81   5.0    5   0.26    0.00   6.173
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS494_1-D2
PFRMAT     TS
TARGET     T0386
MODEL      1
PARENT     2g03_A
ATOM   1444  N   ASN   219       9.215  68.769  80.279  1.00  0.02
ATOM   1446  CA  ASN   219       9.522  68.186  78.970  1.00  0.00
ATOM   1447  CB  ASN   219       8.615  68.846  77.940  1.00  0.02
ATOM   1448  CG  ASN   219       8.693  68.131  76.594  1.00  0.02
ATOM   1449  OD1 ASN   219       9.730  68.151  75.917  1.00  0.02
ATOM   1450  ND2 ASN   219       7.581  67.530  76.214  1.00  0.02
ATOM   1453  C   ASN   219      10.983  68.406  78.596  1.00  0.02
ATOM   1454  O   ASN   219      11.387  69.538  78.301  1.00  0.02
ATOM   1455  N   PRO   220      11.689  67.309  78.364  1.00  0.02
ATOM   1456  CA  PRO   220      13.137  67.369  78.124  1.00  0.00
ATOM   1457  CB  PRO   220      13.593  65.942  78.156  1.00  0.00
ATOM   1458  CG  PRO   220      12.384  65.030  78.287  1.00  0.00
ATOM   1459  CD  PRO   220      11.174  65.939  78.404  1.00  0.02
ATOM   1460  C   PRO   220      13.525  68.027  76.791  1.00  0.00
ATOM   1461  O   PRO   220      14.499  68.790  76.767  1.00  0.02
ATOM   1462  N   GLU   221      12.624  68.011  75.820  1.00  0.02
ATOM   1464  CA  GLU   221      12.907  68.605  74.510  1.00  0.02
ATOM   1465  CB  GLU   221      12.043  67.894  73.471  1.00  0.02
ATOM   1466  CG  GLU   221      12.425  68.261  72.037  1.00  0.02
ATOM   1467  CD  GLU   221      13.840  67.778  71.724  1.00  0.03
ATOM   1468  OE1 GLU   221      14.204  66.736  72.255  1.00  0.02
ATOM   1469  OE2 GLU   221      14.469  68.369  70.858  1.00  0.02
ATOM   1470  C   GLU   221      12.605  70.107  74.511  1.00  0.00
ATOM   1471  O   GLU   221      13.020  70.827  73.596  1.00  0.03
ATOM   1472  N   LYS   222      11.958  70.578  75.567  1.00  0.03
ATOM   1474  CA  LYS   222      11.731  72.014  75.747  1.00  0.02
ATOM   1475  CB  LYS   222      10.374  72.226  76.416  1.00  0.02
ATOM   1476  CG  LYS   222       9.231  71.558  75.657  1.00  0.94
ATOM   1477  CD  LYS   222       9.060  72.124  74.254  1.00  1.59
ATOM   1478  CE  LYS   222       7.912  71.444  73.520  1.00  1.96
ATOM   1479  NZ  LYS   222       7.741  72.011  72.175  1.00  1.94
ATOM   1480  C   LYS   222      12.811  72.614  76.647  1.00  0.03
ATOM   1481  O   LYS   222      12.888  73.839  76.803  1.00  0.00
ATOM   1482  N   ILE   223      13.615  71.750  77.246  1.00  0.00
ATOM   1484  CA  ILE   223      14.674  72.194  78.157  1.00  0.02
ATOM   1485  CB  ILE   223      14.538  71.438  79.478  1.00  0.03
ATOM   1486  CG2 ILE   223      15.533  71.968  80.507  1.00  0.02
ATOM   1487  CG1 ILE   223      13.124  71.554  80.034  1.00  0.02
ATOM   1488  CD1 ILE   223      12.965  70.725  81.303  1.00  0.00
ATOM   1489  C   ILE   223      16.046  71.925  77.540  1.00  0.02
ATOM   1490  O   ILE   223      16.565  72.843  76.919  1.00  0.00
ATOM   1491  OXT ILE   223      16.609  70.874  77.813  1.00  0.00
TER  
END
