
#######################################################
#                                                     #
#                        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   87 (   87),  selected   87 , name T0358TS393_2
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS393_2.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      G      10           #
LGA    T       2      P      11           #
LGA    Q       3      F      12           #
LGA    S       4      T      13           #
LGA    V       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      -       -           -
LGA    T      28      R      14           #
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    L      29      A      17          1.460
LGA    E      30      Q      18          5.216
LGA    D      31      A      19          1.049
LGA    D      32      V      20           -
LGA    Q      33      T      21           -
LGA    G      34      T      22          1.129
LGA    S      35      T      23          3.167
LGA    H      36      Y      24          4.824
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    F      37      T      28           #
LGA    R      38      -       -           -
LGA    L      39      L      29           #
LGA    V      40      E      30           #
LGA    V      41      D      31           #
LGA    R      42      D      32          3.760
LGA    D      43      Q      33           #
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      G      34          2.939
LGA    M      48      S      35          3.771
LGA    V      49      H      36          3.363
LGA    W      50      F      37          2.289
LGA    R      51      R      38          0.914
LGA    A      52      L      39          1.415
LGA    W      53      V      40          2.871
LGA    N      54      V      41          4.481
LGA    F      55      R      42          3.735
LGA    E      56      D      43          2.746
LGA    P      57      T      44           #
LGA    -       -      E      45           -
LGA    D      58      G      46          4.796
LGA    A      59      R      47          5.280
LGA    G      60      M      48          4.038
LGA    E      61      V      49          1.925
LGA    G      62      W      50          4.721
LGA    L      63      R      51          4.722
LGA    N      64      A      52          3.732
LGA    R      65      -       -           -
LGA    Y      66      -       -           -
LGA    I      67      -       -           -
LGA    R      68      W      53           #
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    T      69      A      59          3.766
LGA    S      70      G      60          4.040
LGA    G      71      E      61          4.186
LGA    I      72      G      62           #
LGA    R      73      L      63           -
LGA    T      74      N      64           -
LGA    D      75      R      65           -
LGA    T      76      Y      66           -
LGA    A      77      I      67           -
LGA    T      78      R      68           -
LGA    R      79      T      69           -
LGA    L      80      S      70           -
LGA    E      81      G      71           -
LGA    H      82      I      72           -
LGA    H      83      R      73           -
LGA    H      84      T      74           -
LGA    H      85      D      75           -
LGA    H      86      -       -           -
LGA    H      87      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   87   66    5.0     27    3.59     3.70     24.772     0.731

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.171225 * X  +   0.910392 * Y  +   0.376655 * Z  +  -1.368950
  Y_new =  -0.754955 * X  +   0.124397 * Y  +  -0.643870 * Z  +   6.093789
  Z_new =  -0.633028 * X  +  -0.394604 * Y  +   0.666005 * Z  +   2.797663 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.534882    2.606710  [ DEG:   -30.6465    149.3535 ]
  Theta =   0.685459    2.456134  [ DEG:    39.2739    140.7261 ]
  Phi   =  -1.793824    1.347768  [ DEG:  -102.7786     77.2214 ]
 
# 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: T0358TS393_2                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_2.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   87   66   5.0   27   3.59    3.70  24.772
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_2
PFRMAT TS
TARGET T0358
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      15.611  12.620   3.642  1.00 25.00           C
ATOM      2  CA  THR     2      11.978  11.767   3.085  1.00 25.00           C
ATOM      3  CA  GLN     3      10.148  10.182   0.113  1.00 25.00           C
ATOM      4  CA  SER     4       7.624  10.720  -2.632  1.00 25.00           C
ATOM      5  CA  VAL     5       3.991   9.935  -1.778  1.00 25.00           C
ATOM      6  CA  LEU     6       0.410  11.127  -1.359  1.00 25.00           C
ATOM      7  CA  LEU     7      -1.325  11.573   2.022  1.00 25.00           C
ATOM      8  CA  PRO     8      -0.372  15.021   3.114  1.00 25.00           C
ATOM      9  CA  PRO     9      -0.382  18.593   4.268  1.00 25.00           C
ATOM     10  CA  GLY    10      -2.694  21.222   2.823  1.00 25.00           C
ATOM     11  CA  PRO    11      -6.120  19.712   2.159  1.00 25.00           C
ATOM     12  CA  PHE    12      -5.149  16.947   4.601  1.00 25.00           C
ATOM     13  CA  THR    13      -7.985  14.442   4.441  1.00 25.00           C
ATOM     14  CA  ARG    14     -10.440  12.253   2.531  1.00 25.00           C
ATOM     15  CA  ARG    15      -8.589  13.894  -0.392  1.00 25.00           C
ATOM     16  CA  GLN    16      -6.019  11.054  -0.391  1.00 25.00           C
ATOM     17  CA  ALA    17      -8.842   8.466  -0.409  1.00 25.00           C
ATOM     18  CA  GLN    18     -10.511  10.271  -3.346  1.00 25.00           C
ATOM     19  CA  ALA    19      -7.188  10.298  -5.249  1.00 25.00           C
ATOM     20  CA  VAL    20      -6.752   6.551  -4.593  1.00 25.00           C
ATOM     21  CA  THR    21     -10.307   5.892  -5.859  1.00 25.00           C
ATOM     22  CA  THR    22      -9.587   7.935  -9.017  1.00 25.00           C
ATOM     23  CA  THR    23      -6.362   5.951  -9.596  1.00 25.00           C
ATOM     24  CA  TYR    24      -8.282   2.663  -9.179  1.00 25.00           C
ATOM     25  CA  SER    25      -7.902   0.370  -6.212  1.00 25.00           C
ATOM     26  CA  ASN    26      -4.563  -0.516  -7.765  1.00 25.00           C
ATOM     27  CA  ILE    27      -2.474   2.315  -6.398  1.00 25.00           C
ATOM     28  CA  THR    28       0.748   0.278  -6.848  1.00 25.00           C
ATOM     29  CA  LEU    29       4.101  -0.995  -5.422  1.00 25.00           C
ATOM     30  CA  GLU    30       6.757  -3.425  -4.076  1.00 25.00           C
ATOM     31  CA  ASP    31       6.249  -5.011  -7.529  1.00 25.00           C
ATOM     32  CA  ASP    32       6.154  -5.689 -11.248  1.00 25.00           C
ATOM     33  CA  GLN    33       4.851  -9.203 -10.561  1.00 25.00           C
ATOM     34  CA  GLY    34       2.067  -8.105  -8.174  1.00 25.00           C
ATOM     35  CA  SER    35       1.641  -6.418  -4.797  1.00 25.00           C
ATOM     36  CA  HIS    36       0.745  -3.717  -2.219  1.00 25.00           C
ATOM     37  CA  PHE    37       1.422  -0.281  -0.697  1.00 25.00           C
ATOM     38  CA  ARG    38       1.948   2.907  -2.701  1.00 25.00           C
ATOM     39  CA  LEU    39       2.665   6.018  -4.680  1.00 25.00           C
ATOM     40  CA  VAL    40       0.938   6.266  -8.018  1.00 25.00           C
ATOM     41  CA  VAL    41      -1.708   7.760 -10.309  1.00 25.00           C
ATOM     42  CA  ARG    42      -3.314  11.194 -10.640  1.00 25.00           C
ATOM     43  CA  ASP    43      -4.147  11.428 -14.296  1.00 25.00           C
ATOM     44  CA  THR    44      -3.436  10.026 -17.805  1.00 25.00           C
ATOM     45  CA  GLU    45      -1.318  13.188 -18.234  1.00 25.00           C
ATOM     46  CA  GLY    46       1.924  13.326 -16.167  1.00 25.00           C
ATOM     47  CA  ARG    47       1.475  12.794 -12.456  1.00 25.00           C
ATOM     48  CA  MET    48       0.643  12.143  -8.744  1.00 25.00           C
ATOM     49  CA  VAL    49      -1.266  10.271  -5.994  1.00 25.00           C
ATOM     50  CA  TRP    50      -2.337   7.193  -4.143  1.00 25.00           C
ATOM     51  CA  ARG    51      -1.754   5.617  -0.683  1.00 25.00           C
ATOM     52  CA  ALA    52      -3.013   2.108  -1.430  1.00 25.00           C
ATOM     53  CA  TRP    53      -6.793   2.527  -1.338  1.00 25.00           C
ATOM     54  CA  ASN    54      -6.949  -1.216  -1.277  1.00 25.00           C
ATOM     55  CA  PHE    55      -6.579  -4.978  -1.478  1.00 25.00           C
ATOM     56  CA  GLU    56      -6.288  -6.503   2.024  1.00 25.00           C
ATOM     57  CA  PRO    57      -9.811  -5.104   2.509  1.00 25.00           C
ATOM     58  CA  ASP    58     -12.299  -2.154   2.641  1.00 25.00           C
ATOM     59  CA  ALA    59     -10.084   0.662   3.945  1.00 25.00           C
ATOM     60  CA  GLY    60      -9.396  -0.023   7.625  1.00 25.00           C
ATOM     61  CA  GLU    61      -6.181  -1.502   6.287  1.00 25.00           C
ATOM     62  CA  GLY    62      -2.689  -3.013   5.857  1.00 25.00           C
ATOM     63  CA  LEU    63      -1.927  -0.517   3.054  1.00 25.00           C
ATOM     64  CA  ASN    64      -3.100   2.374   5.276  1.00 25.00           C
ATOM     65  CA  ARG    65      -0.870   1.121   8.126  1.00 25.00           C
ATOM     66  CA  TYR    66       2.113   0.911   5.734  1.00 25.00           C
ATOM     67  CA  ILE    67       1.432   4.484   4.533  1.00 25.00           C
ATOM     68  CA  ARG    68       1.270   5.699   8.162  1.00 25.00           C
ATOM     69  CA  THR    69       4.593   3.950   8.920  1.00 25.00           C
ATOM     70  CA  SER    70       6.065   0.431   9.090  1.00 25.00           C
ATOM     71  CA  GLY    71       6.148  -0.531  12.754  1.00 25.00           C
ATOM     72  CA  ILE    72       4.961   2.932  13.846  1.00 25.00           C
ATOM     73  CA  ARG    73       6.473   2.154  17.302  1.00 25.00           C
ATOM     74  CA  THR    74       7.451   5.295  19.282  1.00 25.00           C
ATOM     75  CA  ASP    75       7.012   3.748  22.740  1.00 25.00           C
ATOM     76  CA  THR    76       3.323   2.762  23.178  1.00 25.00           C
ATOM     77  CA  ALA    77       0.253   1.223  24.814  1.00 25.00           C
ATOM     78  CA  THR    78      -1.383   4.187  26.564  1.00 25.00           C
ATOM     79  CA  ARG    79      -3.715   6.986  27.552  1.00 25.00           C
ATOM     80  CA  LEU    80      -6.200   8.862  29.667  1.00 25.00           C
ATOM     81  CA  GLU    81      -4.552  12.243  29.200  1.00 25.00           C
ATOM     82  CA  HIS    82      -1.180  13.383  30.446  1.00 25.00           C
ATOM     83  CA  HIS    83      -2.204  17.071  30.788  1.00 25.00           C
ATOM     84  CA  HIS    84      -1.760  19.646  27.976  1.00 25.00           C
ATOM     85  CA  HIS    85      -3.427  19.741  24.557  1.00 25.00           C
ATOM     86  CA  HIS    86      -4.162  20.465  20.867  1.00 25.00           C
ATOM     87  CA  HIS    87      -0.776  22.140  20.460  1.00 25.00           C
TER
END
