
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0306AL381_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL381_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    I      44      A      41          3.212
LGA    D      45      V      42          1.874
LGA    N      46      A      43          2.329
LGA    I      47      I      44          3.256
LGA    G      48      D      45          3.815
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    A      49      A      49          2.639
LGA    G      50      G      50          3.291
LGA    T      51      T      51          1.786
LGA    G      52      G      52          4.757
LGA    E      53      E      53          1.924
LGA    W      54      W      54          2.819
LGA    V      55      V      55          0.706
LGA    L      56      L      56          1.385
LGA    L      57      L      57          1.912
LGA    V      58      V      58          0.975
LGA    S      59      S      59          1.298
LGA    G      60      G      60          2.997
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    S      61      R      64          2.511
LGA    S      62      Q      65          3.837
LGA    A      63      A      66          3.793
LGA    R      64      H      67          0.864
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21   95    5.0     21    2.70    66.67     15.020     0.749

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.675641 * X  +  -0.126365 * Y  +   0.726320 * Z  +  15.554163
  Y_new =   0.673346 * X  +   0.506935 * Y  +  -0.538166 * Z  + 122.702675
  Z_new =  -0.300192 * X  +   0.852672 * Y  +   0.427593 * Z  +  98.236938 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.105970   -2.035623  [ DEG:    63.3674   -116.6326 ]
  Theta =   0.304893    2.836699  [ DEG:    17.4691    162.5309 ]
  Phi   =   0.783697   -2.357896  [ DEG:    44.9025   -135.0975 ]
 
# 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: T0306AL381_2                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL381_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   95   5.0   21   2.70   66.67  15.020
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL381_2
REMARK Aligment from pdb entry: 1kekA
ATOM      1  N   ILE    44      34.532  30.552  73.675  1.00  0.00              
ATOM      2  CA  ILE    44      35.256  30.309  72.445  1.00  0.00              
ATOM      3  C   ILE    44      34.878  28.858  72.061  1.00  0.00              
ATOM      4  O   ILE    44      34.976  28.005  72.940  1.00  0.00              
ATOM      5  N   ASP    45      34.500  28.607  70.833  1.00  0.00              
ATOM      6  CA  ASP    45      34.164  27.199  70.485  1.00  0.00              
ATOM      7  C   ASP    45      35.156  26.768  69.422  1.00  0.00              
ATOM      8  O   ASP    45      35.634  27.660  68.716  1.00  0.00              
ATOM      9  N   ASN    46      35.534  25.499  69.366  1.00  0.00              
ATOM     10  CA  ASN    46      36.447  24.992  68.350  1.00  0.00              
ATOM     11  C   ASN    46      35.694  24.046  67.411  1.00  0.00              
ATOM     12  O   ASN    46      34.884  23.234  67.893  1.00  0.00              
ATOM     13  N   ILE    47      36.071  24.048  66.165  1.00  0.00              
ATOM     14  CA  ILE    47      35.522  23.180  65.113  1.00  0.00              
ATOM     15  C   ILE    47      36.663  22.710  64.208  1.00  0.00              
ATOM     16  O   ILE    47      37.631  23.438  63.936  1.00  0.00              
ATOM     17  N   GLY    48      36.578  21.474  63.707  1.00  0.00              
ATOM     18  CA  GLY    48      37.668  20.997  62.840  1.00  0.00              
ATOM     19  C   GLY    48      38.409  19.805  63.433  1.00  0.00              
ATOM     20  O   GLY    48      38.086  19.220  64.485  1.00  0.00              
ATOM     21  N   ALA    49      39.449  19.383  62.735  1.00  0.00              
ATOM     22  CA  ALA    49      40.281  18.262  63.208  1.00  0.00              
ATOM     23  C   ALA    49      40.870  18.437  64.590  1.00  0.00              
ATOM     24  O   ALA    49      41.525  19.420  64.950  1.00  0.00              
ATOM     25  N   GLY    50      40.647  17.460  65.480  1.00  0.00              
ATOM     26  CA  GLY    50      41.126  17.480  66.846  1.00  0.00              
ATOM     27  C   GLY    50      42.633  17.572  66.962  1.00  0.00              
ATOM     28  O   GLY    50      43.212  18.022  67.961  1.00  0.00              
ATOM     29  N   THR    51      43.317  17.123  65.898  1.00  0.00              
ATOM     30  CA  THR    51      44.776  17.163  65.863  1.00  0.00              
ATOM     31  C   THR    51      45.238  18.237  64.869  1.00  0.00              
ATOM     32  O   THR    51      46.297  18.135  64.241  1.00  0.00              
ATOM     33  N   GLY    52      44.452  19.328  64.700  1.00  0.00              
ATOM     34  CA  GLY    52      44.753  20.319  63.699  1.00  0.00              
ATOM     35  C   GLY    52      46.136  20.950  63.922  1.00  0.00              
ATOM     36  O   GLY    52      46.409  21.210  65.086  1.00  0.00              
ATOM     37  N   GLU    53      46.845  21.137  62.833  1.00  0.00              
ATOM     38  CA  GLU    53      48.115  21.853  62.896  1.00  0.00              
ATOM     39  C   GLU    53      48.031  23.351  62.503  1.00  0.00              
ATOM     40  O   GLU    53      48.889  24.171  62.871  1.00  0.00              
ATOM     41  N   TRP    54      47.027  23.667  61.720  1.00  0.00              
ATOM     42  CA  TRP    54      46.787  25.064  61.275  1.00  0.00              
ATOM     43  C   TRP    54      45.382  25.503  61.700  1.00  0.00              
ATOM     44  O   TRP    54      44.404  24.898  61.236  1.00  0.00              
ATOM     45  N   VAL    55      45.245  26.539  62.496  1.00  0.00              
ATOM     46  CA  VAL    55      43.981  26.983  63.056  1.00  0.00              
ATOM     47  C   VAL    55      43.727  28.487  62.766  1.00  0.00              
ATOM     48  O   VAL    55      44.626  29.304  62.918  1.00  0.00              
ATOM     49  N   LEU    56      42.519  28.814  62.404  1.00  0.00              
ATOM     50  CA  LEU    56      42.092  30.220  62.211  1.00  0.00              
ATOM     51  C   LEU    56      41.382  30.616  63.503  1.00  0.00              
ATOM     52  O   LEU    56      40.723  29.793  64.128  1.00  0.00              
ATOM     53  N   LEU    57      41.511  31.867  63.925  1.00  0.00              
ATOM     54  CA  LEU    57      40.667  32.459  64.986  1.00  0.00              
ATOM     55  C   LEU    57      39.838  33.558  64.295  1.00  0.00              
ATOM     56  O   LEU    57      40.443  34.342  63.559  1.00  0.00              
ATOM     57  N   VAL    58      38.507  33.538  64.456  1.00  0.00              
ATOM     58  CA  VAL    58      37.690  34.506  63.683  1.00  0.00              
ATOM     59  C   VAL    58      36.409  34.795  64.426  1.00  0.00              
ATOM     60  O   VAL    58      36.082  34.113  65.433  1.00  0.00              
ATOM     61  N   SER    59      35.670  35.845  64.015  1.00  0.00              
ATOM     62  CA  SER    59      34.490  36.244  64.739  1.00  0.00              
ATOM     63  C   SER    59      33.428  36.744  63.760  1.00  0.00              
ATOM     64  O   SER    59      33.740  37.454  62.804  1.00  0.00              
ATOM     65  N   GLY    60      32.172  36.454  63.979  1.00  0.00              
ATOM     66  CA  GLY    60      31.091  36.915  63.132  1.00  0.00              
ATOM     67  C   GLY    60      30.856  35.940  61.978  1.00  0.00              
ATOM     68  O   GLY    60      31.348  34.781  61.968  1.00  0.00              
ATOM     69  N   SER    61      30.116  36.386  60.959  1.00  0.00              
ATOM     70  CA  SER    61      29.665  35.509  59.883  1.00  0.00              
ATOM     71  C   SER    61      30.727  34.720  59.133  1.00  0.00              
ATOM     72  O   SER    61      30.474  33.630  58.591  1.00  0.00              
ATOM     73  N   SER    62      31.973  35.211  59.115  1.00  0.00              
ATOM     74  CA  SER    62      33.102  34.537  58.499  1.00  0.00              
ATOM     75  C   SER    62      33.256  33.136  59.088  1.00  0.00              
ATOM     76  O   SER    62      33.576  32.180  58.437  1.00  0.00              
ATOM     77  N   ALA    63      32.907  32.944  60.380  1.00  0.00              
ATOM     78  CA  ALA    63      33.020  31.642  61.022  1.00  0.00              
ATOM     79  C   ALA    63      32.166  30.557  60.328  1.00  0.00              
ATOM     80  O   ALA    63      32.538  29.383  60.395  1.00  0.00              
ATOM     81  N   ARG    64      31.006  30.898  59.784  1.00  0.00              
ATOM     82  CA  ARG    64      30.161  29.900  59.157  1.00  0.00              
ATOM     83  C   ARG    64      30.889  29.340  57.929  1.00  0.00              
ATOM     84  O   ARG    64      30.905  28.138  57.649  1.00  0.00              
END
