
#######################################################
#                                                     #
#                        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   83 (   83),  selected   83 , name T0353TS599_3-D1
# Molecule2: number of CA atoms   83 ( 1315),  selected   83 , name T0353_D1.pdb
# PARAMETERS: T0353TS599_3-D1.T0353_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    M       1      Y       6          1.847
LGA    Q       2      D       7          3.558
LGA    I       3      T       8          1.249
LGA    H       4      Y       9          2.553
LGA    V       5      V      10          2.805
LGA    Y       6      K      11          0.672
LGA    D       7      A      12          5.119
LGA    T       8      -       -           -
LGA    Y       9      K      13          1.214
LGA    V      10      D      14          2.467
LGA    K      11      -       -           -
LGA    A      12      -       -           -
LGA    K      13      -       -           -
LGA    D      14      -       -           -
LGA    G      15      -       -           -
LGA    H      16      -       -           -
LGA    V      17      G      15          2.211
LGA    M      18      H      16          4.290
LGA    H      19      V      17          2.762
LGA    F      20      M      18          0.362
LGA    D      21      H      19          1.029
LGA    V      22      F      20          3.701
LGA    F      23      D      21           #
LGA    T      24      V      22           #
LGA    -       -      F      23           -
LGA    -       -      T      24           -
LGA    -       -      D      25           -
LGA    -       -      V      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      D      29           -
LGA    -       -      K      30           -
LGA    -       -      K      31           -
LGA    -       -      A      32           -
LGA    -       -      I      33           -
LGA    -       -      E      34           -
LGA    -       -      F      35           -
LGA    -       -      A      36           -
LGA    -       -      K      37           -
LGA    -       -      Q      38           -
LGA    -       -      W      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    -       -      E      46           -
LGA    -       -      G      47           -
LGA    -       -      A      48           -
LGA    -       -      T      49           -
LGA    -       -      V      50           -
LGA    -       -      T      51           -
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      C      55           -
LGA    -       -      R      56           -
LGA    D      25      F      57          4.547
LGA    V      26      C      58          3.044
LGA    R      27      H      59          2.261
LGA    D      28      S      60          4.871
LGA    D      29      -       -           -
LGA    K      30      E      61          4.245
LGA    K      31      K      62          3.838
LGA    A      32      -       -           -
LGA    I      33      A      63           #
LGA    E      34      P      64           #
LGA    F      35      D      65          4.766
LGA    A      36      E      66          4.421
LGA    K      37      V      67          4.371
LGA    Q      38      I      68          2.981
LGA    W      39      E      69          4.119
LGA    L      40      A      70          4.412
LGA    S      41      I      71           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      K      72          1.342
LGA    A      48      Q      73          3.320
LGA    T      49      N      74          3.621
LGA    V      50      G      75           #
LGA    T      51      Y      76           -
LGA    S      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    C      55      F      77           #
LGA    R      56      I      78           -
LGA    F      57      -       -           -
LGA    C      58      -       -           -
LGA    H      59      Y      79          4.434
LGA    S      60      K      80           #
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      -       -           -
LGA    P      64      M      81          3.040
LGA    D      65      -       -           -
LGA    E      66      -       -           -
LGA    V      67      E      82          1.911
LGA    I      68      -       -           -
LGA    E      69      -       -           -
LGA    A      70      -       -           -
LGA    I      71      G      83          4.815
LGA    K      72      -       -           -
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      -       -           -
LGA    Y      76      -       -           -
LGA    F      77      -       -           -
LGA    I      78      -       -           -
LGA    Y      79      -       -           -
LGA    K      80      -       -           -
LGA    M      81      -       -           -
LGA    E      82      -       -           -
LGA    G      83      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   83   83    5.0     34    3.40     5.88     22.907     0.973

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.870713 * X  +  -0.324996 * Y  +   0.369103 * Z  +   1.797806
  Y_new =   0.129242 * X  +  -0.875361 * Y  +  -0.465876 * Z  +  -1.751354
  Z_new =   0.474506 * X  +  -0.357941 * Y  +   0.804191 * Z  +   5.511779 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.418767    2.722826  [ DEG:   -23.9936    156.0064 ]
  Theta =  -0.494402   -2.647191  [ DEG:   -28.3272   -151.6728 ]
  Phi   =   2.994237   -0.147356  [ DEG:   171.5571     -8.4429 ]
 
# 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: T0353TS599_3-D1                               
REMARK     2: T0353_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_3-D1.T0353_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   83   83   5.0   34   3.40    5.88  22.907
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_3-D1
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       2.537   3.070   0.494  1.00  0.00              
ATOM      2  CA  GLN     2      -0.968   3.854   1.612  1.00  0.00              
ATOM      3  CA  ILE     3      -1.972   3.106   5.203  1.00  0.00              
ATOM      4  CA  HIS     4      -5.480   2.846   6.159  1.00  0.00              
ATOM      5  CA  VAL     5      -6.293   3.934  10.029  1.00  0.00              
ATOM      6  CA  TYR     6      -9.258   2.672  11.768  1.00  0.00              
ATOM      7  CA  ASP     7     -10.303   4.367  14.917  1.00  0.00              
ATOM      8  CA  THR     8     -13.693   2.810  15.561  1.00  0.00              
ATOM      9  CA  TYR     9     -12.035  -0.585  14.975  1.00  0.00              
ATOM     10  CA  VAL    10      -9.546  -0.086  17.804  1.00  0.00              
ATOM     11  CA  LYS    11     -12.438   0.234  20.206  1.00  0.00              
ATOM     12  CA  ALA    12     -15.716   0.300  18.379  1.00  0.00              
ATOM     13  CA  LYS    13     -18.948   0.167  20.302  1.00  0.00              
ATOM     14  CA  ASP    14     -19.383  -3.577  19.508  1.00  0.00              
ATOM     15  CA  GLY    15     -15.909  -4.476  20.597  1.00  0.00              
ATOM     16  CA  HIS    16     -14.243  -5.280  17.361  1.00  0.00              
ATOM     17  CA  VAL    17     -10.685  -4.067  17.395  1.00  0.00              
ATOM     18  CA  MET    18      -8.997  -3.418  14.119  1.00  0.00              
ATOM     19  CA  HIS    19      -6.189  -0.943  13.846  1.00  0.00              
ATOM     20  CA  PHE    20      -4.193  -0.434  10.727  1.00  0.00              
ATOM     21  CA  ASP    21      -1.497   2.037  10.716  1.00  0.00              
ATOM     22  CA  VAL    22      -0.722   3.652   7.190  1.00  0.00              
ATOM     23  CA  PHE    23       2.058   5.954   6.728  1.00  0.00              
ATOM     24  CA  THR    24       2.760   7.125   3.195  1.00  0.00              
ATOM     25  CA  ASP    25       5.818   9.300   2.530  1.00  0.00              
ATOM     26  CA  VAL    26       6.629   9.377  -1.178  1.00  0.00              
ATOM     27  CA  ARG    27      10.379   8.671  -0.961  1.00  0.00              
ATOM     28  CA  ASP    28       9.746   5.620   1.229  1.00  0.00              
ATOM     29  CA  ASP    29       6.990   4.250  -0.987  1.00  0.00              
ATOM     30  CA  LYS    30       9.331   4.091  -4.009  1.00  0.00              
ATOM     31  CA  LYS    31      11.959   2.225  -1.963  1.00  0.00              
ATOM     32  CA  ALA    32       9.462  -0.359  -0.634  1.00  0.00              
ATOM     33  CA  ILE    33       8.183  -1.022  -4.131  1.00  0.00              
ATOM     34  CA  GLU    34      11.755  -1.471  -5.429  1.00  0.00              
ATOM     35  CA  PHE    35      12.715  -3.901  -2.677  1.00  0.00              
ATOM     36  CA  ALA    36       9.617  -5.960  -3.327  1.00  0.00              
ATOM     37  CA  LYS    37      10.331  -6.041  -7.056  1.00  0.00              
ATOM     38  CA  GLN    38      13.926  -7.177  -6.614  1.00  0.00              
ATOM     39  CA  TRP    39      13.017  -9.968  -4.219  1.00  0.00              
ATOM     40  CA  LEU    40      10.161 -11.134  -6.376  1.00  0.00              
ATOM     41  CA  SER    41      12.350 -11.403  -9.449  1.00  0.00              
ATOM     42  CA  SER    42      15.007 -13.386  -7.667  1.00  0.00              
ATOM     43  CA  ILE    43      12.477 -15.900  -6.256  1.00  0.00              
ATOM     44  CA  GLY    44      10.620 -16.411  -9.524  1.00  0.00              
ATOM     45  CA  GLU    45       7.556 -14.277  -8.710  1.00  0.00              
ATOM     46  CA  GLU    46       6.509 -11.900 -11.424  1.00  0.00              
ATOM     47  CA  GLY    47       5.538  -8.555  -9.798  1.00  0.00              
ATOM     48  CA  ALA    48       1.946  -9.050 -10.780  1.00  0.00              
ATOM     49  CA  THR    49       1.420 -12.416  -9.251  1.00  0.00              
ATOM     50  CA  VAL    50       3.172 -12.023  -5.950  1.00  0.00              
ATOM     51  CA  THR    51       2.911 -15.215  -4.011  1.00  0.00              
ATOM     52  CA  SER    52       2.310 -15.202  -0.276  1.00  0.00              
ATOM     53  CA  GLU    53       5.802 -16.617   0.459  1.00  0.00              
ATOM     54  CA  GLU    54       7.616 -14.083  -1.727  1.00  0.00              
ATOM     55  CA  CYS    55       6.122 -10.888  -0.193  1.00  0.00              
ATOM     56  CA  ARG    56       5.860 -11.870   3.478  1.00  0.00              
ATOM     57  CA  PHE    57       9.635 -12.354   3.706  1.00  0.00              
ATOM     58  CA  CYS    58      10.157  -8.587   3.373  1.00  0.00              
ATOM     59  CA  HIS    59       6.981  -7.292   4.969  1.00  0.00              
ATOM     60  CA  SER    60       7.153  -9.180   8.277  1.00  0.00              
ATOM     61  CA  GLN    61      10.885  -8.683   8.668  1.00  0.00              
ATOM     62  CA  LYS    62      11.097  -4.944   7.839  1.00  0.00              
ATOM     63  CA  ALA    63       8.647  -3.211   9.946  1.00  0.00              
ATOM     64  CA  PRO    64       6.879   0.031   9.328  1.00  0.00              
ATOM     65  CA  ASP    65       8.311   1.488  12.523  1.00  0.00              
ATOM     66  CA  GLU    66       7.297  -1.594  14.500  1.00  0.00              
ATOM     67  CA  VAL    67       3.698  -1.384  13.245  1.00  0.00              
ATOM     68  CA  ILE    68       3.487   2.285  14.200  1.00  0.00              
ATOM     69  CA  GLU    69       4.760   1.554  17.682  1.00  0.00              
ATOM     70  CA  ALA    70       2.276  -1.327  18.197  1.00  0.00              
ATOM     71  CA  ILE    71      -0.621   0.721  16.935  1.00  0.00              
ATOM     72  CA  LYS    72       0.231   3.695  19.216  1.00  0.00              
ATOM     73  CA  GLN    73       0.474   1.425  22.223  1.00  0.00              
ATOM     74  CA  ASN    74      -2.895  -0.269  21.550  1.00  0.00              
ATOM     75  CA  GLY    75      -4.807   2.895  20.850  1.00  0.00              
ATOM     76  CA  TYR    76      -5.176   2.385  17.089  1.00  0.00              
ATOM     77  CA  PHE    77      -4.607   5.339  14.814  1.00  0.00              
ATOM     78  CA  ILE    78      -5.065   5.131  11.213  1.00  0.00              
ATOM     79  CA  TYR    79      -3.028   7.663   8.977  1.00  0.00              
ATOM     80  CA  LYS    80      -3.723   7.578   5.384  1.00  0.00              
ATOM     81  CA  MET    81      -1.149   8.755   2.937  1.00  0.00              
ATOM     82  CA  GLU    82      -2.300   9.639  -0.519  1.00  0.00              
ATOM     83  CA  GLY    83      -0.513  12.237  -2.248  1.00  0.00              
TER                                                                             
END
