
#######################################################
#                                                     #
#                        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 (   24),  selected    6 , name T0386AL333_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL333_2-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    N     219      E     221          1.325
LGA    P     220      K     222          1.583
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    E     221      L     225          1.476
LGA    K     222      L     226          0.974
LGA    I     223      K     227          1.687
LGA    -       -      E     228           -
LGA    R     224      F     229          0.877
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
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)    6   81    5.0      6    1.35     0.00      7.023     0.413

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.942883 * X  +   0.316915 * Y  +   0.102646 * Z  + -32.614986
  Y_new =  -0.068990 * X  +   0.487222 * Y  +  -0.870549 * Z  +  63.639500
  Z_new =  -0.325902 * X  +   0.813744 * Y  +   0.481257 * Z  +  52.307800 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.036716   -2.104877  [ DEG:    59.3995   -120.6005 ]
  Theta =   0.331965    2.809628  [ DEG:    19.0202    160.9798 ]
  Phi   =  -0.073039    3.068553  [ DEG:    -4.1848    175.8152 ]
 
# 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: T0386AL333_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL333_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   81   5.0    6   1.35    0.00   7.023
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL333_2-D2
REMARK Aligment from pdb entry: 1oe0_A
ATOM    705  N   ASN   219       3.378  55.960  79.214  1.00  0.00              
ATOM    706  CA  ASN   219       3.531  57.330  78.740  1.00  0.00              
ATOM    707  C   ASN   219       4.772  57.996  79.325  1.00  0.00              
ATOM    708  O   ASN   219       5.018  57.918  80.520  1.00  0.00              
ATOM    709  N   PRO   220       5.552  58.643  78.469  1.00  0.00              
ATOM    710  CA  PRO   220       6.764  59.333  78.890  1.00  0.00              
ATOM    711  C   PRO   220       6.738  60.774  78.402  1.00  0.00              
ATOM    712  O   PRO   220       6.420  61.035  77.241  1.00  0.00              
ATOM    713  N   GLU   221       7.063  61.711  79.284  1.00  0.00              
ATOM    714  CA  GLU   221       7.086  63.116  78.900  1.00  0.00              
ATOM    715  C   GLU   221       8.342  63.330  78.064  1.00  0.00              
ATOM    716  O   GLU   221       9.446  63.402  78.596  1.00  0.00              
ATOM    717  N   LYS   222       8.168  63.428  76.751  1.00  0.00              
ATOM    718  CA  LYS   222       9.294  63.600  75.849  1.00  0.00              
ATOM    719  C   LYS   222       9.637  65.047  75.537  1.00  0.00              
ATOM    720  O   LYS   222      10.208  65.337  74.490  1.00  0.00              
ATOM    721  N   ILE   223       9.286  65.956  76.440  1.00  0.00              
ATOM    722  CA  ILE   223       9.605  67.369  76.250  1.00  0.00              
ATOM    723  C   ILE   223      10.948  67.652  76.923  1.00  0.00              
ATOM    724  O   ILE   223      11.157  68.722  77.496  1.00  0.00              
ATOM    725  N   ARG   224      11.852  66.677  76.840  1.00  0.00              
ATOM    726  CA  ARG   224      13.178  66.775  77.440  1.00  0.00              
ATOM    727  C   ARG   224      13.065  66.936  78.953  1.00  0.00              
ATOM    728  O   ARG   224      13.506  67.987  79.471  1.00  0.00              
END
