
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0304AL586_1
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304AL586_1.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# 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    -       -      D      16           -
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    V     110      M      70          0.419
LGA    Y     111      K      71          2.153
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    L     112      E      74          1.530
LGA    A     113      L      75          1.176
LGA    V     114      M      76          3.107
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    Y     115      G      80          3.708
LGA    P     116      E      81          0.884
LGA    T     117      L      82          2.233
LGA    P     118      N      83          4.572
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    E     119      T     103          2.249
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    M     120      V     110          1.554
LGA    K     121      Y     111          1.634
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -
LGA    -       -      P     118           -
LGA    -       -      E     119           -
LGA    -       -      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  107    5.0     12    2.39     0.00      8.715     0.481

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.526717 * X  +  -0.449647 * Y  +  -0.721379 * Z  +  60.225208
  Y_new =  -0.401893 * X  +   0.616070 * Y  +  -0.677450 * Z  +  24.109594
  Z_new =   0.749033 * X  +   0.646742 * Y  +   0.143784 * Z  +  49.929329 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.352033   -1.789559  [ DEG:    77.4658   -102.5342 ]
  Theta =  -0.846602   -2.294991  [ DEG:   -48.5067   -131.4933 ]
  Phi   =  -0.651780    2.489813  [ DEG:   -37.3442    142.6558 ]
 
# 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: T0304AL586_1                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL586_1.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  107   5.0   12   2.39    0.00   8.715
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL586_1
REMARK Aligment from pdb entry: 1fmb
ATOM      1  N   VAL   110      53.836  22.343  43.547  1.00  0.00              
ATOM      2  CA  VAL   110      54.218  23.688  43.032  1.00  0.00              
ATOM      3  C   VAL   110      55.109  24.342  44.091  1.00  0.00              
ATOM      4  O   VAL   110      55.135  23.959  45.250  1.00  0.00              
ATOM      5  N   TYR   111      55.836  25.311  43.597  1.00  0.00              
ATOM      6  CA  TYR   111      56.829  26.043  44.366  1.00  0.00              
ATOM      7  C   TYR   111      56.460  27.499  44.500  1.00  0.00              
ATOM      8  O   TYR   111      56.149  28.124  43.515  1.00  0.00              
ATOM      9  N   LEU   112      56.534  28.031  45.723  1.00  0.00              
ATOM     10  CA  LEU   112      56.255  29.441  45.965  1.00  0.00              
ATOM     11  C   LEU   112      57.608  30.034  46.338  1.00  0.00              
ATOM     12  O   LEU   112      58.213  29.602  47.323  1.00  0.00              
ATOM     13  N   ALA   113      58.044  30.992  45.588  1.00  0.00              
ATOM     14  CA  ALA   113      59.322  31.684  45.701  1.00  0.00              
ATOM     15  C   ALA   113      59.262  32.919  46.605  1.00  0.00              
ATOM     16  O   ALA   113      60.259  33.647  46.748  1.00  0.00              
ATOM     17  N   VAL   114      58.049  33.136  47.153  1.00  0.00              
ATOM     18  CA  VAL   114      57.839  34.208  48.132  1.00  0.00              
ATOM     19  C   VAL   114      57.933  35.634  47.697  1.00  0.00              
ATOM     20  O   VAL   114      57.839  36.558  48.514  1.00  0.00              
ATOM     21  N   TYR   115      57.903  35.890  46.369  1.00  0.00              
ATOM     22  CA  TYR   115      57.766  37.233  45.821  1.00  0.00              
ATOM     23  C   TYR   115      56.357  37.766  46.166  1.00  0.00              
ATOM     24  O   TYR   115      56.200  38.978  46.312  1.00  0.00              
ATOM     25  N   PRO   116      55.408  36.856  46.276  1.00  0.00              
ATOM     26  CA  PRO   116      54.038  37.262  46.658  1.00  0.00              
ATOM     27  C   PRO   116      53.597  36.421  47.835  1.00  0.00              
ATOM     28  O   PRO   116      54.273  35.429  48.238  1.00  0.00              
ATOM     29  N   THR   117      52.498  36.811  48.545  1.00  0.00              
ATOM     30  CA  THR   117      52.160  35.921  49.686  1.00  0.00              
ATOM     31  C   THR   117      51.777  34.564  49.073  1.00  0.00              
ATOM     32  O   THR   117      51.073  34.579  48.035  1.00  0.00              
ATOM     33  N   PRO   118      52.145  33.480  49.697  1.00  0.00              
ATOM     34  CA  PRO   118      51.859  32.134  49.171  1.00  0.00              
ATOM     35  C   PRO   118      50.418  31.757  49.541  1.00  0.00              
ATOM     36  O   PRO   118      50.026  31.324  50.637  1.00  0.00              
ATOM     37  N   GLU   119      49.549  31.948  48.534  1.00  0.00              
ATOM     38  CA  GLU   119      48.135  31.637  48.697  1.00  0.00              
ATOM     39  C   GLU   119      47.700  30.523  47.727  1.00  0.00              
ATOM     40  O   GLU   119      48.298  30.416  46.656  1.00  0.00              
ATOM     41  N   MET   120      46.658  29.806  48.181  1.00  0.00              
ATOM     42  CA  MET   120      46.146  28.759  47.276  1.00  0.00              
ATOM     43  C   MET   120      44.667  28.584  47.574  1.00  0.00              
ATOM     44  O   MET   120      44.189  29.068  48.608  1.00  0.00              
ATOM     45  N   LYS   121      43.954  27.966  46.629  1.00  0.00              
ATOM     46  CA  LYS   121      42.540  27.682  46.841  1.00  0.00              
ATOM     47  C   LYS   121      42.420  26.268  47.377  1.00  0.00              
ATOM     48  O   LYS   121      42.985  25.283  46.840  1.00  0.00              
END
