
#######################################################
#                                                     #
#                        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 T0335TS102_3
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS102_3.T0335.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    -       -      S       3           -
LGA    -       -      N       4           -
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    -       -      K      27           -
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    H      81      Q      30          2.044
LGA    H      82      Q      31          2.055
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    H      83      R      34          0.716
LGA    H      84      Q      35          1.903
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    H      85      L      38          1.712
LGA    -       -      K      39           -
LGA    -       -      G      40           -
LGA    -       -      F      41           -
LGA    -       -      R      42           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   42    5.0      5    1.76     0.00     11.184     0.269

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.105759 * X  +   0.772010 * Y  +  -0.626750 * Z  +  25.296879
  Y_new =  -0.843096 * X  +  -0.264583 * Y  +  -0.468171 * Z  +  28.387924
  Z_new =  -0.527260 * X  +   0.577924 * Y  +   0.622897 * Z  + -42.114426 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.747964   -2.393629  [ DEG:    42.8552   -137.1448 ]
  Theta =   0.555373    2.586220  [ DEG:    31.8205    148.1795 ]
  Phi   =  -1.446007    1.695586  [ DEG:   -82.8501     97.1499 ]
 
# 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: T0335TS102_3                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS102_3.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   42   5.0    5   1.76    0.00  11.184
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS102_3
PFRMAT TS
TARGET T0335
MODEL 3
PARENT 1zko_A
ATOM      1  N   HIS    81       2.580   1.976   3.854  1.00  1.00
ATOM      2  CA  HIS    81       3.426   1.949   2.629  1.00  1.00
ATOM      3  C   HIS    81       2.609   2.319   1.409  1.00  1.00
ATOM      4  O   HIS    81       1.449   1.927   1.282  1.00  1.00
ATOM      5  CB  HIS    81       4.066   0.575   2.447  1.00  1.00
ATOM      6  N   HIS    82       3.235   3.072   0.516  1.00  1.00
ATOM      7  CA  HIS    82       2.559   3.632  -0.642  1.00  1.00
ATOM      8  C   HIS    82       3.085   3.012  -1.923  1.00  1.00
ATOM      9  O   HIS    82       4.238   2.580  -1.976  1.00  1.00
ATOM     10  CB  HIS    82       2.711   5.150  -0.637  1.00  1.00
ATOM     11  N   HIS    83       2.222   2.939  -2.935  1.00  1.00
ATOM     12  CA  HIS    83       2.563   2.321  -4.213  1.00  1.00
ATOM     13  C   HIS    83       3.810   2.958  -4.822  1.00  1.00
ATOM     14  O   HIS    83       3.870   4.172  -5.022  1.00  1.00
ATOM     15  CB  HIS    83       1.369   2.429  -5.168  1.00  1.00
ATOM     16  N   HIS    84       4.810   2.130  -5.103  1.00  1.00
ATOM     17  CA  HIS    84       6.055   2.609  -5.681  1.00  1.00
ATOM     18  C   HIS    84       5.839   3.058  -7.117  1.00  1.00
ATOM     19  O   HIS    84       5.207   2.353  -7.897  1.00  1.00
ATOM     20  CB  HIS    84       7.095   1.492  -5.643  1.00  1.00
ATOM     21  N   HIS    85       6.356   4.238  -7.445  1.00  1.00
ATOM     22  CA  HIS    85       6.401   4.699  -8.824  1.00  1.00
ATOM     23  C   HIS    85       7.472   3.924  -9.576  1.00  1.00
ATOM     24  O   HIS    85       8.419   3.417  -8.975  1.00  1.00
ATOM     25  CB  HIS    85       6.762   6.173  -8.905  1.00  1.00
TER
END
