
#######################################################
#                                                     #
#                        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 T0356AL381_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL381_3-D1.T0356_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    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    L      85      D      81          1.713
LGA    R      86      V      82          1.130
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    E      87      V     334           #
LGA    V      88      A     335          3.337
LGA    G      89      L     336          0.892
LGA    K      90      N     337          1.714
LGA    L      91      E     338          1.435
LGA    L      92      V     339          1.350
LGA    A      93      F     340          1.445
LGA    F      94      V     341          0.313
LGA    L      95      P     342          1.369
LGA    K      96      I     343          0.891
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  124    5.0     11    1.59     0.00      7.958     0.651

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.036645 * X  +   0.999198 * Y  +   0.016138 * Z  +  40.689564
  Y_new =  -0.198580 * X  +  -0.008546 * Y  +   0.980047 * Z  + 100.971184
  Z_new =   0.979399 * X  +  -0.039118 * Y  +   0.198108 * Z  +  68.097328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.194952    2.946641  [ DEG:   -11.1699    168.8301 ]
  Theta =  -1.367465   -1.774127  [ DEG:   -78.3500   -101.6500 ]
  Phi   =  -1.388315    1.753277  [ DEG:   -79.5446    100.4554 ]
 
# 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: T0356AL381_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL381_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  124   5.0   11   1.59    0.00   7.958
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL381_3-D1
REMARK Aligment from pdb entry: 1om2A
ATOM      1  N   LEU    85      60.361  82.286  73.462  1.00  0.00              
ATOM      2  CA  LEU    85      58.969  82.643  73.648  1.00  0.00              
ATOM      3  C   LEU    85      58.053  81.462  73.340  1.00  0.00              
ATOM      4  O   LEU    85      56.900  81.473  73.764  1.00  0.00              
ATOM      5  N   ARG    86      58.548  80.443  72.624  1.00  0.00              
ATOM      6  CA  ARG    86      57.733  79.274  72.310  1.00  0.00              
ATOM      7  C   ARG    86      57.794  78.257  73.450  1.00  0.00              
ATOM      8  O   ARG    86      56.757  77.797  73.926  1.00  0.00              
ATOM      9  N   GLU    87      59.005  77.899  73.892  1.00  0.00              
ATOM     10  CA  GLU    87      59.212  76.945  74.974  1.00  0.00              
ATOM     11  C   GLU    87      59.076  75.487  74.521  1.00  0.00              
ATOM     12  O   GLU    87      59.140  74.581  75.349  1.00  0.00              
ATOM     13  N   VAL    88      61.053  74.021  71.637  1.00  0.00              
ATOM     14  CA  VAL    88      62.027  74.049  70.563  1.00  0.00              
ATOM     15  C   VAL    88      61.875  72.901  69.580  1.00  0.00              
ATOM     16  O   VAL    88      61.782  73.135  68.386  1.00  0.00              
ATOM     17  N   GLY    89      61.874  71.673  70.092  1.00  0.00              
ATOM     18  CA  GLY    89      61.815  70.449  69.302  1.00  0.00              
ATOM     19  C   GLY    89      60.650  70.425  68.317  1.00  0.00              
ATOM     20  O   GLY    89      60.825  69.977  67.183  1.00  0.00              
ATOM     21  N   LYS    90      59.471  70.914  68.716  1.00  0.00              
ATOM     22  CA  LYS    90      58.338  70.955  67.798  1.00  0.00              
ATOM     23  C   LYS    90      58.701  71.866  66.634  1.00  0.00              
ATOM     24  O   LYS    90      58.543  71.499  65.470  1.00  0.00              
ATOM     25  N   LEU    91      59.207  73.054  66.964  1.00  0.00              
ATOM     26  CA  LEU    91      59.605  74.006  65.952  1.00  0.00              
ATOM     27  C   LEU    91      60.744  73.442  65.095  1.00  0.00              
ATOM     28  O   LEU    91      60.757  73.652  63.890  1.00  0.00              
ATOM     29  N   LEU    92      61.703  72.716  65.672  1.00  0.00              
ATOM     30  CA  LEU    92      62.797  72.162  64.881  1.00  0.00              
ATOM     31  C   LEU    92      62.267  71.180  63.836  1.00  0.00              
ATOM     32  O   LEU    92      62.729  71.187  62.695  1.00  0.00              
ATOM     33  N   ALA    93      61.277  70.359  64.198  1.00  0.00              
ATOM     34  CA  ALA    93      60.675  69.430  63.252  1.00  0.00              
ATOM     35  C   ALA    93      59.966  70.230  62.157  1.00  0.00              
ATOM     36  O   ALA    93      60.035  69.878  60.978  1.00  0.00              
ATOM     37  N   PHE    94      59.292  71.314  62.549  1.00  0.00              
ATOM     38  CA  PHE    94      58.570  72.189  61.634  1.00  0.00              
ATOM     39  C   PHE    94      59.516  72.922  60.679  1.00  0.00              
ATOM     40  O   PHE    94      59.173  73.147  59.520  1.00  0.00              
ATOM     41  N   LEU    95      60.718  73.261  61.150  1.00  0.00              
ATOM     42  CA  LEU    95      61.730  73.947  60.355  1.00  0.00              
ATOM     43  C   LEU    95      62.430  72.946  59.440  1.00  0.00              
ATOM     44  O   LEU    95      62.845  73.330  58.352  1.00  0.00              
ATOM     45  N   LYS    96      62.575  71.684  59.855  1.00  0.00              
ATOM     46  CA  LYS    96      63.261  70.686  59.040  1.00  0.00              
ATOM     47  C   LYS    96      62.388  70.207  57.877  1.00  0.00              
ATOM     48  O   LYS    96      62.914  69.766  56.858  1.00  0.00              
END
