
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0378AL333_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL333_1-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    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    R      16      R      43          1.778
LGA    K      17      M      44          0.814
LGA    Y      18      L      45          0.498
LGA    R      19      V      46          0.504
LGA    V      87      G      47          0.653
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    F      88      P      83          2.369
LGA    D      89      L      84          1.544
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)    7   89    5.0      7    1.35    14.29      7.441     0.483

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.261322 * X  +   0.964640 * Y  +  -0.034346 * Z  + -83.841370
  Y_new =  -0.085185 * X  +  -0.058491 * Y  +  -0.994647 * Z  +  60.073284
  Z_new =  -0.961485 * X  +  -0.256997 * Y  +   0.097458 * Z  +  90.118546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.208332    1.933261  [ DEG:   -69.2323    110.7677 ]
  Theta =   1.292357    1.849236  [ DEG:    74.0466    105.9534 ]
  Phi   =  -2.826476    0.315117  [ DEG:  -161.9451     18.0549 ]
 
# 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: T0378AL333_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL333_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   89   5.0    7   1.35   14.29   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL333_1-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   ARG    16       5.687  20.679  56.625  1.00  0.00              
ATOM      2  CA  ARG    16       5.538  21.010  55.205  1.00  0.00              
ATOM      3  C   ARG    16       4.213  21.719  54.953  1.00  0.00              
ATOM      4  O   ARG    16       3.148  21.124  55.107  1.00  0.00              
ATOM      5  N   LYS    17       4.269  22.991  54.577  1.00  0.00              
ATOM      6  CA  LYS    17       3.041  23.720  54.305  1.00  0.00              
ATOM      7  C   LYS    17       2.809  23.713  52.797  1.00  0.00              
ATOM      8  O   LYS    17       3.650  24.183  52.029  1.00  0.00              
ATOM      9  N   TYR    18       1.677  23.160  52.373  1.00  0.00              
ATOM     10  CA  TYR    18       1.365  23.087  50.954  1.00  0.00              
ATOM     11  C   TYR    18       0.729  24.362  50.450  1.00  0.00              
ATOM     12  O   TYR    18      -0.170  24.902  51.088  1.00  0.00              
ATOM     13  N   ARG    19       1.202  24.844  49.305  1.00  0.00              
ATOM     14  CA  ARG    19       0.639  26.043  48.700  1.00  0.00              
ATOM     15  C   ARG    19      -0.156  25.573  47.488  1.00  0.00              
ATOM     16  O   ARG    19       0.063  24.469  46.984  1.00  0.00              
ATOM     17  N   VAL    87      -1.075  26.412  47.030  1.00  0.00              
ATOM     18  CA  VAL    87      -1.924  26.107  45.888  1.00  0.00              
ATOM     19  C   VAL    87      -1.148  25.492  44.745  1.00  0.00              
ATOM     20  O   VAL    87      -1.624  24.582  44.070  1.00  0.00              
ATOM     21  N   PHE    88       0.063  25.995  44.547  1.00  0.00              
ATOM     22  CA  PHE    88       0.931  25.535  43.473  1.00  0.00              
ATOM     23  C   PHE    88       1.292  24.060  43.558  1.00  0.00              
ATOM     24  O   PHE    88       1.296  23.372  42.539  1.00  0.00              
ATOM     25  N   ASP    89       1.597  23.564  44.752  1.00  0.00              
ATOM     26  CA  ASP    89       1.978  22.159  44.864  1.00  0.00              
ATOM     27  C   ASP    89       0.825  21.180  45.077  1.00  0.00              
ATOM     28  O   ASP    89       1.038  20.035  45.474  1.00  0.00              
END
