
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0283TS393_1-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS393_1-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    S       2      S       2           -
LGA    F       3      F       3           -
LGA    I       4      I       4           -
LGA    E       5      E       5           -
LGA    K       6      K       6           -
LGA    M       7      M       7           -
LGA    I       8      I       8           -
LGA    G       9      G       9           -
LGA    S      10      S      10           -
LGA    L      11      L      11           -
LGA    N      12      -       -           -
LGA    D      13      -       -           -
LGA    K      14      -       -           -
LGA    R      15      -       -           -
LGA    E      16      -       -           -
LGA    W      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    A      22      N      12          3.821
LGA    R      23      -       -           -
LGA    A      24      -       -           -
LGA    K      25      D      13          2.880
LGA    A      26      K      14          3.260
LGA    L      27      R      15           -
LGA    P      28      E      16           -
LGA    K      29      W      17           -
LGA    E      30      K      18           #
LGA    Y      31      A      19           -
LGA    H      32      M      20           -
LGA    H      33      -       -           -
LGA    A      34      E      21           #
LGA    Y      35      A      22           -
LGA    K      36      R      23           -
LGA    A      37      A      24           -
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      K      25           #
LGA    D      50      A      26          4.722
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      L      27          5.401
LGA    T      54      P      28          2.084
LGA    K      55      K      29          2.179
LGA    R      56      E      30          1.899
LGA    I      57      Y      31          1.624
LGA    F      58      H      32          1.228
LGA    G      59      H      33          0.941
LGA    G      60      A      34          1.048
LGA    I      61      Y      35          0.747
LGA    L      62      K      36          0.300
LGA    D      63      A      37          0.586
LGA    L      64      I      38          0.604
LGA    F      65      Q      39          0.320
LGA    E      66      K      40          0.615
LGA    E      67      Y      41          0.753
LGA    G      68      M      42          0.599
LGA    A      69      W      43          1.379
LGA    A      70      T      44          2.984
LGA    E      71      S      45           -
LGA    G      72      G      46           -
LGA    K      73      -       -           -
LGA    K      74      -       -           -
LGA    V      75      G      47           #
LGA    T      76      -       -           -
LGA    D      77      P      48           #
LGA    L      78      T      49           -
LGA    T      79      D      50           #
LGA    G      80      W      51          4.393
LGA    E      81      Q      52          3.781
LGA    D      82      D      53          2.147
LGA    V      83      T      54          2.052
LGA    A      84      K      55          1.380
LGA    A      85      R      56          1.540
LGA    F      86      I      57          2.073
LGA    C      87      F      58          1.443
LGA    D      88      G      59          3.654
LGA    E      89      G      60          5.323
LGA    L      90      I      61           #
LGA    M      91      -       -           -
LGA    K      92      L      62           #
LGA    D      93      D      63           -
LGA    T      94      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    -       -      K      73           -
LGA    -       -      K      74           -
LGA    K      95      V      75          3.459
LGA    T      96      T      76          3.722
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    W      97      E      81          4.176
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     35    2.70     8.57     25.923     1.249

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.041136 * X  +  -0.944578 * Y  +  -0.325699 * Z  +  22.411686
  Y_new =   0.668694 * X  +  -0.216181 * Y  +   0.711417 * Z  +  24.747345
  Z_new =  -0.742399 * X  +  -0.247058 * Y  +   0.622741 * Z  +  -6.268755 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.377681    2.763911  [ DEG:   -21.6396    158.3604 ]
  Theta =   0.836644    2.304949  [ DEG:    47.9361    132.0639 ]
  Phi   =   1.509356   -1.632236  [ DEG:    86.4797    -93.5203 ]
 
# 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: T0283TS393_1-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_1-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   35   2.70    8.57  25.923
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_1-D1
PFRMAT TS
TARGET T0283
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -0.365   1.196 -15.561  1.00 25.00           C
ATOM      2  CA  SER     2      -0.576   4.978 -15.069  1.00 25.00           C
ATOM      3  CA  PHE     3       2.809   5.270 -13.235  1.00 25.00           C
ATOM      4  CA  ILE     4       5.101   2.597 -11.730  1.00 25.00           C
ATOM      5  CA  GLU     5       8.069   3.995 -13.705  1.00 25.00           C
ATOM      6  CA  LYS     6       7.264   7.527 -12.462  1.00 25.00           C
ATOM      7  CA  MET     7       7.093   6.246  -8.858  1.00 25.00           C
ATOM      8  CA  ILE     8      10.476   4.503  -9.290  1.00 25.00           C
ATOM      9  CA  GLY     9      11.990   7.733 -10.683  1.00 25.00           C
ATOM     10  CA  SER    10      10.599   9.698  -7.705  1.00 25.00           C
ATOM     11  CA  LEU    11      12.086   7.130  -5.284  1.00 25.00           C
ATOM     12  CA  ASN    12      15.478   7.401  -7.042  1.00 25.00           C
ATOM     13  CA  ASP    13      15.330  11.220  -6.790  1.00 25.00           C
ATOM     14  CA  LYS    14      14.508  10.966  -3.059  1.00 25.00           C
ATOM     15  CA  ARG    15      17.459   8.580  -2.544  1.00 25.00           C
ATOM     16  CA  GLU    16      19.775  11.006  -4.393  1.00 25.00           C
ATOM     17  CA  TRP    17      18.538  13.894  -2.203  1.00 25.00           C
ATOM     18  CA  LYS    18      19.169  11.809   0.947  1.00 25.00           C
ATOM     19  CA  ALA    19      22.705  10.989  -0.276  1.00 25.00           C
ATOM     20  CA  MET    20      23.363  14.703  -0.939  1.00 25.00           C
ATOM     21  CA  GLU    21      22.117  15.578   2.575  1.00 25.00           C
ATOM     22  CA  ALA    22      24.409  12.904   4.079  1.00 25.00           C
ATOM     23  CA  ARG    23      27.377  14.303   2.104  1.00 25.00           C
ATOM     24  CA  ALA    24      26.572  17.834   3.347  1.00 25.00           C
ATOM     25  CA  LYS    25      26.402  16.554   6.952  1.00 25.00           C
ATOM     26  CA  ALA    26      29.784  14.811   6.519  1.00 25.00           C
ATOM     27  CA  LEU    27      31.119  18.405   6.411  1.00 25.00           C
ATOM     28  CA  PRO    28      34.009  18.961   4.091  1.00 25.00           C
ATOM     29  CA  LYS    29      35.531  17.261   0.994  1.00 25.00           C
ATOM     30  CA  GLU    30      32.489  17.117  -1.327  1.00 25.00           C
ATOM     31  CA  TYR    31      31.167  20.388   0.162  1.00 25.00           C
ATOM     32  CA  HIS    32      34.583  22.037  -0.362  1.00 25.00           C
ATOM     33  CA  HIS    33      34.634  20.833  -3.997  1.00 25.00           C
ATOM     34  CA  ALA    34      31.114  22.243  -4.539  1.00 25.00           C
ATOM     35  CA  TYR    35      32.202  25.597  -3.043  1.00 25.00           C
ATOM     36  CA  LYS    36      35.259  25.662  -5.350  1.00 25.00           C
ATOM     37  CA  ALA    37      33.025  24.926  -8.371  1.00 25.00           C
ATOM     38  CA  ILE    38      30.659  27.757  -7.344  1.00 25.00           C
ATOM     39  CA  GLN    39      33.630  30.150  -7.006  1.00 25.00           C
ATOM     40  CA  LYS    40      34.879  29.128 -10.479  1.00 25.00           C
ATOM     41  CA  TYR    41      31.390  29.731 -11.939  1.00 25.00           C
ATOM     42  CA  MET    42      31.267  33.183 -10.287  1.00 25.00           C
ATOM     43  CA  TRP    43      34.714  34.022 -11.729  1.00 25.00           C
ATOM     44  CA  THR    44      33.554  32.919 -15.208  1.00 25.00           C
ATOM     45  CA  SER    45      32.728  29.544 -16.754  1.00 25.00           C
ATOM     46  CA  GLY    46      33.861  26.434 -14.879  1.00 25.00           C
ATOM     47  CA  GLY    47      31.027  24.693 -16.601  1.00 25.00           C
ATOM     48  CA  PRO    48      31.551  20.944 -16.653  1.00 25.00           C
ATOM     49  CA  THR    49      28.318  18.933 -16.220  1.00 25.00           C
ATOM     50  CA  ASP    50      24.509  19.186 -16.400  1.00 25.00           C
ATOM     51  CA  TRP    51      22.610  20.882 -19.303  1.00 25.00           C
ATOM     52  CA  GLN    52      23.252  24.652 -19.522  1.00 25.00           C
ATOM     53  CA  ASP    53      20.134  25.331 -17.405  1.00 25.00           C
ATOM     54  CA  THR    54      21.316  22.782 -14.802  1.00 25.00           C
ATOM     55  CA  LYS    55      24.765  24.445 -14.704  1.00 25.00           C
ATOM     56  CA  ARG    56      23.126  27.873 -14.222  1.00 25.00           C
ATOM     57  CA  ILE    57      20.987  26.476 -11.369  1.00 25.00           C
ATOM     58  CA  PHE    58      24.110  24.991  -9.723  1.00 25.00           C
ATOM     59  CA  GLY    59      25.905  28.359 -10.030  1.00 25.00           C
ATOM     60  CA  GLY    60      22.900  30.132  -8.450  1.00 25.00           C
ATOM     61  CA  ILE    61      22.889  27.604  -5.574  1.00 25.00           C
ATOM     62  CA  LEU    62      26.639  28.166  -5.033  1.00 25.00           C
ATOM     63  CA  ASP    63      26.087  31.956  -4.979  1.00 25.00           C
ATOM     64  CA  LEU    64      23.270  31.534  -2.419  1.00 25.00           C
ATOM     65  CA  PHE    65      25.541  29.348  -0.243  1.00 25.00           C
ATOM     66  CA  GLU    66      28.310  31.986  -0.440  1.00 25.00           C
ATOM     67  CA  GLU    67      25.818  34.712   0.571  1.00 25.00           C
ATOM     68  CA  GLY    68      24.656  32.585   3.535  1.00 25.00           C
ATOM     69  CA  ALA    69      28.292  32.053   4.613  1.00 25.00           C
ATOM     70  CA  ALA    70      28.933  35.823   4.393  1.00 25.00           C
ATOM     71  CA  GLU    71      32.353  34.618   3.215  1.00 25.00           C
ATOM     72  CA  GLY    72      33.619  31.051   2.817  1.00 25.00           C
ATOM     73  CA  LYS    73      34.188  27.347   3.335  1.00 25.00           C
ATOM     74  CA  LYS    74      30.797  27.111   5.074  1.00 25.00           C
ATOM     75  CA  VAL    75      29.238  26.936   1.626  1.00 25.00           C
ATOM     76  CA  THR    76      26.286  24.505   1.433  1.00 25.00           C
ATOM     77  CA  ASP    77      26.547  23.853   5.198  1.00 25.00           C
ATOM     78  CA  LEU    78      23.497  21.580   4.842  1.00 25.00           C
ATOM     79  CA  THR    79      21.363  19.041   6.801  1.00 25.00           C
ATOM     80  CA  GLY    80      18.586  18.324   9.352  1.00 25.00           C
ATOM     81  CA  GLU    81      15.132  19.546   8.236  1.00 25.00           C
ATOM     82  CA  ASP    82      16.037  23.121   9.269  1.00 25.00           C
ATOM     83  CA  VAL    83      19.316  22.884   7.303  1.00 25.00           C
ATOM     84  CA  ALA    84      17.412  21.620   4.231  1.00 25.00           C
ATOM     85  CA  ALA    85      14.933  24.524   4.540  1.00 25.00           C
ATOM     86  CA  PHE    86      17.837  27.008   4.783  1.00 25.00           C
ATOM     87  CA  CYS    87      19.446  25.469   1.666  1.00 25.00           C
ATOM     88  CA  ASP    88      16.123  25.748  -0.216  1.00 25.00           C
ATOM     89  CA  GLU    89      15.807  29.417   0.831  1.00 25.00           C
ATOM     90  CA  LEU    90      19.379  30.094  -0.373  1.00 25.00           C
ATOM     91  CA  MET    91      18.593  28.417  -3.725  1.00 25.00           C
ATOM     92  CA  LYS    92      15.433  30.551  -4.079  1.00 25.00           C
ATOM     93  CA  ASP    93      17.456  33.715  -3.326  1.00 25.00           C
ATOM     94  CA  THR    94      20.052  32.710  -5.956  1.00 25.00           C
ATOM     95  CA  LYS    95      17.267  32.123  -8.519  1.00 25.00           C
ATOM     96  CA  THR    96      15.777  35.560  -7.721  1.00 25.00           C
ATOM     97  CA  TRP    97      19.219  37.181  -8.158  1.00 25.00           C
TER
END
