
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0378AL242_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL242_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    -       -      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      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    M      85      T      77          0.979
LGA    A      86      Q      78          0.855
LGA    V      87      T      79          0.495
LGA    F      88      T      80          0.787
LGA    D      89      P      81          0.843
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    0.81     0.00      5.618     0.551

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.677593 * X  +  -0.607744 * Y  +  -0.414143 * Z  +  93.935501
  Y_new =   0.309709 * X  +  -0.746561 * Y  +   0.588835 * Z  +  73.973129
  Z_new =  -0.667044 * X  +   0.270727 * Y  +   0.694089 * Z  +   6.892302 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.371896   -2.769697  [ DEG:    21.3081   -158.6919 ]
  Theta =   0.730234    2.411359  [ DEG:    41.8393    138.1607 ]
  Phi   =   2.712873   -0.428720  [ DEG:   155.4362    -24.5638 ]
 
# 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: T0378AL242_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL242_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   0.81    0.00   5.618
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL242_3-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   MET    85      12.548  26.548  41.930  1.00  0.00              
ATOM      2  CA  MET    85      11.545  26.915  40.941  1.00  0.00              
ATOM      3  C   MET    85      12.053  26.736  39.529  1.00  0.00              
ATOM      4  O   MET    85      13.171  27.137  39.216  1.00  0.00              
ATOM      5  N   ALA    86      11.232  26.130  38.679  1.00  0.00              
ATOM      6  CA  ALA    86      11.596  25.941  37.281  1.00  0.00              
ATOM      7  C   ALA    86      10.742  26.920  36.485  1.00  0.00              
ATOM      8  O   ALA    86       9.712  27.392  36.969  1.00  0.00              
ATOM      9  N   VAL    87      11.178  27.220  35.268  1.00  0.00              
ATOM     10  CA  VAL    87      10.482  28.145  34.387  1.00  0.00              
ATOM     11  C   VAL    87       8.989  27.913  34.375  1.00  0.00              
ATOM     12  O   VAL    87       8.199  28.855  34.339  1.00  0.00              
ATOM     13  N   PHE    88       8.612  26.642  34.421  1.00  0.00              
ATOM     14  CA  PHE    88       7.213  26.243  34.390  1.00  0.00              
ATOM     15  C   PHE    88       6.390  26.781  35.550  1.00  0.00              
ATOM     16  O   PHE    88       5.260  27.218  35.347  1.00  0.00              
ATOM     17  N   ASP    89       6.936  26.754  36.762  1.00  0.00              
ATOM     18  CA  ASP    89       6.161  27.234  37.902  1.00  0.00              
ATOM     19  C   ASP    89       6.286  28.727  38.199  1.00  0.00              
ATOM     20  O   ASP    89       5.927  29.184  39.285  1.00  0.00              
END
