
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0306TS393_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS393_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      -       -           -
LGA    L       3      -       -           -
LGA    A       4      K       2          1.547
LGA    V       5      L       3          2.423
LGA    V       6      A       4           #
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    I      10      -       -           -
LGA    V      11      V       5          4.857
LGA    C      12      V       6          1.396
LGA    T      13      T       7          2.982
LGA    V      14      G       8          4.249
LGA    R      15      Q       9          2.117
LGA    H      16      I      10          1.962
LGA    H      17      V      11          3.874
LGA    G      18      C      12           -
LGA    L      19      T      13           -
LGA    A      20      V      14           -
LGA    H      21      R      15           -
LGA    D      22      H      16           -
LGA    K      23      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    L      24      M      26          1.610
LGA    L      25      V      27          3.349
LGA    M      26      E      28           -
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    A      41      -       -           -
LGA    V      42      -       -           -
LGA    A      43      -       -           -
LGA    I      44      -       -           -
LGA    D      45      M      29          2.167
LGA    N      46      I      30          2.420
LGA    I      47      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    G      48      G      38          1.997
LGA    A      49      Q      39          2.248
LGA    G      50      C      40           -
LGA    T      51      A      41           -
LGA    G      52      V      42           -
LGA    E      53      A      43           -
LGA    W      54      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    V      55      W      54          4.960
LGA    L      56      V      55          3.155
LGA    L      57      L      56          0.228
LGA    V      58      L      57          1.692
LGA    S      59      V      58          5.408
LGA    G      60      -       -           -
LGA    S      61      S      59           #
LGA    S      62      G      60           -
LGA    -       -      S      61           -
LGA    A      63      S      62           #
LGA    R      64      A      63          1.447
LGA    -       -      R      64           -
LGA    Q      65      Q      65          2.285
LGA    A      66      A      66          2.920
LGA    H      67      H      67          2.187
LGA    K      68      K      68          1.812
LGA    S      69      S      69          1.945
LGA    E      70      E      70          1.491
LGA    T      71      T      71          2.842
LGA    S      72      S      72          3.011
LGA    P      73      P      73          3.122
LGA    V      74      V      74          3.362
LGA    D      75      D      75          3.574
LGA    L      76      L      76          3.582
LGA    C      77      C      77          3.903
LGA    V      78      -       -           -
LGA    I      79      -       -           -
LGA    G      80      V      78           #
LGA    I      81      I      79           -
LGA    V      82      G      80           -
LGA    D      83      I      81           -
LGA    E      84      -       -           -
LGA    V      85      V      82           #
LGA    V      86      -       -           -
LGA    S      87      -       -           -
LGA    G      88      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    G      89      I      92          1.990
LGA    Q      90      F      93          1.794
LGA    V      91      H      94           #
LGA    I      92      K      95           #
LGA    F      93      -       -           -
LGA    H      94      -       -           -
LGA    K      95      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     36    2.89    47.22     23.033     1.205

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.455432 * X  +  -0.879568 * Y  +  -0.137630 * Z  +  41.503078
  Y_new =   0.798366 * X  +   0.471915 * Y  +  -0.374043 * Z  +  26.726400
  Z_new =   0.393946 * X  +   0.060472 * Y  +   0.917142 * Z  +  64.872734 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.065840   -3.075752  [ DEG:     3.7724   -176.2276 ]
  Theta =  -0.404921   -2.736672  [ DEG:   -23.2002   -156.7998 ]
  Phi   =   1.052384   -2.089209  [ DEG:    60.2972   -119.7028 ]
 
# 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: T0306TS393_2                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS393_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   36   2.89   47.22  23.033
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS393_2
PFRMAT TS
TARGET T0306
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      39.481  43.165  71.036  1.00 25.00           C
ATOM      2  CA  LYS     2      40.158  39.531  71.820  1.00 25.00           C
ATOM      3  CA  LEU     3      41.729  37.282  69.192  1.00 25.00           C
ATOM      4  CA  ALA     4      43.774  35.645  66.382  1.00 25.00           C
ATOM      5  CA  VAL     5      46.356  33.806  64.256  1.00 25.00           C
ATOM      6  CA  VAL     6      49.604  31.834  64.164  1.00 25.00           C
ATOM      7  CA  THR     7      50.186  33.718  60.966  1.00 25.00           C
ATOM      8  CA  GLY     8      48.050  31.089  59.320  1.00 25.00           C
ATOM      9  CA  GLN     9      47.674  27.452  60.377  1.00 25.00           C
ATOM     10  CA  ILE    10      44.793  25.146  61.305  1.00 25.00           C
ATOM     11  CA  VAL    11      43.165  24.217  64.560  1.00 25.00           C
ATOM     12  CA  CYS    12      42.860  21.576  67.338  1.00 25.00           C
ATOM     13  CA  THR    13      41.250  20.196  70.529  1.00 25.00           C
ATOM     14  CA  VAL    14      38.169  19.291  68.408  1.00 25.00           C
ATOM     15  CA  ARG    15      35.030  18.324  70.268  1.00 25.00           C
ATOM     16  CA  HIS    16      34.086  18.060  74.002  1.00 25.00           C
ATOM     17  CA  HIS    17      32.689  14.506  73.648  1.00 25.00           C
ATOM     18  CA  GLY    18      33.788  12.696  76.740  1.00 25.00           C
ATOM     19  CA  LEU    19      37.062  14.616  76.110  1.00 25.00           C
ATOM     20  CA  ALA    20      38.581  16.917  78.729  1.00 25.00           C
ATOM     21  CA  HIS    21      35.973  19.677  78.493  1.00 25.00           C
ATOM     22  CA  ASP    22      37.149  23.002  77.230  1.00 25.00           C
ATOM     23  CA  LYS    23      40.108  22.836  74.875  1.00 25.00           C
ATOM     24  CA  LEU    24      38.072  24.382  72.023  1.00 25.00           C
ATOM     25  CA  LEU    25      39.030  24.685  68.336  1.00 25.00           C
ATOM     26  CA  MET    26      37.278  23.186  65.238  1.00 25.00           C
ATOM     27  CA  VAL    27      39.542  20.675  63.475  1.00 25.00           C
ATOM     28  CA  GLU    28      40.443  22.218  60.113  1.00 25.00           C
ATOM     29  CA  MET    29      43.714  20.571  59.168  1.00 25.00           C
ATOM     30  CA  ILE    30      45.629  22.474  56.469  1.00 25.00           C
ATOM     31  CA  ASP    31      44.122  20.985  53.327  1.00 25.00           C
ATOM     32  CA  PRO    32      42.832  18.221  51.026  1.00 25.00           C
ATOM     33  CA  GLN    33      39.384  16.506  51.084  1.00 25.00           C
ATOM     34  CA  GLY    34      39.924  16.419  47.284  1.00 25.00           C
ATOM     35  CA  ASN    35      40.543  20.038  46.247  1.00 25.00           C
ATOM     36  CA  PRO    36      41.555  23.684  45.586  1.00 25.00           C
ATOM     37  CA  ASP    37      44.671  22.686  47.527  1.00 25.00           C
ATOM     38  CA  GLY    38      44.852  26.306  48.706  1.00 25.00           C
ATOM     39  CA  GLN    39      44.026  25.957  52.372  1.00 25.00           C
ATOM     40  CA  CYS    40      42.079  26.175  55.585  1.00 25.00           C
ATOM     41  CA  ALA    41      40.410  27.743  58.604  1.00 25.00           C
ATOM     42  CA  VAL    42      38.738  26.956  61.892  1.00 25.00           C
ATOM     43  CA  ALA    43      40.223  28.415  65.124  1.00 25.00           C
ATOM     44  CA  ILE    44      41.833  31.120  67.320  1.00 25.00           C
ATOM     45  CA  ASP    45      43.663  32.566  70.325  1.00 25.00           C
ATOM     46  CA  ASN    46      46.737  30.878  71.871  1.00 25.00           C
ATOM     47  CA  ILE    47      45.169  28.474  74.377  1.00 25.00           C
ATOM     48  CA  GLY    48      45.036  30.001  77.828  1.00 25.00           C
ATOM     49  CA  ALA    49      44.875  33.348  75.925  1.00 25.00           C
ATOM     50  CA  GLY    50      47.506  35.060  78.062  1.00 25.00           C
ATOM     51  CA  THR    51      49.667  31.951  77.655  1.00 25.00           C
ATOM     52  CA  GLY    52      52.533  33.173  75.386  1.00 25.00           C
ATOM     53  CA  GLU    53      51.567  30.249  73.141  1.00 25.00           C
ATOM     54  CA  TRP    54      50.609  28.164  70.129  1.00 25.00           C
ATOM     55  CA  VAL    55      47.858  28.300  67.527  1.00 25.00           C
ATOM     56  CA  LEU    56      45.464  28.866  64.641  1.00 25.00           C
ATOM     57  CA  LEU    57      43.494  30.201  61.702  1.00 25.00           C
ATOM     58  CA  VAL    58      40.397  32.392  62.081  1.00 25.00           C
ATOM     59  CA  SER    59      41.536  34.001  58.860  1.00 25.00           C
ATOM     60  CA  GLY    60      40.894  37.235  60.852  1.00 25.00           C
ATOM     61  CA  SER    61      37.487  37.356  59.194  1.00 25.00           C
ATOM     62  CA  SER    62      36.609  33.705  58.380  1.00 25.00           C
ATOM     63  CA  ALA    63      35.170  32.676  61.776  1.00 25.00           C
ATOM     64  CA  ARG    64      32.243  35.099  61.297  1.00 25.00           C
ATOM     65  CA  GLN    65      31.588  33.657  57.810  1.00 25.00           C
ATOM     66  CA  ALA    66      31.633  30.106  59.244  1.00 25.00           C
ATOM     67  CA  HIS    67      28.732  27.879  58.054  1.00 25.00           C
ATOM     68  CA  LYS    68      28.077  30.502  55.423  1.00 25.00           C
ATOM     69  CA  SER    69      24.556  30.529  56.934  1.00 25.00           C
ATOM     70  CA  GLU    70      24.821  33.926  58.551  1.00 25.00           C
ATOM     71  CA  THR    71      23.951  31.985  61.684  1.00 25.00           C
ATOM     72  CA  SER    72      25.029  30.138  64.850  1.00 25.00           C
ATOM     73  CA  PRO    73      26.685  32.365  67.497  1.00 25.00           C
ATOM     74  CA  VAL    74      30.147  33.799  66.703  1.00 25.00           C
ATOM     75  CA  ASP    75      30.873  30.362  65.232  1.00 25.00           C
ATOM     76  CA  LEU    76      34.039  28.314  64.615  1.00 25.00           C
ATOM     77  CA  CYS    77      35.968  31.015  66.587  1.00 25.00           C
ATOM     78  CA  VAL    78      35.608  28.322  69.272  1.00 25.00           C
ATOM     79  CA  ILE    79      37.949  30.633  71.221  1.00 25.00           C
ATOM     80  CA  GLY    80      41.027  28.410  71.448  1.00 25.00           C
ATOM     81  CA  ILE    81      43.681  26.090  70.021  1.00 25.00           C
ATOM     82  CA  VAL    82      46.696  23.839  69.723  1.00 25.00           C
ATOM     83  CA  ASP    83      47.089  20.100  69.658  1.00 25.00           C
ATOM     84  CA  GLU    84      50.557  20.704  71.221  1.00 25.00           C
ATOM     85  CA  VAL    85      51.626  23.151  68.572  1.00 25.00           C
ATOM     86  CA  VAL    86      52.949  20.638  66.048  1.00 25.00           C
ATOM     87  CA  SER    87      55.691  19.092  63.886  1.00 25.00           C
ATOM     88  CA  GLY    88      58.235  21.815  64.162  1.00 25.00           C
ATOM     89  CA  GLY    89      58.799  25.448  63.289  1.00 25.00           C
ATOM     90  CA  GLN    90      55.256  26.670  62.783  1.00 25.00           C
ATOM     91  CA  VAL    91      51.768  26.307  64.334  1.00 25.00           C
ATOM     92  CA  ILE    92      49.180  23.543  64.125  1.00 25.00           C
ATOM     93  CA  PHE    93      46.738  20.627  64.061  1.00 25.00           C
ATOM     94  CA  HIS    94      46.155  17.057  65.048  1.00 25.00           C
ATOM     95  CA  LYS    95      48.362  13.960  64.830  1.00 25.00           C
TER
END
