
#######################################################
#                                                     #
#                        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 (   25),  selected    5 , name T0352TS102_4
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS102_4.T0352.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    -       -      T       2           -
LGA    -       -      T       3           -
LGA    -       -      H       4           -
LGA    -       -      D       5           -
LGA    -       -      R       6           -
LGA    -       -      V       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      L      11           -
LGA    -       -      Q      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      L      18           -
LGA    -       -      R      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    -       -      T      37           -
LGA    -       -      Q      38           -
LGA    -       -      P      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    -       -      L      55           -
LGA    -       -      I      56           -
LGA    -       -      P      57           -
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    -       -      A      76           -
LGA    H     113      P      77          0.768
LGA    H     114      Y      78          1.862
LGA    -       -      Y      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    H     115      A      82          1.300
LGA    H     116      L      83          0.953
LGA    H     117      A      84          0.333
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  109    5.0      5    1.16     0.00      4.446     0.396

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.556060 * X  +  -0.166253 * Y  +  -0.814345 * Z  +  18.099676
  Y_new =  -0.624680 * X  +  -0.562699 * Y  +   0.541428 * Z  +  48.079128
  Z_new =  -0.548245 * X  +   0.809772 * Y  +   0.209039 * Z  +  43.250278 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.318165   -1.823427  [ DEG:    75.5253   -104.4747 ]
  Theta =   0.580264    2.561329  [ DEG:    33.2467    146.7533 ]
  Phi   =  -2.298143    0.843449  [ DEG:  -131.6739     48.3261 ]
 
# 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: T0352TS102_4                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS102_4.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  109   5.0    5   1.16    0.00   4.446
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS102_4
PFRMAT TS
TARGET T0352
MODEL 4
PARENT 2afb_A
ATOM      1  N   HIS   113     -21.312   7.874   9.653  1.00  1.00
ATOM      2  CA  HIS   113     -22.028   6.997   8.660  1.00  1.00
ATOM      3  C   HIS   113     -23.371   7.616   8.188  1.00  1.00
ATOM      4  O   HIS   113     -23.796   8.659   8.702  1.00  1.00
ATOM      5  CB  HIS   113     -22.240   5.595   9.263  1.00  1.00
ATOM      6  N   HIS   114     -24.024   6.974   7.213  1.00  1.00
ATOM      7  CA  HIS   114     -25.281   7.478   6.607  1.00  1.00
ATOM      8  C   HIS   114     -26.465   6.507   6.805  1.00  1.00
ATOM      9  O   HIS   114     -26.265   5.300   6.743  1.00  1.00
ATOM     10  CB  HIS   114     -25.098   7.649   5.090  1.00  1.00
ATOM     11  N   HIS   115     -27.689   7.020   6.979  1.00  1.00
ATOM     12  CA  HIS   115     -28.902   6.188   6.828  1.00  1.00
ATOM     13  C   HIS   115     -28.928   5.551   5.425  1.00  1.00
ATOM     14  O   HIS   115     -28.562   6.194   4.453  1.00  1.00
ATOM     15  CB  HIS   115     -30.190   7.009   7.033  1.00  1.00
ATOM     16  N   HIS   116     -29.352   4.295   5.321  1.00  1.00
ATOM     17  CA  HIS   116     -29.540   3.659   4.026  1.00  1.00
ATOM     18  C   HIS   116     -30.981   3.255   3.881  1.00  1.00
ATOM     19  O   HIS   116     -31.414   2.354   4.558  1.00  1.00
ATOM     20  CB  HIS   116     -28.655   2.415   3.887  1.00  1.00
ATOM     21  N   HIS   117     -31.716   3.866   2.962  1.00  1.00
ATOM     22  CA  HIS   117     -33.125   3.531   2.769  1.00  1.00
ATOM     23  C   HIS   117     -33.202   2.234   1.993  1.00  1.00
ATOM     24  O   HIS   117     -33.599   2.229   0.851  1.00  1.00
ATOM     25  CB  HIS   117     -33.893   4.676   2.090  1.00  1.00
TER
END
