
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS393_1.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    K       2      L       3          4.950
LGA    L       3      A       4          3.691
LGA    A       4      V       5          1.000
LGA    V       5      V       6          2.373
LGA    V       6      T       7          2.650
LGA    -       -      G       8           -
LGA    T       7      Q       9          3.465
LGA    G       8      I      10          2.173
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    Q       9      K      23           #
LGA    I      10      L      24          1.549
LGA    V      11      -       -           -
LGA    C      12      -       -           -
LGA    T      13      -       -           -
LGA    V      14      -       -           -
LGA    R      15      -       -           -
LGA    H      16      -       -           -
LGA    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    M      26      -       -           -
LGA    V      27      -       -           -
LGA    E      28      L      25           #
LGA    -       -      M      26           -
LGA    M      29      V      27          1.364
LGA    I      30      E      28          4.165
LGA    D      31      M      29           -
LGA    P      32      I      30           -
LGA    Q      33      D      31           -
LGA    G      34      P      32           -
LGA    N      35      Q      33           -
LGA    P      36      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    D      37      D      37          4.868
LGA    G      38      G      38          4.107
LGA    Q      39      Q      39          2.590
LGA    C      40      C      40          4.713
LGA    A      41      A      41          4.684
LGA    V      42      V      42          2.673
LGA    -       -      A      43           -
LGA    A      43      I      44          4.105
LGA    I      44      D      45           #
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    D      45      A      49          4.678
LGA    N      46      -       -           -
LGA    I      47      -       -           -
LGA    G      48      -       -           -
LGA    A      49      -       -           -
LGA    G      50      -       -           -
LGA    T      51      -       -           -
LGA    G      52      -       -           -
LGA    E      53      G      50          4.498
LGA    W      54      T      51          3.833
LGA    V      55      G      52          4.852
LGA    L      56      E      53          2.586
LGA    L      57      W      54          2.417
LGA    V      58      V      55          3.275
LGA    S      59      L      56          2.407
LGA    G      60      L      57          1.043
LGA    S      61      V      58          2.880
LGA    S      62      S      59          4.610
LGA    A      63      G      60           -
LGA    R      64      S      61           #
LGA    Q      65      S      62          4.208
LGA    A      66      A      63          2.673
LGA    H      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      R      64          4.624
LGA    E      70      Q      65          4.468
LGA    T      71      -       -           -
LGA    S      72      -       -           -
LGA    P      73      A      66           #
LGA    V      74      H      67          3.458
LGA    D      75      K      68          4.946
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    L      76      C      77          4.974
LGA    C      77      V      78          0.895
LGA    V      78      I      79          2.185
LGA    I      79      G      80          1.767
LGA    G      80      I      81          2.127
LGA    I      81      V      82          4.644
LGA    V      82      D      83           #
LGA    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    I      92      -       -           -
LGA    F      93      -       -           -
LGA    H      94      -       -           -
LGA    K      95      E      84          2.396
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
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     41    3.54    24.39     22.558     1.127

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.142111 * X  +   0.891628 * Y  +  -0.429889 * Z  +  40.964592
  Y_new =  -0.703870 * X  +   0.396381 * Y  +   0.589448 * Z  +  24.339949
  Z_new =   0.695968 * X  +   0.218819 * Y  +   0.683920 * Z  +  64.351791 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.309656   -2.831937  [ DEG:    17.7420   -162.2580 ]
  Theta =  -0.769767   -2.371825  [ DEG:   -44.1044   -135.8956 ]
  Phi   =  -1.371575    1.770017  [ DEG:   -78.5855    101.4145 ]
 
# 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_1                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS393_1.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   41   3.54   24.39  22.558
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS393_1
PFRMAT TS
TARGET T0306
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      51.865  34.243  65.282  1.00 25.00           C
ATOM      2  CA  LYS     2      50.831  30.785  66.463  1.00 25.00           C
ATOM      3  CA  LEU     3      48.767  27.747  67.175  1.00 25.00           C
ATOM      4  CA  ALA     4      46.848  25.052  68.947  1.00 25.00           C
ATOM      5  CA  VAL     5      45.231  21.732  69.786  1.00 25.00           C
ATOM      6  CA  VAL     6      41.989  19.829  70.359  1.00 25.00           C
ATOM      7  CA  THR     7      38.815  20.803  72.237  1.00 25.00           C
ATOM      8  CA  GLY     8      35.313  19.540  72.932  1.00 25.00           C
ATOM      9  CA  GLN     9      34.601  21.143  69.557  1.00 25.00           C
ATOM     10  CA  ILE    10      32.917  22.114  66.328  1.00 25.00           C
ATOM     11  CA  VAL    11      34.090  21.627  62.761  1.00 25.00           C
ATOM     12  CA  CYS    12      36.248  20.537  59.862  1.00 25.00           C
ATOM     13  CA  THR    13      37.113  22.607  56.746  1.00 25.00           C
ATOM     14  CA  VAL    14      40.534  23.197  55.061  1.00 25.00           C
ATOM     15  CA  ARG    15      40.653  23.983  51.301  1.00 25.00           C
ATOM     16  CA  HIS    16      39.719  21.018  49.058  1.00 25.00           C
ATOM     17  CA  HIS    17      41.896  20.332  46.041  1.00 25.00           C
ATOM     18  CA  GLY    18      45.701  20.485  45.931  1.00 25.00           C
ATOM     19  CA  LEU    19      46.053  18.828  49.363  1.00 25.00           C
ATOM     20  CA  ALA    20      44.886  15.692  47.564  1.00 25.00           C
ATOM     21  CA  HIS    21      41.394  14.666  48.790  1.00 25.00           C
ATOM     22  CA  ASP    22      42.064  15.564  52.440  1.00 25.00           C
ATOM     23  CA  LYS    23      42.292  18.414  54.945  1.00 25.00           C
ATOM     24  CA  LEU    24      40.072  17.422  57.808  1.00 25.00           C
ATOM     25  CA  LEU    25      41.218  20.094  60.203  1.00 25.00           C
ATOM     26  CA  MET    26      40.143  23.512  61.487  1.00 25.00           C
ATOM     27  CA  VAL    27      41.314  26.240  63.867  1.00 25.00           C
ATOM     28  CA  GLU    28      41.975  25.354  67.456  1.00 25.00           C
ATOM     29  CA  MET    29      42.471  25.979  71.218  1.00 25.00           C
ATOM     30  CA  ILE    30      40.027  27.013  73.981  1.00 25.00           C
ATOM     31  CA  ASP    31      39.809  26.365  77.767  1.00 25.00           C
ATOM     32  CA  PRO    32      40.986  27.973  80.975  1.00 25.00           C
ATOM     33  CA  GLN    33      37.824  30.089  81.628  1.00 25.00           C
ATOM     34  CA  GLY    34      37.930  33.896  81.177  1.00 25.00           C
ATOM     35  CA  ASN    35      40.780  35.415  83.078  1.00 25.00           C
ATOM     36  CA  PRO    36      44.373  34.045  82.988  1.00 25.00           C
ATOM     37  CA  ASP    37      46.345  33.543  79.777  1.00 25.00           C
ATOM     38  CA  GLY    38      44.581  35.134  76.804  1.00 25.00           C
ATOM     39  CA  GLN    39      42.976  33.375  73.912  1.00 25.00           C
ATOM     40  CA  CYS    40      41.886  31.020  71.156  1.00 25.00           C
ATOM     41  CA  ALA    41      39.047  29.364  69.188  1.00 25.00           C
ATOM     42  CA  VAL    42      37.215  26.010  69.183  1.00 25.00           C
ATOM     43  CA  ALA    43      37.165  24.775  65.525  1.00 25.00           C
ATOM     44  CA  ILE    44      38.757  21.544  66.776  1.00 25.00           C
ATOM     45  CA  ASP    45      37.771  18.780  64.352  1.00 25.00           C
ATOM     46  CA  ASN    46      36.928  15.096  64.522  1.00 25.00           C
ATOM     47  CA  ILE    47      36.042  15.984  68.128  1.00 25.00           C
ATOM     48  CA  GLY    48      36.210  12.251  68.760  1.00 25.00           C
ATOM     49  CA  ALA    49      39.965  12.673  68.189  1.00 25.00           C
ATOM     50  CA  GLY    50      40.064   9.423  66.123  1.00 25.00           C
ATOM     51  CA  THR    51      37.654   9.817  63.161  1.00 25.00           C
ATOM     52  CA  GLY    52      40.532  10.079  60.672  1.00 25.00           C
ATOM     53  CA  GLU    53      41.326  13.247  62.697  1.00 25.00           C
ATOM     54  CA  TRP    54      42.343  16.677  63.990  1.00 25.00           C
ATOM     55  CA  VAL    55      43.276  20.205  65.089  1.00 25.00           C
ATOM     56  CA  LEU    56      45.517  23.170  64.424  1.00 25.00           C
ATOM     57  CA  LEU    57      46.229  26.380  62.594  1.00 25.00           C
ATOM     58  CA  VAL    58      44.830  29.355  64.479  1.00 25.00           C
ATOM     59  CA  SER    59      43.051  32.251  62.845  1.00 25.00           C
ATOM     60  CA  GLY    60      39.645  31.166  64.261  1.00 25.00           C
ATOM     61  CA  SER    61      37.187  33.816  65.553  1.00 25.00           C
ATOM     62  CA  SER    62      34.570  31.412  66.908  1.00 25.00           C
ATOM     63  CA  ALA    63      33.110  29.068  64.254  1.00 25.00           C
ATOM     64  CA  ARG    64      30.080  31.374  63.848  1.00 25.00           C
ATOM     65  CA  GLN    65      32.402  34.395  63.453  1.00 25.00           C
ATOM     66  CA  ALA    66      34.435  32.516  60.805  1.00 25.00           C
ATOM     67  CA  HIS    67      34.259  35.744  58.748  1.00 25.00           C
ATOM     68  CA  LYS    68      32.813  38.691  60.683  1.00 25.00           C
ATOM     69  CA  SER    69      29.107  38.069  61.053  1.00 25.00           C
ATOM     70  CA  GLU    70      29.070  38.755  57.262  1.00 25.00           C
ATOM     71  CA  THR    71      29.003  35.601  55.148  1.00 25.00           C
ATOM     72  CA  SER    72      27.969  32.812  57.524  1.00 25.00           C
ATOM     73  CA  PRO    73      26.310  29.832  59.320  1.00 25.00           C
ATOM     74  CA  VAL    74      28.384  26.673  59.807  1.00 25.00           C
ATOM     75  CA  ASP    75      31.524  27.050  57.724  1.00 25.00           C
ATOM     76  CA  LEU    76      34.410  25.907  59.897  1.00 25.00           C
ATOM     77  CA  CYS    77      37.367  27.860  61.248  1.00 25.00           C
ATOM     78  CA  VAL    78      39.076  27.076  57.967  1.00 25.00           C
ATOM     79  CA  ILE    79      42.618  27.889  59.124  1.00 25.00           C
ATOM     80  CA  GLY    80      45.725  26.486  57.497  1.00 25.00           C
ATOM     81  CA  ILE    81      45.304  22.807  58.559  1.00 25.00           C
ATOM     82  CA  VAL    82      48.057  21.010  60.446  1.00 25.00           C
ATOM     83  CA  ASP    83      45.905  17.828  60.418  1.00 25.00           C
ATOM     84  CA  GLU    84      47.341  17.176  63.924  1.00 25.00           C
ATOM     85  CA  VAL    85      47.577  17.369  67.683  1.00 25.00           C
ATOM     86  CA  VAL    86      51.331  16.618  67.522  1.00 25.00           C
ATOM     87  CA  SER    87      54.939  15.897  68.350  1.00 25.00           C
ATOM     88  CA  GLY    88      53.787  14.015  71.428  1.00 25.00           C
ATOM     89  CA  GLY    89      51.996  16.241  73.963  1.00 25.00           C
ATOM     90  CA  GLN    90      50.918  19.902  73.573  1.00 25.00           C
ATOM     91  CA  VAL    91      50.273  20.953  69.947  1.00 25.00           C
ATOM     92  CA  ILE    92      50.016  21.857  66.258  1.00 25.00           C
ATOM     93  CA  PHE    93      51.046  24.319  63.525  1.00 25.00           C
ATOM     94  CA  HIS    94      51.799  27.922  62.358  1.00 25.00           C
ATOM     95  CA  LYS    95      53.385  28.114  58.950  1.00 25.00           C
TER
END
