
#######################################################
#                                                     #
#                        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 (   39),  selected    5 , name T0378TS186_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS186_3-D1.T0378_D1.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    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    M      85      K      31          0.614
LGA    A      86      L      32          0.213
LGA    V      87      V      33          0.185
LGA    F      88      G      34          0.581
LGA    D      89      E      35          0.728
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   89    5.0      5    0.51    20.00      5.618     0.813

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.072429 * X  +   0.881065 * Y  +  -0.467416 * Z  +   6.200227
  Y_new =   0.416864 * X  +  -0.452491 * Y  +  -0.788338 * Z  +   4.439358
  Z_new =  -0.906079 * X  +  -0.137750 * Y  +  -0.400058 * Z  +  78.358871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.809983    0.331610  [ DEG:  -161.0001     18.9999 ]
  Theta =   1.133922    2.007671  [ DEG:    64.9689    115.0311 ]
  Phi   =   1.398765   -1.742827  [ DEG:    80.1433    -99.8567 ]
 
# 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: T0378TS186_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS186_3-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   89   5.0    5   0.51   20.00   5.618
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS186_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1v2x_A
ATOM      1  N   MET    85       2.011  16.431  40.857  1.00  0.00
ATOM      2  CA  MET    85       2.253  15.001  40.493  1.00  0.00
ATOM      3  C   MET    85       3.256  14.317  41.415  1.00  0.00
ATOM      4  O   MET    85       3.024  13.194  41.867  1.00  0.00
ATOM      5  CB  MET    85       2.756  14.893  39.052  1.00  0.00
ATOM      6  CG  MET    85       3.160  13.478  38.660  1.00  0.00
ATOM      7  SD  MET    85       4.045  13.392  37.091  1.00  0.00
ATOM      8  CE  MET    85       2.773  12.700  36.009  1.00  0.00
ATOM      9  N   ALA    86       4.379  14.978  41.684  1.00  0.00
ATOM     10  CA  ALA    86       5.382  14.382  42.553  1.00  0.00
ATOM     11  C   ALA    86       5.000  14.644  44.010  1.00  0.00
ATOM     12  O   ALA    86       5.473  13.971  44.922  1.00  0.00
ATOM     13  CB  ALA    86       6.750  14.986  42.278  1.00  0.00
ATOM     14  N   VAL    87       4.134  15.621  44.230  1.00  0.00
ATOM     15  CA  VAL    87       3.692  15.921  45.583  1.00  0.00
ATOM     16  C   VAL    87       2.771  14.760  45.981  1.00  0.00
ATOM     17  O   VAL    87       2.741  14.305  47.129  1.00  0.00
ATOM     18  CB  VAL    87       2.931  17.259  45.644  1.00  0.00
ATOM     19  CG1 VAL    87       2.316  17.459  47.022  1.00  0.00
ATOM     20  CG2 VAL    87       3.870  18.421  45.363  1.00  0.00
ATOM     21  N   PHE    88       2.039  14.279  44.985  1.00  0.00
ATOM     22  CA  PHE    88       1.015  13.036  45.135  1.00  0.00
ATOM     23  C   PHE    88       1.685  11.697  45.392  1.00  0.00
ATOM     24  O   PHE    88       1.110  10.643  45.118  1.00  0.00
ATOM     25  CB  PHE    88       0.188  12.867  43.858  1.00  0.00
ATOM     26  CG  PHE    88      -0.791  13.980  43.618  1.00  0.00
ATOM     27  CD1 PHE    88      -0.496  15.001  42.731  1.00  0.00
ATOM     28  CD2 PHE    88      -2.007  14.005  44.278  1.00  0.00
ATOM     29  CE1 PHE    88      -1.397  16.025  42.510  1.00  0.00
ATOM     30  CE2 PHE    88      -2.908  15.030  44.056  1.00  0.00
ATOM     31  CZ  PHE    88      -2.607  16.038  43.178  1.00  0.00
ATOM     32  N   ASP    89       2.602  11.727  45.788  1.00  0.00
ATOM     33  CA  ASP    89       3.315  10.526  46.066  1.00  0.00
ATOM     34  C   ASP    89       2.790   9.814  47.303  1.00  0.00
ATOM     35  O   ASP    89       2.370  10.456  48.266  1.00  0.00
ATOM     36  CB  ASP    89       4.797  10.826  46.304  1.00  0.00
ATOM     37  CG  ASP    89       5.524  11.211  45.032  1.00  0.00
ATOM     38  OD1 ASP    89       4.950  11.025  43.939  1.00  0.00
ATOM     39  OD2 ASP    89       6.669  11.701  45.128  1.00  0.00
TER
END
