
#######################################################
#                                                     #
#                        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 T0351TS102_1
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS102_1.T0351.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    -       -      I       2           -
LGA    -       -      L       3           -
LGA    -       -      Y       4           -
LGA    -       -      D       5           -
LGA    -       -      A       6           -
LGA    -       -      I       7           -
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      S      16           -
LGA    -       -      R      17           -
LGA    H     113      K      18          1.357
LGA    H     114      D      19          0.406
LGA    H     115      F      20          0.535
LGA    H     116      E      21          0.672
LGA    H     117      L      22          0.828
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    -       -      I      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      W      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    -       -      A      38           -
LGA    -       -      P      39           -
LGA    -       -      L      40           -
LGA    -       -      P      41           -
LGA    -       -      T      42           -
LGA    -       -      Q      43           -
LGA    -       -      A      44           -
LGA    -       -      E      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      T      48           -
LGA    -       -      W      49           -
LGA    -       -      W      50           -
LGA    -       -      E      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      K      55           -
LGA    -       -      N      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   56    5.0      5    0.83     0.00      8.788     0.539

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.895365 * X  +  -0.116780 * Y  +  -0.429748 * Z  + -138.908417
  Y_new =   0.430224 * X  +   0.476056 * Y  +   0.766993 * Z  + -201.060822
  Z_new =   0.115014 * X  +  -0.871627 * Y  +   0.476485 * Z  + 105.744255 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.070519    2.071073  [ DEG:   -61.3362    118.6637 ]
  Theta =  -0.115269   -3.026323  [ DEG:    -6.6044   -173.3956 ]
  Phi   =   0.447927   -2.693666  [ DEG:    25.6643   -154.3357 ]
 
# 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: T0351TS102_1                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS102_1.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   56   5.0    5   0.83    0.00   8.788
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS102_1
PFRMAT TS
TARGET T0351
MODEL 1
PARENT 1vlv_A
ATOM      1  N   HIS   113      -2.373  13.831   2.887  1.00  1.00
ATOM      2  CA  HIS   113      -1.137  13.251   3.486  1.00  1.00
ATOM      3  C   HIS   113      -0.203  12.750   2.394  1.00  1.00
ATOM      4  O   HIS   113       0.557  11.801   2.661  1.00  1.00
ATOM      5  CB  HIS   113      -1.434  12.014   4.389  1.00  1.00
ATOM      6  N   HIS   114      -0.220  13.376   1.203  1.00  1.00
ATOM      7  CA  HIS   114       0.252  12.767  -0.098  1.00  1.00
ATOM      8  C   HIS   114      -0.733  11.708  -0.641  1.00  1.00
ATOM      9  O   HIS   114      -1.139  11.810  -1.800  1.00  1.00
ATOM     10  CB  HIS   114       1.654  12.159  -0.054  1.00  1.00
ATOM     11  N   HIS   115      -1.034  10.674   0.155  1.00  1.00
ATOM     12  CA  HIS   115      -2.279   9.887  -0.014  1.00  1.00
ATOM     13  C   HIS   115      -3.068  10.101   1.245  1.00  1.00
ATOM     14  O   HIS   115      -2.693   9.630   2.315  1.00  1.00
ATOM     15  CB  HIS   115      -2.057   8.388  -0.272  1.00  1.00
ATOM     16  N   HIS   116      -4.148  10.858   1.110  1.00  1.00
ATOM     17  CA  HIS   116      -5.061  11.113   2.207  1.00  1.00
ATOM     18  C   HIS   116      -5.809   9.826   2.679  1.00  1.00
ATOM     19  O   HIS   116      -6.419   9.119   1.866  1.00  1.00
ATOM     20  CB  HIS   116      -6.042  12.204   1.752  1.00  1.00
ATOM     21  N   HIS   117      -5.763   9.542   3.986  1.00  1.00
ATOM     22  CA  HIS   117      -6.458   8.403   4.569  1.00  1.00
ATOM     23  C   HIS   117      -7.957   8.710   4.707  1.00  1.00
ATOM     24  O   HIS   117      -8.311   9.739   5.311  1.00  1.00
ATOM     25  CB  HIS   117      -5.893   8.047   5.958  1.00  1.00
TER
END
