
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0283AL381_4
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283AL381_4.T0283  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    -       -      E       5           -
LGA    -       -      K       6           -
LGA    -       -      M       7           -
LGA    -       -      I       8           -
LGA    -       -      G       9           -
LGA    -       -      S      10           -
LGA    -       -      L      11           -
LGA    -       -      N      12           -
LGA    -       -      D      13           -
LGA    -       -      K      14           -
LGA    -       -      R      15           -
LGA    -       -      E      16           -
LGA    -       -      W      17           -
LGA    E      81      K      18          1.532
LGA    D      82      A      19          0.405
LGA    V      83      M      20          0.891
LGA    A      84      E      21          1.098
LGA    A      85      A      22          0.905
LGA    F      86      R      23          0.791
LGA    C      87      A      24          0.728
LGA    D      88      K      25          0.978
LGA    E      89      A      26          1.307
LGA    L      90      L      27          0.734
LGA    M      91      P      28          1.166
LGA    K      92      K      29          3.172
LGA    -       -      E      30           -
LGA    D      93      Y      31          1.537
LGA    T      94      H      32          1.850
LGA    K      95      H      33          0.884
LGA    T      96      A      34          3.524
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      I      57           -
LGA    -       -      F      58           -
LGA    -       -      G      59           -
LGA    -       -      G      60           -
LGA    -       -      I      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    -       -      F      65           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    -       -      K      74           -
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    -       -      V      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      F      86           -
LGA    -       -      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -
LGA    -       -      M      98           -
LGA    -       -      D      99           -
LGA    -       -      K     100           -
LGA    -       -      Y     101           -
LGA    -       -      R     102           -
LGA    -       -      T     103           -
LGA    -       -      K     104           -
LGA    -       -      L     105           -
LGA    -       -      N     106           -
LGA    -       -      D     107           -
LGA    -       -      S     108           -
LGA    -       -      I     109           -
LGA    -       -      G     110           -
LGA    -       -      R     111           -
LGA    -       -      D     112           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  112    5.0     16    1.58    18.75     13.499     0.951

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.303623 * X  +  -0.599204 * Y  +  -0.740789 * Z  +  47.990959
  Y_new =  -0.374380 * X  +   0.789986 * Y  +  -0.485553 * Z  +  11.577420
  Z_new =   0.876158 * X  +   0.129912 * Y  +  -0.464188 * Z  + -28.963354 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.868705   -0.272888  [ DEG:   164.3647    -15.6353 ]
  Theta =  -1.067833   -2.073760  [ DEG:   -61.1823   -118.8177 ]
  Phi   =  -2.252209    0.889383  [ DEG:  -129.0421     50.9579 ]
 
# 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: T0283AL381_4                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_4.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  112   5.0   16   1.58   18.75  13.499
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_4
REMARK Aligment from pdb entry: 1kw4A
ATOM      1  N   GLU    81      24.840  16.851   0.504  1.00  0.00              
ATOM      2  CA  GLU    81      25.657  16.549  -0.674  1.00  0.00              
ATOM      3  C   GLU    81      24.789  16.137  -1.866  1.00  0.00              
ATOM      4  O   GLU    81      25.082  16.510  -3.006  1.00  0.00              
ATOM      5  N   ASP    82      23.730  15.372  -1.607  1.00  0.00              
ATOM      6  CA  ASP    82      22.823  14.940  -2.673  1.00  0.00              
ATOM      7  C   ASP    82      22.164  16.163  -3.325  1.00  0.00              
ATOM      8  O   ASP    82      22.055  16.246  -4.549  1.00  0.00              
ATOM      9  N   VAL    83      21.705  17.101  -2.501  1.00  0.00              
ATOM     10  CA  VAL    83      21.072  18.313  -3.018  1.00  0.00              
ATOM     11  C   VAL    83      22.066  19.132  -3.851  1.00  0.00              
ATOM     12  O   VAL    83      21.702  19.678  -4.890  1.00  0.00              
ATOM     13  N   ALA    84      23.321  19.205  -3.410  1.00  0.00              
ATOM     14  CA  ALA    84      24.323  19.978  -4.150  1.00  0.00              
ATOM     15  C   ALA    84      24.560  19.394  -5.546  1.00  0.00              
ATOM     16  O   ALA    84      24.814  20.128  -6.504  1.00  0.00              
ATOM     17  N   ALA    85      24.475  18.074  -5.667  1.00  0.00              
ATOM     18  CA  ALA    85      24.660  17.433  -6.966  1.00  0.00              
ATOM     19  C   ALA    85      23.446  17.687  -7.867  1.00  0.00              
ATOM     20  O   ALA    85      23.582  17.844  -9.085  1.00  0.00              
ATOM     21  N   PHE    86      22.267  17.732  -7.257  1.00  0.00              
ATOM     22  CA  PHE    86      21.019  18.006  -7.970  1.00  0.00              
ATOM     23  C   PHE    86      21.087  19.418  -8.572  1.00  0.00              
ATOM     24  O   PHE    86      20.759  19.625  -9.746  1.00  0.00              
ATOM     25  N   CYS    87      21.529  20.385  -7.771  1.00  0.00              
ATOM     26  CA  CYS    87      21.647  21.772  -8.226  1.00  0.00              
ATOM     27  C   CYS    87      22.718  21.895  -9.322  1.00  0.00              
ATOM     28  O   CYS    87      22.522  22.592 -10.322  1.00  0.00              
ATOM     29  N   ASP    88      23.841  21.203  -9.143  1.00  0.00              
ATOM     30  CA  ASP    88      24.934  21.237 -10.113  1.00  0.00              
ATOM     31  C   ASP    88      24.492  20.829 -11.517  1.00  0.00              
ATOM     32  O   ASP    88      24.986  21.369 -12.513  1.00  0.00              
ATOM     33  N   GLU    89      23.557  19.887 -11.593  1.00  0.00              
ATOM     34  CA  GLU    89      23.075  19.381 -12.873  1.00  0.00              
ATOM     35  C   GLU    89      21.881  20.111 -13.489  1.00  0.00              
ATOM     36  O   GLU    89      21.475  19.795 -14.609  1.00  0.00              
ATOM     37  N   LEU    90      21.315  21.076 -12.768  1.00  0.00              
ATOM     38  CA  LEU    90      20.187  21.850 -13.291  1.00  0.00              
ATOM     39  C   LEU    90      20.718  22.970 -14.177  1.00  0.00              
ATOM     40  O   LEU    90      21.517  23.793 -13.739  1.00  0.00              
ATOM     41  N   MET    91      20.264  23.026 -15.437  1.00  0.00              
ATOM     42  CA  MET    91      20.724  24.066 -16.362  1.00  0.00              
ATOM     43  C   MET    91      20.681  25.495 -15.823  1.00  0.00              
ATOM     44  O   MET    91      19.633  25.982 -15.399  1.00  0.00              
ATOM     45  N   LYS    92      21.837  26.152 -15.833  1.00  0.00              
ATOM     46  CA  LYS    92      21.933  27.524 -15.365  1.00  0.00              
ATOM     47  C   LYS    92      21.984  27.756 -13.864  1.00  0.00              
ATOM     48  O   LYS    92      21.933  28.903 -13.416  1.00  0.00              
ATOM     49  N   ASP    93      22.109  26.690 -13.077  1.00  0.00              
ATOM     50  CA  ASP    93      22.135  26.837 -11.622  1.00  0.00              
ATOM     51  C   ASP    93      23.469  26.473 -10.969  1.00  0.00              
ATOM     52  O   ASP    93      23.608  26.571  -9.749  1.00  0.00              
ATOM     53  N   THR    94      24.454  26.083 -11.771  1.00  0.00              
ATOM     54  CA  THR    94      25.745  25.675 -11.222  1.00  0.00              
ATOM     55  C   THR    94      26.470  26.696 -10.343  1.00  0.00              
ATOM     56  O   THR    94      27.255  26.312  -9.476  1.00  0.00              
ATOM     57  N   LYS    95      26.212  27.985 -10.543  1.00  0.00              
ATOM     58  CA  LYS    95      26.875  29.010  -9.738  1.00  0.00              
ATOM     59  C   LYS    95      26.369  29.073  -8.299  1.00  0.00              
ATOM     60  O   LYS    95      26.942  29.782  -7.471  1.00  0.00              
ATOM     61  N   THR    96      25.308  28.332  -7.999  1.00  0.00              
ATOM     62  CA  THR    96      24.728  28.352  -6.657  1.00  0.00              
ATOM     63  C   THR    96      25.009  27.108  -5.805  1.00  0.00              
ATOM     64  O   THR    96      24.525  27.000  -4.676  1.00  0.00              
END
