
#######################################################
#                                                     #
#                        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 T0283AL044_4
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283AL044_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    H      32      G       9          2.403
LGA    H      33      S      10          3.845
LGA    K      40      L      11          1.960
LGA    -       -      N      12           -
LGA    -       -      D      13           -
LGA    -       -      K      14           -
LGA    Y      41      R      15          1.409
LGA    M      42      E      16          2.165
LGA    T      54      W      17          0.973
LGA    K      55      K      18          1.664
LGA    R      56      A      19          2.354
LGA    I      57      M      20          2.864
LGA    F      58      E      21          2.599
LGA    -       -      A      22           -
LGA    -       -      R      23           -
LGA    -       -      A      24           -
LGA    -       -      K      25           -
LGA    -       -      A      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      K      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    G      59      K      36          4.302
LGA    G      60      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    I      61      K      73          2.567
LGA    L      62      K      74           -
LGA    D      63      V      75           -
LGA    A      84      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     12    2.59     8.33      7.938     0.446

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.057590 * X  +   0.732221 * Y  +  -0.678628 * Z  +  33.196033
  Y_new =   0.916677 * X  +   0.308045 * Y  +   0.254580 * Z  + -14.490115
  Z_new =   0.395457 * X  +  -0.607422 * Y  +  -0.688950 * Z  +  47.845379 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.419002    0.722591  [ DEG:  -138.5986     41.4014 ]
  Theta =  -0.406565   -2.735028  [ DEG:   -23.2945   -156.7055 ]
  Phi   =   1.633539   -1.508054  [ DEG:    93.5949    -86.4051 ]
 
# 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: T0283AL044_4                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL044_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   12   2.59    8.33   7.938
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL044_4
REMARK Aligment from pdb entry: 1kzy_C
ATOM      1  N   HIS    32      24.634  15.192  11.788  1.00  0.00              
ATOM      2  CA  HIS    32      25.109  13.922  12.305  1.00  0.00              
ATOM      3  C   HIS    32      25.161  12.867  11.171  1.00  0.00              
ATOM      4  O   HIS    32      26.102  12.070  11.085  1.00  0.00              
ATOM      5  N   HIS    33      24.170  12.903  10.294  1.00  0.00              
ATOM      6  CA  HIS    33      24.106  12.019   9.124  1.00  0.00              
ATOM      7  C   HIS    33      25.192  12.511   8.167  1.00  0.00              
ATOM      8  O   HIS    33      25.016  13.541   7.531  1.00  0.00              
ATOM      9  N   LYS    40      26.299  11.783   8.064  1.00  0.00              
ATOM     10  CA  LYS    40      27.416  12.201   7.229  1.00  0.00              
ATOM     11  C   LYS    40      27.113  12.361   5.750  1.00  0.00              
ATOM     12  O   LYS    40      27.896  12.987   5.031  1.00  0.00              
ATOM     13  N   TYR    41      26.017  11.783   5.270  1.00  0.00              
ATOM     14  CA  TYR    41      25.671  11.937   3.846  1.00  0.00              
ATOM     15  C   TYR    41      24.383  12.737   3.645  1.00  0.00              
ATOM     16  O   TYR    41      23.627  12.471   2.733  1.00  0.00              
ATOM     17  N   MET    42      24.150  13.719   4.490  1.00  0.00              
ATOM     18  CA  MET    42      22.947  14.528   4.400  1.00  0.00              
ATOM     19  C   MET    42      22.824  15.313   3.107  1.00  0.00              
ATOM     20  O   MET    42      21.740  15.374   2.525  1.00  0.00              
ATOM     21  N   THR    54      23.918  15.910   2.651  1.00  0.00              
ATOM     22  CA  THR    54      23.849  16.707   1.434  1.00  0.00              
ATOM     23  C   THR    54      24.396  16.028   0.192  1.00  0.00              
ATOM     24  O   THR    54      24.561  16.681  -0.847  1.00  0.00              
ATOM     25  N   LYS    55      24.652  14.720   0.295  1.00  0.00              
ATOM     26  CA  LYS    55      25.201  13.940  -0.814  1.00  0.00              
ATOM     27  C   LYS    55      24.351  14.050  -2.097  1.00  0.00              
ATOM     28  O   LYS    55      23.124  13.843  -2.082  1.00  0.00              
ATOM     29  N   ARG    56      25.017  14.369  -3.207  1.00  0.00              
ATOM     30  CA  ARG    56      24.304  14.533  -4.456  1.00  0.00              
ATOM     31  C   ARG    56      23.964  15.996  -4.711  1.00  0.00              
ATOM     32  O   ARG    56      23.248  16.315  -5.666  1.00  0.00              
ATOM     33  N   ILE    57      24.479  16.885  -3.862  1.00  0.00              
ATOM     34  CA  ILE    57      24.257  18.309  -4.017  1.00  0.00              
ATOM     35  C   ILE    57      25.572  19.041  -4.138  1.00  0.00              
ATOM     36  O   ILE    57      26.586  18.625  -3.556  1.00  0.00              
ATOM     37  N   PHE    58      25.546  20.138  -4.890  1.00  0.00              
ATOM     38  CA  PHE    58      26.732  20.979  -5.050  1.00  0.00              
ATOM     39  C   PHE    58      26.269  22.341  -4.597  1.00  0.00              
ATOM     40  O   PHE    58      25.110  22.713  -4.838  1.00  0.00              
ATOM     41  N   GLY    59      27.151  23.091  -3.954  1.00  0.00              
ATOM     42  CA  GLY    59      26.742  24.395  -3.507  1.00  0.00              
ATOM     43  C   GLY    59      27.698  25.502  -3.905  1.00  0.00              
ATOM     44  O   GLY    59      28.911  25.331  -3.957  1.00  0.00              
ATOM     45  N   GLY    60      24.531  17.605 -14.826  1.00  0.00              
ATOM     46  CA  GLY    60      24.507  16.166 -14.777  1.00  0.00              
ATOM     47  C   GLY    60      24.752  15.546 -13.413  1.00  0.00              
ATOM     48  O   GLY    60      23.918  14.823 -12.904  1.00  0.00              
ATOM     49  N   ILE    61      10.600  30.881 -14.633  1.00  0.00              
ATOM     50  CA  ILE    61      10.671  31.766 -15.813  1.00  0.00              
ATOM     51  C   ILE    61      11.358  31.094 -16.993  1.00  0.00              
ATOM     52  O   ILE    61      12.128  30.155 -16.814  1.00  0.00              
ATOM     53  N   LEU    62      39.952  47.499 -30.695  1.00  0.00              
ATOM     54  CA  LEU    62      39.323  46.525 -31.594  1.00  0.00              
ATOM     55  C   LEU    62      38.901  47.304 -32.842  1.00  0.00              
ATOM     56  O   LEU    62      38.391  48.419 -32.740  1.00  0.00              
ATOM     57  N   ASP    63      39.139  46.722 -34.015  1.00  0.00              
ATOM     58  CA  ASP    63      38.779  47.349 -35.286  1.00  0.00              
ATOM     59  C   ASP    63      37.445  46.806 -35.810  1.00  0.00              
ATOM     60  O   ASP    63      37.316  45.622 -36.152  1.00  0.00              
ATOM     61  N   ALA    84      36.466  47.709 -35.870  1.00  0.00              
ATOM     62  CA  ALA    84      35.088  47.423 -36.280  1.00  0.00              
ATOM     63  C   ALA    84      34.834  46.678 -37.598  1.00  0.00              
ATOM     64  O   ALA    84      34.264  47.245 -38.540  1.00  0.00              
END
