
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0378AL333_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL333_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    M       1      L      45          1.879
LGA    L       2      V      46          1.339
LGA    Q       6      G      47          1.641
LGA    I       7      T      48          4.064
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    K       8      V      64          4.064
LGA    F       9      E      65          3.600
LGA    L      10      L      66          2.929
LGA    R      11      -       -           -
LGA    V      87      -       -           -
LGA    F      88      P      67          1.932
LGA    D      89      E      68          2.481
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    -       -      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)   11   89    5.0      9    2.84    11.11      7.124     0.306

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.568017 * X  +   0.003716 * Y  +  -0.823008 * Z  + -15.046292
  Y_new =  -0.338774 * X  +   0.912400 * Y  +  -0.229692 * Z  +  40.970409
  Z_new =   0.750059 * X  +   0.409283 * Y  +   0.519518 * Z  +  19.090694 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.667265   -2.474327  [ DEG:    38.2315   -141.7685 ]
  Theta =  -0.848152   -2.293441  [ DEG:   -48.5955   -131.4045 ]
  Phi   =  -0.537779    2.603813  [ DEG:   -30.8125    149.1875 ]
 
# 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_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL333_3-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   89   5.0    9   2.84   11.11   7.124
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL333_3-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   MET     1       0.728  22.539  50.383  1.00  0.00              
ATOM      2  CA  MET     1      -0.364  23.187  51.171  1.00  0.00              
ATOM      3  C   MET     1      -0.710  24.584  50.666  1.00  0.00              
ATOM      4  O   MET     1      -1.886  24.920  50.517  1.00  0.00              
ATOM      5  N   LEU     2       0.307  25.407  50.420  1.00  0.00              
ATOM      6  CA  LEU     2       0.048  26.755  49.940  1.00  0.00              
ATOM      7  C   LEU     2      -0.155  26.717  48.425  1.00  0.00              
ATOM      8  O   LEU     2      -0.716  27.637  47.835  1.00  0.00              
ATOM      9  N   GLN     6       0.297  25.645  47.793  1.00  0.00              
ATOM     10  CA  GLN     6       0.120  25.510  46.355  1.00  0.00              
ATOM     11  C   GLN     6      -1.375  25.236  46.149  1.00  0.00              
ATOM     12  O   GLN     6      -2.003  25.692  45.188  1.00  0.00              
ATOM     13  N   ILE     7      -1.930  24.494  47.099  1.00  0.00              
ATOM     14  CA  ILE     7      -3.331  24.109  47.118  1.00  0.00              
ATOM     15  C   ILE     7      -4.229  25.281  47.515  1.00  0.00              
ATOM     16  O   ILE     7      -5.341  25.439  47.007  1.00  0.00              
ATOM     17  N   LYS     8      -3.731  26.120  48.412  1.00  0.00              
ATOM     18  CA  LYS     8      -4.520  27.234  48.897  1.00  0.00              
ATOM     19  C   LYS     8      -4.016  28.588  48.372  1.00  0.00              
ATOM     20  O   LYS     8      -4.762  29.333  47.737  1.00  0.00              
ATOM     21  N   PHE     9      -2.744  28.887  48.600  1.00  0.00              
ATOM     22  CA  PHE     9      -2.171  30.155  48.163  1.00  0.00              
ATOM     23  C   PHE     9      -2.339  30.379  46.669  1.00  0.00              
ATOM     24  O   PHE     9      -2.392  31.515  46.218  1.00  0.00              
ATOM     25  N   LEU    10      -2.443  29.305  45.901  1.00  0.00              
ATOM     26  CA  LEU    10      -2.576  29.463  44.461  1.00  0.00              
ATOM     27  C   LEU    10      -3.990  29.267  43.929  1.00  0.00              
ATOM     28  O   LEU    10      -4.746  30.225  43.781  1.00  0.00              
ATOM     29  N   ARG    11      -4.325  28.018  43.629  1.00  0.00              
ATOM     30  CA  ARG    11      -5.624  27.667  43.092  1.00  0.00              
ATOM     31  C   ARG    11      -6.733  28.394  43.844  1.00  0.00              
ATOM     32  O   ARG    11      -7.505  29.146  43.255  1.00  0.00              
ATOM     33  N   VAL    87      -6.782  28.169  45.153  1.00  0.00              
ATOM     34  CA  VAL    87      -7.780  28.761  46.028  1.00  0.00              
ATOM     35  C   VAL    87      -7.911  30.284  45.887  1.00  0.00              
ATOM     36  O   VAL    87      -9.003  30.791  45.647  1.00  0.00              
ATOM     37  N   PHE    88      -6.796  30.993  46.028  1.00  0.00              
ATOM     38  CA  PHE    88      -6.755  32.458  45.942  1.00  0.00              
ATOM     39  C   PHE    88      -7.079  33.020  44.555  1.00  0.00              
ATOM     40  O   PHE    88      -7.840  33.985  44.452  1.00  0.00              
ATOM     41  N   ASP    89      -6.519  32.443  43.492  1.00  0.00              
ATOM     42  CA  ASP    89      -6.815  32.962  42.159  1.00  0.00              
ATOM     43  C   ASP    89      -8.281  32.742  41.765  1.00  0.00              
ATOM     44  O   ASP    89      -8.892  33.599  41.136  1.00  0.00              
END
