
#######################################################
#                                                     #
#                        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 T0306TS168_5
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS168_5.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      M       1          5.083
LGA    L       3      K       2           #
LGA    A       4      L       3           #
LGA    V       5      A       4           -
LGA    V       6      V       5           -
LGA    T       7      V       6           -
LGA    G       8      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
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    Q       9      D      22          4.438
LGA    I      10      K      23          2.174
LGA    V      11      L      24          2.026
LGA    C      12      L      25          1.722
LGA    T      13      M      26          3.785
LGA    V      14      V      27          3.920
LGA    R      15      -       -           -
LGA    H      16      -       -           -
LGA    H      17      -       -           -
LGA    G      18      -       -           -
LGA    L      19      -       -           -
LGA    A      20      -       -           -
LGA    H      21      -       -           -
LGA    D      22      E      28          4.404
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    K      23      Q      39           #
LGA    L      24      C      40           #
LGA    L      25      A      41           #
LGA    M      26      V      42           #
LGA    V      27      A      43           #
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      I      44           #
LGA    A      43      D      45          2.549
LGA    I      44      N      46          4.763
LGA    D      45      I      47           -
LGA    N      46      -       -           -
LGA    I      47      G      48          2.879
LGA    G      48      A      49           #
LGA    A      49      G      50          3.269
LGA    G      50      -       -           -
LGA    T      51      T      51          3.440
LGA    G      52      G      52          2.477
LGA    E      53      E      53          3.054
LGA    W      54      W      54          4.525
LGA    V      55      V      55          2.776
LGA    L      56      L      56          1.420
LGA    L      57      L      57          1.766
LGA    V      58      V      58          1.779
LGA    S      59      S      59          2.561
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    G      60      A      63          1.203
LGA    S      61      R      64          1.246
LGA    S      62      Q      65           #
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    A      63      T      71          4.667
LGA    R      64      S      72          3.059
LGA    Q      65      P      73          4.072
LGA    A      66      V      74          1.146
LGA    H      67      D      75          4.864
LGA    K      68      -       -           -
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    C      77      -       -           -
LGA    V      78      L      76          3.045
LGA    I      79      C      77           #
LGA    G      80      V      78           -
LGA    I      81      I      79           -
LGA    V      82      -       -           -
LGA    D      83      G      80           #
LGA    E      84      I      81          4.455
LGA    V      85      V      82          2.076
LGA    V      86      D      83          2.711
LGA    S      87      E      84          3.157
LGA    G      88      V      85           #
LGA    G      89      V      86           -
LGA    Q      90      S      87           -
LGA    V      91      G      88           -
LGA    I      92      G      89           -
LGA    F      93      Q      90           -
LGA    H      94      V      91           -
LGA    K      95      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     33    3.26    33.33     21.019     0.981

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.425402 * X  +   0.464954 * Y  +  -0.776435 * Z  +  37.862652
  Y_new =   0.655374 * X  +   0.749923 * Y  +   0.090004 * Z  +  27.934942
  Z_new =   0.624114 * X  +  -0.470568 * Y  +  -0.623737 * Z  +  62.604080 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.495261    0.646332  [ DEG:  -142.9679     37.0321 ]
  Theta =  -0.673997   -2.467596  [ DEG:   -38.6172   -141.3828 ]
  Phi   =   2.146537   -0.995056  [ DEG:   122.9875    -57.0125 ]
 
# 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: T0306TS168_5                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS168_5.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   33   3.26   33.33  21.019
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS168_5
PFRMAT TS
TARGET T0306
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      42.259  41.749  57.965  1.00 25.00           C
ATOM      2  CA  LYS     2      41.821  37.938  57.512  1.00 25.00           C
ATOM      3  CA  LEU     3      41.899  34.200  57.645  1.00 25.00           C
ATOM      4  CA  ALA     4      41.536  30.572  56.753  1.00 25.00           C
ATOM      5  CA  VAL     5      42.092  26.830  56.934  1.00 25.00           C
ATOM      6  CA  VAL     6      40.455  23.405  57.127  1.00 25.00           C
ATOM      7  CA  THR     7      37.079  22.058  55.968  1.00 25.00           C
ATOM      8  CA  GLY     8      35.659  18.665  56.870  1.00 25.00           C
ATOM      9  CA  GLN     9      33.833  20.690  59.523  1.00 25.00           C
ATOM     10  CA  ILE    10      33.939  19.966  63.220  1.00 25.00           C
ATOM     11  CA  VAL    11      34.049  22.374  66.141  1.00 25.00           C
ATOM     12  CA  CYS    12      36.804  23.316  68.543  1.00 25.00           C
ATOM     13  CA  THR    13      36.733  26.179  71.100  1.00 25.00           C
ATOM     14  CA  VAL    14      39.386  28.883  71.836  1.00 25.00           C
ATOM     15  CA  ARG    15      40.869  30.406  75.037  1.00 25.00           C
ATOM     16  CA  HIS    16      40.774  28.060  78.068  1.00 25.00           C
ATOM     17  CA  HIS    17      42.527  30.713  80.116  1.00 25.00           C
ATOM     18  CA  GLY    18      46.175  31.649  79.537  1.00 25.00           C
ATOM     19  CA  LEU    19      48.256  29.993  76.783  1.00 25.00           C
ATOM     20  CA  ALA    20      47.318  26.692  78.412  1.00 25.00           C
ATOM     21  CA  HIS    21      44.984  23.715  79.074  1.00 25.00           C
ATOM     22  CA  ASP    22      43.625  24.591  75.616  1.00 25.00           C
ATOM     23  CA  LYS    23      43.563  25.971  72.075  1.00 25.00           C
ATOM     24  CA  LEU    24      41.782  23.359  70.045  1.00 25.00           C
ATOM     25  CA  LEU    25      41.032  25.547  67.072  1.00 25.00           C
ATOM     26  CA  MET    26      37.997  27.302  65.590  1.00 25.00           C
ATOM     27  CA  VAL    27      37.100  29.741  62.810  1.00 25.00           C
ATOM     28  CA  GLU    28      37.636  28.524  59.298  1.00 25.00           C
ATOM     29  CA  MET    29      37.174  28.427  55.481  1.00 25.00           C
ATOM     30  CA  ILE    30      34.125  27.318  53.446  1.00 25.00           C
ATOM     31  CA  ASP    31      31.968  27.801  50.297  1.00 25.00           C
ATOM     32  CA  PRO    32      31.880  25.656  47.192  1.00 25.00           C
ATOM     33  CA  GLN    33      31.503  26.571  43.461  1.00 25.00           C
ATOM     34  CA  GLY    34      28.233  28.445  44.172  1.00 25.00           C
ATOM     35  CA  ASN    35      29.178  32.056  44.507  1.00 25.00           C
ATOM     36  CA  PRO    36      32.917  32.077  43.601  1.00 25.00           C
ATOM     37  CA  ASP    37      35.195  34.075  45.899  1.00 25.00           C
ATOM     38  CA  GLY    38      32.973  35.499  48.640  1.00 25.00           C
ATOM     39  CA  GLN    39      33.299  33.026  51.435  1.00 25.00           C
ATOM     40  CA  CYS    40      33.855  32.248  55.098  1.00 25.00           C
ATOM     41  CA  ALA    41      32.991  29.877  57.980  1.00 25.00           C
ATOM     42  CA  VAL    42      33.209  26.130  58.697  1.00 25.00           C
ATOM     43  CA  ALA    43      34.364  25.943  62.377  1.00 25.00           C
ATOM     44  CA  ILE    44      37.335  23.888  61.160  1.00 25.00           C
ATOM     45  CA  ASP    45      38.568  21.719  64.035  1.00 25.00           C
ATOM     46  CA  ASN    46      39.848  18.192  64.512  1.00 25.00           C
ATOM     47  CA  ILE    47      38.143  17.606  61.147  1.00 25.00           C
ATOM     48  CA  GLY    48      40.333  14.521  60.926  1.00 25.00           C
ATOM     49  CA  ALA    49      43.139  17.104  60.678  1.00 25.00           C
ATOM     50  CA  GLY    50      45.172  14.560  62.736  1.00 25.00           C
ATOM     51  CA  THR    51      44.015  14.191  66.378  1.00 25.00           C
ATOM     52  CA  GLY    52      46.754  16.739  67.125  1.00 25.00           C
ATOM     53  CA  GLU    53      44.670  19.364  65.247  1.00 25.00           C
ATOM     54  CA  TRP    54      43.509  22.596  63.610  1.00 25.00           C
ATOM     55  CA  VAL    55      41.982  25.615  61.855  1.00 25.00           C
ATOM     56  CA  LEU    56      42.183  29.377  61.617  1.00 25.00           C
ATOM     57  CA  LEU    57      41.165  32.787  62.840  1.00 25.00           C
ATOM     58  CA  VAL    58      38.079  34.016  61.018  1.00 25.00           C
ATOM     59  CA  SER    59      35.246  35.720  62.833  1.00 25.00           C
ATOM     60  CA  GLY    60      32.851  32.759  62.306  1.00 25.00           C
ATOM     61  CA  SER    61      29.649  33.099  60.217  1.00 25.00           C
ATOM     62  CA  SER    62      28.278  29.617  60.904  1.00 25.00           C
ATOM     63  CA  ALA    63      25.622  31.911  62.439  1.00 25.00           C
ATOM     64  CA  ARG    64      24.285  28.998  64.537  1.00 25.00           C
ATOM     65  CA  GLN    65      27.834  28.200  65.734  1.00 25.00           C
ATOM     66  CA  ALA    66      28.368  31.872  66.682  1.00 25.00           C
ATOM     67  CA  HIS    67      26.612  35.163  67.559  1.00 25.00           C
ATOM     68  CA  LYS    68      23.123  35.001  66.037  1.00 25.00           C
ATOM     69  CA  SER    69      22.006  37.160  68.927  1.00 25.00           C
ATOM     70  CA  GLU    70      23.320  36.494  72.488  1.00 25.00           C
ATOM     71  CA  THR    71      22.050  32.940  72.070  1.00 25.00           C
ATOM     72  CA  SER    72      22.969  29.371  71.113  1.00 25.00           C
ATOM     73  CA  PRO    73      23.503  25.878  69.574  1.00 25.00           C
ATOM     74  CA  VAL    74      27.007  24.455  69.103  1.00 25.00           C
ATOM     75  CA  ASP    75      29.159  27.249  70.483  1.00 25.00           C
ATOM     76  CA  LEU    76      31.989  26.583  68.053  1.00 25.00           C
ATOM     77  CA  CYS    77      33.378  29.503  66.071  1.00 25.00           C
ATOM     78  CA  VAL    78      35.598  30.579  68.938  1.00 25.00           C
ATOM     79  CA  ILE    79      37.892  32.761  66.813  1.00 25.00           C
ATOM     80  CA  GLY    80      41.374  33.777  67.863  1.00 25.00           C
ATOM     81  CA  ILE    81      42.721  30.287  66.942  1.00 25.00           C
ATOM     82  CA  VAL    82      46.006  29.905  65.090  1.00 25.00           C
ATOM     83  CA  ASP    83      46.092  26.173  66.000  1.00 25.00           C
ATOM     84  CA  GLU    84      47.105  25.878  62.303  1.00 25.00           C
ATOM     85  CA  VAL    85      46.739  25.025  58.647  1.00 25.00           C
ATOM     86  CA  VAL    86      50.227  26.467  57.988  1.00 25.00           C
ATOM     87  CA  SER    87      52.793  28.077  55.741  1.00 25.00           C
ATOM     88  CA  GLY    88      52.968  24.675  54.087  1.00 25.00           C
ATOM     89  CA  GLY    89      50.490  24.772  51.181  1.00 25.00           C
ATOM     90  CA  GLN    90      47.659  25.655  53.615  1.00 25.00           C
ATOM     91  CA  VAL    91      46.566  28.859  55.405  1.00 25.00           C
ATOM     92  CA  ILE    92      46.331  30.304  58.920  1.00 25.00           C
ATOM     93  CA  PHE    93      45.947  33.326  61.224  1.00 25.00           C
ATOM     94  CA  HIS    94      48.467  35.842  62.717  1.00 25.00           C
ATOM     95  CA  LYS    95      46.044  38.755  63.093  1.00 25.00           C
TER
END
