
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0372AL257_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL257_5-D1.T0372_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    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    D      13      L      29          2.659
LGA    T      14      S      30          1.379
LGA    I      15      F      31          0.824
LGA    T      16      S      32          0.956
LGA    A      17      N      33          1.054
LGA    F      18      L      34          0.513
LGA    T      19      C      35          0.466
LGA    M      20      S      36          0.630
LGA    K      21      W      37          0.644
LGA    S      22      R      38          0.717
LGA    D      23      F      39          0.610
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    K     290      L     295          1.902
LGA    Y     291      K     296          1.038
LGA    M     292      D     297          1.735
LGA    A     293      H     298          4.212
LGA    C     294      -       -           -
LGA    L     295      -       -           -
LGA    K     296      -       -           -
LGA    D     297      -       -           -
LGA    H     298      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20  126    5.0     15    1.62     0.00     11.219     0.873

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.857202 * X  +   0.450856 * Y  +  -0.248865 * Z  +   5.125581
  Y_new =  -0.403962 * X  +   0.288955 * Y  +  -0.867940 * Z  + 134.353210
  Z_new =  -0.319405 * X  +   0.844532 * Y  +   0.429821 * Z  + -86.654411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.100018   -2.041575  [ DEG:    63.0264   -116.9736 ]
  Theta =   0.325101    2.816491  [ DEG:    18.6269    161.3731 ]
  Phi   =  -0.440390    2.701203  [ DEG:   -25.2325    154.7675 ]
 
# 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: T0372AL257_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL257_5-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  126   5.0   15   1.62    0.00  11.219
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL257_5-D1
REMARK Aligment from pdb entry: 1lrz_A
ATOM      1  N   ASP    13      35.578  50.297  13.332  1.00  0.00              
ATOM      2  CA  ASP    13      36.916  49.731  13.427  1.00  0.00              
ATOM      3  C   ASP    13      37.943  50.788  13.759  1.00  0.00              
ATOM      4  O   ASP    13      37.758  51.964  13.440  1.00  0.00              
ATOM      5  N   THR    14      39.006  50.365  14.436  1.00  0.00              
ATOM      6  CA  THR    14      40.103  51.247  14.796  1.00  0.00              
ATOM      7  C   THR    14      41.259  50.843  13.897  1.00  0.00              
ATOM      8  O   THR    14      41.200  49.819  13.203  1.00  0.00              
ATOM      9  N   ILE    15      42.319  51.639  13.932  1.00  0.00              
ATOM     10  CA  ILE    15      43.504  51.364  13.138  1.00  0.00              
ATOM     11  C   ILE    15      44.083  49.990  13.492  1.00  0.00              
ATOM     12  O   ILE    15      44.566  49.266  12.613  1.00  0.00              
ATOM     13  N   THR    16      44.037  49.626  14.778  1.00  0.00              
ATOM     14  CA  THR    16      44.565  48.327  15.209  1.00  0.00              
ATOM     15  C   THR    16      43.757  47.193  14.600  1.00  0.00              
ATOM     16  O   THR    16      44.318  46.162  14.249  1.00  0.00              
ATOM     17  N   ALA    17      42.441  47.379  14.496  1.00  0.00              
ATOM     18  CA  ALA    17      41.572  46.372  13.880  1.00  0.00              
ATOM     19  C   ALA    17      41.966  46.215  12.408  1.00  0.00              
ATOM     20  O   ALA    17      42.027  45.104  11.868  1.00  0.00              
ATOM     21  N   PHE    18      42.213  47.343  11.752  1.00  0.00              
ATOM     22  CA  PHE    18      42.550  47.307  10.335  1.00  0.00              
ATOM     23  C   PHE    18      43.858  46.566  10.098  1.00  0.00              
ATOM     24  O   PHE    18      43.946  45.716   9.207  1.00  0.00              
ATOM     25  N   THR    19      44.870  46.878  10.896  1.00  0.00              
ATOM     26  CA  THR    19      46.158  46.209  10.762  1.00  0.00              
ATOM     27  C   THR    19      46.006  44.724  11.080  1.00  0.00              
ATOM     28  O   THR    19      46.599  43.877  10.412  1.00  0.00              
ATOM     29  N   MET    20      45.205  44.402  12.091  1.00  0.00              
ATOM     30  CA  MET    20      45.029  42.999  12.463  1.00  0.00              
ATOM     31  C   MET    20      44.372  42.181  11.362  1.00  0.00              
ATOM     32  O   MET    20      44.649  40.996  11.238  1.00  0.00              
ATOM     33  N   LYS    21      43.514  42.812  10.559  1.00  0.00              
ATOM     34  CA  LYS    21      42.823  42.098   9.490  1.00  0.00              
ATOM     35  C   LYS    21      43.604  42.033   8.176  1.00  0.00              
ATOM     36  O   LYS    21      43.143  41.412   7.227  1.00  0.00              
ATOM     37  N   SER    22      44.764  42.687   8.115  1.00  0.00              
ATOM     38  CA  SER    22      45.603  42.653   6.912  1.00  0.00              
ATOM     39  C   SER    22      46.240  41.269   6.845  1.00  0.00              
ATOM     40  O   SER    22      46.341  40.592   7.865  1.00  0.00              
ATOM     41  N   ASP    23      46.677  40.846   5.659  1.00  0.00              
ATOM     42  CA  ASP    23      47.350  39.559   5.578  1.00  0.00              
ATOM     43  C   ASP    23      48.811  39.779   6.018  1.00  0.00              
ATOM     44  O   ASP    23      49.254  40.926   6.205  1.00  0.00              
ATOM    561  N   LYS   290      28.881  46.979  -9.382  1.00  0.00              
ATOM    562  CA  LYS   290      27.738  47.864  -9.551  1.00  0.00              
ATOM    563  C   LYS   290      26.850  47.449 -10.728  1.00  0.00              
ATOM    564  O   LYS   290      27.256  46.653 -11.573  1.00  0.00              
ATOM    565  N   TYR   291      25.634  47.986 -10.781  1.00  0.00              
ATOM    566  CA  TYR   291      24.698  47.626 -11.840  1.00  0.00              
ATOM    567  C   TYR   291      25.183  47.926 -13.251  1.00  0.00              
ATOM    568  O   TYR   291      24.850  47.197 -14.183  1.00  0.00              
ATOM    569  N   MET   292      25.970  48.985 -13.415  1.00  0.00              
ATOM    570  CA  MET   292      26.466  49.305 -14.744  1.00  0.00              
ATOM    571  C   MET   292      25.804  50.498 -15.417  1.00  0.00              
ATOM    572  O   MET   292      25.274  51.401 -14.753  1.00  0.00              
ATOM    573  N   ALA   293      25.815  50.479 -16.747  1.00  0.00              
ATOM    574  CA  ALA   293      25.287  51.566 -17.569  1.00  0.00              
ATOM    575  C   ALA   293      23.970  51.309 -18.282  1.00  0.00              
ATOM    576  O   ALA   293      23.717  50.210 -18.768  1.00  0.00              
ATOM    577  N   CYS   294      23.142  52.346 -18.355  1.00  0.00              
ATOM    578  CA  CYS   294      21.857  52.257 -19.033  1.00  0.00              
ATOM    579  C   CYS   294      21.707  53.458 -19.964  1.00  0.00              
ATOM    580  O   CYS   294      22.024  54.602 -19.605  1.00  0.00              
ATOM    581  N   LEU   295      21.206  53.192 -21.163  1.00  0.00              
ATOM    582  CA  LEU   295      21.033  54.230 -22.160  1.00  0.00              
ATOM    583  C   LEU   295      19.593  54.284 -22.638  1.00  0.00              
ATOM    584  O   LEU   295      19.002  53.262 -22.972  1.00  0.00              
ATOM    585  N   LYS   296      19.015  55.479 -22.633  1.00  0.00              
ATOM    586  CA  LYS   296      17.658  55.638 -23.114  1.00  0.00              
ATOM    587  C   LYS   296      17.693  56.550 -24.329  1.00  0.00              
ATOM    588  O   LYS   296      17.923  57.758 -24.213  1.00  0.00              
ATOM    589  N   ASP   297      17.495  55.976 -25.520  1.00  0.00              
ATOM    590  CA  ASP   297      17.503  56.770 -26.754  1.00  0.00              
ATOM    591  C   ASP   297      16.244  57.631 -26.757  1.00  0.00              
ATOM    592  O   ASP   297      15.158  57.113 -26.499  1.00  0.00              
ATOM    593  N   HIS   298      16.377  58.929 -27.032  1.00  0.00              
ATOM    594  CA  HIS   298      15.209  59.811 -27.072  1.00  0.00              
ATOM    595  C   HIS   298      14.638  59.892 -28.495  1.00  0.00              
ATOM    596  O   HIS   298      13.419  59.885 -28.683  1.00  0.00              
END
