
#######################################################
#                                                     #
#                        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   86 (   86),  selected   86 , name T0292TS168_2-D1
# Molecule2: number of CA atoms   77 (  591),  selected   77 , name T0292_D1.pdb
# PARAMETERS: T0292TS168_2-D1.T0292_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S       1           -
LGA    S       1      R       2          1.762
LGA    R       2      A       3          3.216
LGA    A       3      E       4          1.447
LGA    E       4      D       5          3.222
LGA    D       5      Y       6          3.489
LGA    Y       6      -       -           -
LGA    E       7      E       7          2.548
LGA    V       8      V       8          1.655
LGA    L       9      L       9          1.700
LGA    Y      10      Y      10          1.374
LGA    T      11      T      11          1.480
LGA    I      12      I      12          0.785
LGA    G      13      G      13          0.879
LGA    T      14      T      14          1.873
LGA    G      15      G      15          3.193
LGA    S      16      S      16          2.954
LGA    Y      17      Y      17          2.809
LGA    G      18      G      18          3.259
LGA    R      19      R      19          1.350
LGA    C      20      C      20          0.772
LGA    Q      21      Q      21          0.098
LGA    K      22      K      22          1.447
LGA    I      23      I      23          1.878
LGA    R      24      R      24          2.299
LGA    R      25      R      25          1.668
LGA    K      26      K      26          1.868
LGA    S      27      S      27          1.584
LGA    D      28      D      28          1.132
LGA    G      29      G      29          0.193
LGA    K      30      K      30          0.781
LGA    I      31      I      31          1.067
LGA    L      32      L      32          1.007
LGA    V      33      V      33          0.719
LGA    W      34      W      34          0.762
LGA    K      35      K      35          0.480
LGA    E      36      E      36          0.933
LGA    L      37      L      37          0.857
LGA    D      38      D      38          2.065
LGA    Y      39      Y      39          2.856
LGA    G      40      G      40          2.724
LGA    S      41      S      41          2.383
LGA    M      42      M      42          4.406
LGA    T      43      T      43          3.270
LGA    E      44      -       -           -
LGA    A      45      -       -           -
LGA    E      46      -       -           -
LGA    K      47      -       -           -
LGA    Q      48      -       -           -
LGA    M      49      M      49          1.734
LGA    L      50      L      50          1.936
LGA    V      51      V      51          1.716
LGA    S      52      S      52          1.196
LGA    E      53      E      53          0.873
LGA    V      54      V      54          1.111
LGA    N      55      N      55          1.219
LGA    L      56      L      56          1.402
LGA    L      57      L      57          1.543
LGA    R      58      R      58          1.533
LGA    E      59      E      59          1.514
LGA    L      60      L      60          1.023
LGA    K      61      K      61          2.795
LGA    H      62      H      62          3.698
LGA    P      63      P      63          2.964
LGA    N      64      N      64          0.895
LGA    I      65      I      65          0.708
LGA    V      66      V      66          0.845
LGA    R      67      R      67          0.904
LGA    Y      68      Y      68          0.320
LGA    Y      69      Y      69          0.903
LGA    D      70      D      70          0.756
LGA    R      71      R      71          1.022
LGA    I      72      I      72          0.856
LGA    I      73      I      73          2.494
LGA    D      74      D      74          2.963
LGA    R      75      -       -           -
LGA    T      76      -       -           -
LGA    N      77      -       -           -
LGA    T      78      -       -           -
LGA    T      79      T      79          1.642
LGA    L      80      L      80          1.318
LGA    Y      81      Y      81          0.554
LGA    I      82      I      82          1.460
LGA    V      83      V      83          2.498
LGA    M      84      M      84          1.077
LGA    E      85      E      85          0.832
LGA    Y      86      Y      86          0.883

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   86   77    5.0     76    1.90    93.42     87.491     3.808

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.512899 * X  +  -0.170433 * Y  +   0.841360 * Z  +   5.993401
  Y_new =   0.852675 * X  +   0.012337 * Y  +   0.522296 * Z  +  14.469178
  Z_new =  -0.099397 * X  +   0.985292 * Y  +   0.138996 * Z  +  16.233683 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.430650   -1.710943  [ DEG:    81.9702    -98.0298 ]
  Theta =   0.099561    3.042032  [ DEG:     5.7044    174.2956 ]
  Phi   =   2.112331   -1.029261  [ DEG:   121.0277    -58.9723 ]
 
# 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: T0292TS168_2-D1                               
REMARK     2: T0292_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0292TS168_2-D1.T0292_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   86   77   5.0   76   1.90   93.42  87.491
REMARK  ---------------------------------------------------------- 
MOLECULE T0292TS168_2-D1
PFRMAT TS
TARGET T0292
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1      -8.836  -8.465   5.781  1.00 25.00           C
ATOM      2  CA  ARG     2     -11.948  -6.241   5.700  1.00 25.00           C
ATOM      3  CA  ALA     3     -14.694  -5.953   8.292  1.00 25.00           C
ATOM      4  CA  GLU     4     -13.553  -9.302   9.610  1.00 25.00           C
ATOM      5  CA  ASP     5     -12.941  -8.037  13.183  1.00 25.00           C
ATOM      6  CA  TYR     6     -15.991  -5.676  13.309  1.00 25.00           C
ATOM      7  CA  GLU     7     -16.998  -2.782  15.630  1.00 25.00           C
ATOM      8  CA  VAL     8     -16.192   0.910  14.989  1.00 25.00           C
ATOM      9  CA  LEU     9     -16.362   2.957  18.166  1.00 25.00           C
ATOM     10  CA  TYR    10     -15.711   6.545  17.060  1.00 25.00           C
ATOM     11  CA  THR    11     -13.364   9.568  17.007  1.00 25.00           C
ATOM     12  CA  ILE    12      -9.666   9.762  17.859  1.00 25.00           C
ATOM     13  CA  GLY    13      -9.089  12.957  15.805  1.00 25.00           C
ATOM     14  CA  THR    14      -9.182  15.182  12.705  1.00 25.00           C
ATOM     15  CA  GLY    15      -5.696  15.451  11.211  1.00 25.00           C
ATOM     16  CA  SER    16      -5.355  17.043   7.826  1.00 25.00           C
ATOM     17  CA  TYR    17      -3.641  13.853   6.790  1.00 25.00           C
ATOM     18  CA  GLY    18      -5.826  10.812   7.471  1.00 25.00           C
ATOM     19  CA  ARG    19      -8.994  11.001   9.570  1.00 25.00           C
ATOM     20  CA  CYS    20      -8.905   8.889  12.675  1.00 25.00           C
ATOM     21  CA  GLN    21     -10.307   5.913  14.667  1.00 25.00           C
ATOM     22  CA  LYS    22     -11.088   3.268  17.325  1.00 25.00           C
ATOM     23  CA  ILE    23     -10.332   0.197  15.134  1.00 25.00           C
ATOM     24  CA  ARG    24     -12.151  -2.411  17.171  1.00 25.00           C
ATOM     25  CA  ARG    25     -10.821  -6.030  17.344  1.00 25.00           C
ATOM     26  CA  LYS    26     -13.071  -9.029  18.155  1.00 25.00           C
ATOM     27  CA  SER    27     -10.034 -11.123  17.491  1.00 25.00           C
ATOM     28  CA  ASP    28      -8.917 -11.322  21.167  1.00 25.00           C
ATOM     29  CA  GLY    29      -9.813  -7.712  21.959  1.00 25.00           C
ATOM     30  CA  LYS    30      -7.229  -4.998  21.302  1.00 25.00           C
ATOM     31  CA  ILE    31      -6.358  -1.360  21.489  1.00 25.00           C
ATOM     32  CA  LEU    32      -5.921  -0.667  17.793  1.00 25.00           C
ATOM     33  CA  VAL    33      -5.998   3.035  16.811  1.00 25.00           C
ATOM     34  CA  TRP    34      -6.148   3.560  13.028  1.00 25.00           C
ATOM     35  CA  LYS    35      -6.080   5.734   9.838  1.00 25.00           C
ATOM     36  CA  GLU    36      -9.303   5.888   7.808  1.00 25.00           C
ATOM     37  CA  LEU    37      -7.492   6.748   4.573  1.00 25.00           C
ATOM     38  CA  ASP    38     -10.457   7.739   2.442  1.00 25.00           C
ATOM     39  CA  TYR    39      -9.211   8.324  -1.119  1.00 25.00           C
ATOM     40  CA  GLY    40     -11.641   8.949  -3.959  1.00 25.00           C
ATOM     41  CA  SER    41      -8.554   8.470  -6.158  1.00 25.00           C
ATOM     42  CA  MET    42      -5.736   5.870  -6.523  1.00 25.00           C
ATOM     43  CA  THR    43      -4.138   7.214  -9.745  1.00 25.00           C
ATOM     44  CA  GLU    44      -2.038   4.031  -9.823  1.00 25.00           C
ATOM     45  CA  ALA    45       0.630   6.352  -8.317  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.614   8.116  -5.154  1.00 25.00           C
ATOM     47  CA  LYS    47      -1.703   4.753  -3.678  1.00 25.00           C
ATOM     48  CA  GLN    48       1.734   3.262  -4.475  1.00 25.00           C
ATOM     49  CA  MET    49       3.445   6.247  -2.792  1.00 25.00           C
ATOM     50  CA  LEU    50       1.229   5.806   0.300  1.00 25.00           C
ATOM     51  CA  VAL    51       2.103   2.079   0.425  1.00 25.00           C
ATOM     52  CA  SER    52       5.830   2.918   0.170  1.00 25.00           C
ATOM     53  CA  GLU    53       5.477   5.458   3.015  1.00 25.00           C
ATOM     54  CA  VAL    54       3.688   2.841   5.163  1.00 25.00           C
ATOM     55  CA  ASN    55       6.477   0.315   4.453  1.00 25.00           C
ATOM     56  CA  LEU    56       9.114   2.914   5.433  1.00 25.00           C
ATOM     57  CA  LEU    57       7.224   3.642   8.684  1.00 25.00           C
ATOM     58  CA  ARG    58       7.059  -0.106   9.455  1.00 25.00           C
ATOM     59  CA  GLU    59      10.821  -0.427   8.818  1.00 25.00           C
ATOM     60  CA  LEU    60      10.985   0.460  12.514  1.00 25.00           C
ATOM     61  CA  LYS    61      11.787   0.084  16.220  1.00 25.00           C
ATOM     62  CA  HIS    62      13.224   2.855  18.341  1.00 25.00           C
ATOM     63  CA  PRO    63      11.753   1.150  21.356  1.00 25.00           C
ATOM     64  CA  ASN    64      10.326   4.512  22.371  1.00 25.00           C
ATOM     65  CA  ILE    65       8.409   4.323  19.130  1.00 25.00           C
ATOM     66  CA  VAL    66       4.963   3.684  17.552  1.00 25.00           C
ATOM     67  CA  ARG    67       4.461   0.003  16.588  1.00 25.00           C
ATOM     68  CA  TYR    68       2.679  -0.043  13.228  1.00 25.00           C
ATOM     69  CA  TYR    69      -0.037  -2.740  13.409  1.00 25.00           C
ATOM     70  CA  ASP    70      -0.678  -4.227   9.959  1.00 25.00           C
ATOM     71  CA  ARG    71      -1.722  -3.051   6.527  1.00 25.00           C
ATOM     72  CA  ILE    72      -5.048  -2.752   4.603  1.00 25.00           C
ATOM     73  CA  ILE    73      -5.080  -3.146   0.827  1.00 25.00           C
ATOM     74  CA  ASP    74      -8.837  -3.753   0.948  1.00 25.00           C
ATOM     75  CA  ARG    75      -9.222  -2.960  -2.805  1.00 25.00           C
ATOM     76  CA  THR    76     -12.923  -2.378  -3.505  1.00 25.00           C
ATOM     77  CA  ASN    77     -13.514   1.356  -3.728  1.00 25.00           C
ATOM     78  CA  THR    78     -10.834   3.609  -2.280  1.00 25.00           C
ATOM     79  CA  THR    79      -8.462   3.163   0.644  1.00 25.00           C
ATOM     80  CA  LEU    80      -5.311   2.656   2.673  1.00 25.00           C
ATOM     81  CA  TYR    81      -6.441   1.832   6.221  1.00 25.00           C
ATOM     82  CA  ILE    82      -2.929   2.721   7.287  1.00 25.00           C
ATOM     83  CA  VAL    83      -1.697   1.761  10.809  1.00 25.00           C
ATOM     84  CA  MET    84      -1.382   2.661  14.477  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.225   2.206  18.113  1.00 25.00           C
ATOM     86  CA  TYR    86      -2.947   2.505  20.811  1.00 25.00           C
TER
END
