
#######################################################
#                                                     #
#                        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 T0378AL243_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL243_4-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    T      79      G      29          2.384
LGA    T      80      P      30          2.976
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    P      81      M      44           #
LGA    Q      82      L      45          3.161
LGA    P      83      V      46          4.013
LGA    L      84      G      47          3.724
LGA    M      85      -       -           -
LGA    A      86      T      48          4.191
LGA    V      87      A      49          3.778
LGA    F      88      A      50          3.222
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    D      89      E      65          4.606
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    -       -      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    3.62     0.00      6.119     0.242

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.506612 * X  +  -0.721243 * Y  +  -0.472390 * Z  + -11.412090
  Y_new =  -0.861859 * X  +  -0.438457 * Y  +  -0.254860 * Z  +  50.015789
  Z_new =  -0.023307 * X  +   0.536249 * Y  +  -0.843738 * Z  +  53.678596 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.575433   -0.566160  [ DEG:   147.5614    -32.4386 ]
  Theta =   0.023309    3.118284  [ DEG:     1.3355    178.6645 ]
  Phi   =  -1.039386    2.102206  [ DEG:   -59.5524    120.4476 ]
 
# 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: T0378AL243_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL243_4-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   3.62    0.00   6.119
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL243_4-D1
REMARK Aligment from pdb entry: 1v2xA
ATOM      1  N   THR    79       4.811  20.300  44.635  1.00  0.00              
ATOM      2  CA  THR    79       4.141  20.695  43.407  1.00  0.00              
ATOM      3  C   THR    79       2.626  20.510  43.510  1.00  0.00              
ATOM      4  O   THR    79       1.845  21.302  42.979  1.00  0.00              
ATOM      5  N   THR    80       2.214  19.468  44.218  1.00  0.00              
ATOM      6  CA  THR    80       0.800  19.171  44.334  1.00  0.00              
ATOM      7  C   THR    80       0.248  19.464  45.738  1.00  0.00              
ATOM      8  O   THR    80      -0.690  20.246  45.893  1.00  0.00              
ATOM      9  N   PRO    81       0.853  18.874  46.759  1.00  0.00              
ATOM     10  CA  PRO    81       0.394  19.068  48.131  1.00  0.00              
ATOM     11  C   PRO    81       0.360  20.535  48.523  1.00  0.00              
ATOM     12  O   PRO    81      -0.423  20.927  49.379  1.00  0.00              
ATOM     13  N   GLN    82       1.188  21.355  47.892  1.00  0.00              
ATOM     14  CA  GLN    82       1.216  22.764  48.250  1.00  0.00              
ATOM     15  C   GLN    82       0.489  23.682  47.275  1.00  0.00              
ATOM     16  O   GLN    82      -0.687  23.989  47.455  1.00  0.00              
ATOM     17  N   PRO    83       1.212  24.125  46.253  1.00  0.00              
ATOM     18  CA  PRO    83       0.677  25.023  45.251  1.00  0.00              
ATOM     19  C   PRO    83      -0.716  24.578  44.818  1.00  0.00              
ATOM     20  O   PRO    83      -1.684  25.323  44.949  1.00  0.00              
ATOM     21  N   LEU    84      -0.797  23.349  44.319  1.00  0.00              
ATOM     22  CA  LEU    84      -2.037  22.762  43.840  1.00  0.00              
ATOM     23  C   LEU    84      -3.200  22.858  44.836  1.00  0.00              
ATOM     24  O   LEU    84      -4.264  23.370  44.497  1.00  0.00              
ATOM     25  N   MET    85      -2.983  22.374  46.054  1.00  0.00              
ATOM     26  CA  MET    85      -3.998  22.372  47.115  1.00  0.00              
ATOM     27  C   MET    85      -4.399  23.765  47.610  1.00  0.00              
ATOM     28  O   MET    85      -5.592  24.030  47.781  1.00  0.00              
ATOM     29  N   ALA    86      -3.435  24.654  47.844  1.00  0.00              
ATOM     30  CA  ALA    86      -3.795  25.990  48.317  1.00  0.00              
ATOM     31  C   ALA    86      -4.561  26.791  47.256  1.00  0.00              
ATOM     32  O   ALA    86      -5.490  27.523  47.579  1.00  0.00              
ATOM     33  N   VAL    87      -4.180  26.656  45.990  1.00  0.00              
ATOM     34  CA  VAL    87      -4.863  27.378  44.929  1.00  0.00              
ATOM     35  C   VAL    87      -6.329  26.931  44.777  1.00  0.00              
ATOM     36  O   VAL    87      -7.230  27.742  44.519  1.00  0.00              
ATOM     37  N   PHE    88      -6.571  25.634  44.916  1.00  0.00              
ATOM     38  CA  PHE    88      -7.928  25.151  44.747  1.00  0.00              
ATOM     39  C   PHE    88      -8.709  25.580  45.956  1.00  0.00              
ATOM     40  O   PHE    88      -9.878  25.922  45.840  1.00  0.00              
ATOM     41  N   ASP    89      -8.071  25.549  47.114  1.00  0.00              
ATOM     42  CA  ASP    89      -8.759  25.957  48.336  1.00  0.00              
ATOM     43  C   ASP    89      -9.336  27.352  48.152  1.00  0.00              
ATOM     44  O   ASP    89     -10.485  27.614  48.507  1.00  0.00              
END
