
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0372AL257_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL257_3-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    F       4      M       1           -
LGA    K       5      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    K     290      R      25          0.760
LGA    Y     291      N      26          1.613
LGA    M     292      C      27          1.206
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    A     293      S      30          1.522
LGA    C     294      F      31          1.798
LGA    L     295      S      32          3.021
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    K     296      C      35          2.362
LGA    H     298      S      36          2.735
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
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    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  126    5.0      8    2.01     0.00      5.335     0.379

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.380378 * X  +  -0.918015 * Y  +  -0.112076 * Z  +  37.276939
  Y_new =   0.882242 * X  +   0.323836 * Y  +   0.341730 * Z  +  33.177914
  Z_new =  -0.277419 * X  +  -0.228864 * Y  +   0.933092 * Z  +  -1.770488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.240527    2.901066  [ DEG:   -13.7812    166.2188 ]
  Theta =   0.281107    2.860486  [ DEG:    16.1062    163.8938 ]
  Phi   =   1.163729   -1.977864  [ DEG:    66.6768   -113.3232 ]
 
# 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_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL257_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  126   5.0    8   2.01    0.00   5.335
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL257_3-D1
REMARK Aligment from pdb entry: 1ne9_A
ATOM      1  N   PHE     4      11.800  61.839   5.213  1.00  0.00              
ATOM      2  CA  PHE     4      11.834  62.693   6.383  1.00  0.00              
ATOM      3  C   PHE     4      10.559  63.181   7.031  1.00  0.00              
ATOM      4  O   PHE     4       9.493  63.202   6.415  1.00  0.00              
ATOM      5  N   LYS     5      10.664  63.578   8.309  1.00  0.00              
ATOM      6  CA  LYS     5       9.503  64.085   9.036  1.00  0.00              
ATOM      7  C   LYS     5       9.243  65.473   8.463  1.00  0.00              
ATOM      8  O   LYS     5      10.123  66.066   7.833  1.00  0.00              
ATOM    581  N   LYS   290      28.704  53.053  14.415  1.00  0.00              
ATOM    582  CA  LYS   290      30.017  53.078  15.047  1.00  0.00              
ATOM    583  C   LYS   290      30.760  51.854  14.543  1.00  0.00              
ATOM    584  O   LYS   290      30.364  50.725  14.814  1.00  0.00              
ATOM    585  N   TYR   291      31.841  52.083  13.813  1.00  0.00              
ATOM    586  CA  TYR   291      32.612  50.992  13.248  1.00  0.00              
ATOM    587  C   TYR   291      33.667  50.421  14.186  1.00  0.00              
ATOM    588  O   TYR   291      34.051  51.042  15.182  1.00  0.00              
ATOM    589  N   MET   292      34.128  49.226  13.841  1.00  0.00              
ATOM    590  CA  MET   292      35.129  48.502  14.611  1.00  0.00              
ATOM    591  C   MET   292      36.433  49.284  14.738  1.00  0.00              
ATOM    592  O   MET   292      37.217  49.054  15.656  1.00  0.00              
ATOM    593  N   ALA   293      36.663  50.214  13.819  1.00  0.00              
ATOM    594  CA  ALA   293      37.877  51.006  13.880  1.00  0.00              
ATOM    595  C   ALA   293      39.023  50.413  13.092  1.00  0.00              
ATOM    596  O   ALA   293      38.818  49.761  12.069  1.00  0.00              
ATOM    597  N   CYS   294      40.242  50.629  13.567  1.00  0.00              
ATOM    598  CA  CYS   294      41.402  50.111  12.860  1.00  0.00              
ATOM    599  C   CYS   294      41.827  48.749  13.377  1.00  0.00              
ATOM    600  O   CYS   294      41.966  48.538  14.582  1.00  0.00              
ATOM    601  N   LEU   295      41.998  47.820  12.444  1.00  0.00              
ATOM    602  CA  LEU   295      42.437  46.474  12.766  1.00  0.00              
ATOM    603  C   LEU   295      43.861  46.421  12.247  1.00  0.00              
ATOM    604  O   LEU   295      44.102  46.497  11.038  1.00  0.00              
ATOM    605  N   LYS   296      44.809  46.311  13.170  1.00  0.00              
ATOM    606  CA  LYS   296      46.215  46.292  12.804  1.00  0.00              
ATOM    607  C   LYS   296      46.868  44.927  12.899  1.00  0.00              
ATOM    608  O   LYS   296      46.787  44.264  13.932  1.00  0.00              
ATOM    609  N   HIS   298      47.501  44.510  11.810  1.00  0.00              
ATOM    610  CA  HIS   298      48.247  43.258  11.804  1.00  0.00              
ATOM    611  C   HIS   298      49.662  43.787  12.019  1.00  0.00              
ATOM    612  O   HIS   298      50.268  44.359  11.111  1.00  0.00              
END
