
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS168_1.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      -       -           -
LGA    L       3      -       -           -
LGA    A       4      -       -           -
LGA    V       5      -       -           -
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    I      10      -       -           -
LGA    V      11      -       -           -
LGA    C      12      -       -           -
LGA    T      13      M       1          3.778
LGA    V      14      K       2          1.633
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      L       3          2.179
LGA    L      25      A       4          2.547
LGA    M      26      -       -           -
LGA    V      27      V       5          1.039
LGA    E      28      V       6          1.614
LGA    M      29      T       7          3.360
LGA    I      30      G       8          3.425
LGA    D      31      Q       9          4.924
LGA    P      32      I      10           -
LGA    Q      33      V      11           -
LGA    G      34      C      12           -
LGA    N      35      T      13           -
LGA    P      36      V      14           -
LGA    D      37      R      15           -
LGA    G      38      H      16           -
LGA    Q      39      H      17           -
LGA    C      40      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    A      41      L      24           #
LGA    V      42      L      25          4.491
LGA    A      43      M      26          4.073
LGA    I      44      V      27          4.130
LGA    D      45      E      28           #
LGA    N      46      -       -           -
LGA    I      47      M      29          3.480
LGA    G      48      I      30          1.771
LGA    A      49      D      31           #
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    G      50      N      35          3.084
LGA    T      51      P      36          2.868
LGA    G      52      D      37          2.793
LGA    -       -      G      38           -
LGA    E      53      Q      39          1.425
LGA    W      54      C      40          3.163
LGA    V      55      A      41          2.546
LGA    L      56      V      42          1.626
LGA    L      57      A      43          1.382
LGA    -       -      I      44           -
LGA    V      58      D      45          1.695
LGA    S      59      N      46          2.999
LGA    G      60      I      47           #
LGA    S      61      G      48           -
LGA    S      62      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    -       -      W      54           -
LGA    -       -      V      55           -
LGA    -       -      L      56           -
LGA    -       -      L      57           -
LGA    -       -      V      58           -
LGA    A      63      S      59           #
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    R      64      H      67          1.751
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    Q      65      S      72          3.915
LGA    A      66      P      73          3.075
LGA    H      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    E      70      -       -           -
LGA    T      71      -       -           -
LGA    S      72      -       -           -
LGA    P      73      -       -           -
LGA    V      74      V      74          4.393
LGA    D      75      D      75          1.129
LGA    L      76      L      76          1.040
LGA    C      77      C      77          3.971
LGA    V      78      V      78          2.761
LGA    I      79      I      79          2.076
LGA    G      80      -       -           -
LGA    I      81      G      80          0.508
LGA    V      82      I      81          1.722
LGA    D      83      V      82          1.808
LGA    E      84      D      83          4.245
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    V      85      F      93           #
LGA    V      86      H      94          4.330
LGA    S      87      -       -           -
LGA    G      88      -       -           -
LGA    G      89      -       -           -
LGA    Q      90      -       -           -
LGA    V      91      -       -           -
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     38    2.94    21.05     23.697     1.249

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.183537 * X  +  -0.100571 * Y  +  -0.977855 * Z  +  39.982475
  Y_new =   0.076119 * X  +   0.993220 * Y  +  -0.087864 * Z  +  25.441788
  Z_new =   0.980061 * X  +  -0.058307 * Y  +   0.189948 * Z  +  65.990974 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.297834    2.843758  [ DEG:   -17.0646    162.9353 ]
  Theta =  -1.370770   -1.770823  [ DEG:   -78.5393   -101.4607 ]
  Phi   =   0.393145   -2.748448  [ DEG:    22.5255   -157.4745 ]
 
# 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_1                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS168_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   38   2.94   21.05  23.697
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS168_1
PFRMAT TS
TARGET T0306
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      39.334  22.026  81.518  1.00 25.00           C
ATOM      2  CA  LYS     2      40.617  22.620  77.932  1.00 25.00           C
ATOM      3  CA  LEU     3      42.112  23.735  74.660  1.00 25.00           C
ATOM      4  CA  ALA     4      38.735  23.587  72.912  1.00 25.00           C
ATOM      5  CA  VAL     5      36.881  21.863  70.072  1.00 25.00           C
ATOM      6  CA  VAL     6      35.490  20.178  67.017  1.00 25.00           C
ATOM      7  CA  THR     7      36.000  18.298  63.701  1.00 25.00           C
ATOM      8  CA  GLY     8      35.938  19.853  60.200  1.00 25.00           C
ATOM      9  CA  GLN     9      39.422  20.005  58.576  1.00 25.00           C
ATOM     10  CA  ILE    10      40.181  22.773  61.028  1.00 25.00           C
ATOM     11  CA  VAL    11      40.265  26.108  62.970  1.00 25.00           C
ATOM     12  CA  CYS    12      41.562  29.673  62.409  1.00 25.00           C
ATOM     13  CA  THR    13      40.394  33.190  61.842  1.00 25.00           C
ATOM     14  CA  VAL    14      42.381  34.992  64.599  1.00 25.00           C
ATOM     15  CA  ARG    15      42.655  38.662  63.642  1.00 25.00           C
ATOM     16  CA  HIS    16      43.091  39.816  60.044  1.00 25.00           C
ATOM     17  CA  HIS    17      43.075  41.030  56.499  1.00 25.00           C
ATOM     18  CA  GLY    18      46.302  42.577  55.265  1.00 25.00           C
ATOM     19  CA  LEU    19      48.255  39.361  55.987  1.00 25.00           C
ATOM     20  CA  ALA    20      50.598  40.916  58.575  1.00 25.00           C
ATOM     21  CA  HIS    21      51.348  37.317  59.757  1.00 25.00           C
ATOM     22  CA  ASP    22      48.548  34.982  58.642  1.00 25.00           C
ATOM     23  CA  LYS    23      45.749  33.764  60.915  1.00 25.00           C
ATOM     24  CA  LEU    24      46.464  30.916  63.300  1.00 25.00           C
ATOM     25  CA  LEU    25      46.963  28.116  65.847  1.00 25.00           C
ATOM     26  CA  MET    26      44.994  24.900  65.475  1.00 25.00           C
ATOM     27  CA  VAL    27      45.586  24.659  69.242  1.00 25.00           C
ATOM     28  CA  GLU    28      44.290  21.053  68.848  1.00 25.00           C
ATOM     29  CA  MET    29      41.272  19.307  70.456  1.00 25.00           C
ATOM     30  CA  ILE    30      39.346  16.019  70.305  1.00 25.00           C
ATOM     31  CA  ASP    31      37.106  13.291  71.823  1.00 25.00           C
ATOM     32  CA  PRO    32      39.397  10.327  71.162  1.00 25.00           C
ATOM     33  CA  GLN    33      39.406   9.748  74.930  1.00 25.00           C
ATOM     34  CA  GLY    34      36.108   7.974  75.415  1.00 25.00           C
ATOM     35  CA  ASN    35      33.739   6.201  73.091  1.00 25.00           C
ATOM     36  CA  PRO    36      36.555   6.250  70.554  1.00 25.00           C
ATOM     37  CA  ASP    37      34.609   7.053  67.424  1.00 25.00           C
ATOM     38  CA  GLY    38      34.806  10.022  64.991  1.00 25.00           C
ATOM     39  CA  GLN    39      38.309  11.462  64.373  1.00 25.00           C
ATOM     40  CA  CYS    40      39.674  14.972  64.911  1.00 25.00           C
ATOM     41  CA  ALA    41      41.192  18.449  65.454  1.00 25.00           C
ATOM     42  CA  VAL    42      40.344  22.122  66.010  1.00 25.00           C
ATOM     43  CA  ALA    43      40.646  24.967  68.473  1.00 25.00           C
ATOM     44  CA  ILE    44      42.123  28.417  67.594  1.00 25.00           C
ATOM     45  CA  ASP    45      40.150  31.655  67.768  1.00 25.00           C
ATOM     46  CA  ASN    46      42.381  33.929  69.855  1.00 25.00           C
ATOM     47  CA  ILE    47      45.422  32.423  68.027  1.00 25.00           C
ATOM     48  CA  GLY    48      47.572  32.306  71.171  1.00 25.00           C
ATOM     49  CA  ALA    49      48.229  28.618  71.725  1.00 25.00           C
ATOM     50  CA  GLY    50      51.001  29.325  74.211  1.00 25.00           C
ATOM     51  CA  THR    51      49.695  32.147  76.380  1.00 25.00           C
ATOM     52  CA  GLY    52      46.118  33.075  77.181  1.00 25.00           C
ATOM     53  CA  GLU    53      42.952  33.032  75.056  1.00 25.00           C
ATOM     54  CA  TRP    54      43.031  29.838  73.042  1.00 25.00           C
ATOM     55  CA  VAL    55      39.550  28.672  71.875  1.00 25.00           C
ATOM     56  CA  LEU    56      36.470  27.180  70.245  1.00 25.00           C
ATOM     57  CA  LEU    57      36.052  26.289  66.532  1.00 25.00           C
ATOM     58  CA  VAL    58      35.590  23.940  63.523  1.00 25.00           C
ATOM     59  CA  SER    59      34.212  24.981  60.171  1.00 25.00           C
ATOM     60  CA  GLY    60      31.606  22.449  58.953  1.00 25.00           C
ATOM     61  CA  SER    61      28.680  22.688  61.318  1.00 25.00           C
ATOM     62  CA  SER    62      29.967  24.783  64.199  1.00 25.00           C
ATOM     63  CA  ALA    63      31.688  28.128  63.482  1.00 25.00           C
ATOM     64  CA  ARG    64      30.122  28.213  59.988  1.00 25.00           C
ATOM     65  CA  GLN    65      26.673  27.494  61.489  1.00 25.00           C
ATOM     66  CA  ALA    66      27.165  30.314  64.033  1.00 25.00           C
ATOM     67  CA  HIS    67      25.668  27.789  66.478  1.00 25.00           C
ATOM     68  CA  LYS    68      22.304  27.180  64.736  1.00 25.00           C
ATOM     69  CA  SER    69      19.708  26.730  67.516  1.00 25.00           C
ATOM     70  CA  GLU    70      21.102  29.430  69.812  1.00 25.00           C
ATOM     71  CA  THR    71      23.403  28.098  72.555  1.00 25.00           C
ATOM     72  CA  SER    72      25.379  31.026  74.112  1.00 25.00           C
ATOM     73  CA  PRO    73      28.957  32.184  73.447  1.00 25.00           C
ATOM     74  CA  VAL    74      28.970  33.154  69.750  1.00 25.00           C
ATOM     75  CA  ASP    75      31.560  34.442  67.279  1.00 25.00           C
ATOM     76  CA  LEU    76      33.646  31.267  67.078  1.00 25.00           C
ATOM     77  CA  CYS    77      36.195  33.023  64.918  1.00 25.00           C
ATOM     78  CA  VAL    78      36.595  29.747  63.118  1.00 25.00           C
ATOM     79  CA  ILE    79      37.568  28.668  59.549  1.00 25.00           C
ATOM     80  CA  GLY    80      38.742  26.047  57.122  1.00 25.00           C
ATOM     81  CA  ILE    81      42.137  27.752  57.177  1.00 25.00           C
ATOM     82  CA  VAL    82      44.116  25.831  59.818  1.00 25.00           C
ATOM     83  CA  ASP    83      47.101  25.879  57.571  1.00 25.00           C
ATOM     84  CA  GLU    84      48.740  23.718  60.205  1.00 25.00           C
ATOM     85  CA  VAL    85      49.853  24.508  63.730  1.00 25.00           C
ATOM     86  CA  VAL    86      52.614  21.931  63.070  1.00 25.00           C
ATOM     87  CA  SER    87      55.763  20.859  64.892  1.00 25.00           C
ATOM     88  CA  GLY    88      55.820  19.425  68.414  1.00 25.00           C
ATOM     89  CA  GLY    89      54.076  16.120  68.105  1.00 25.00           C
ATOM     90  CA  GLN    90      50.823  17.998  68.074  1.00 25.00           C
ATOM     91  CA  VAL    91      48.719  19.893  65.539  1.00 25.00           C
ATOM     92  CA  ILE    92      45.559  20.125  63.438  1.00 25.00           C
ATOM     93  CA  PHE    93      44.583  20.610  59.783  1.00 25.00           C
ATOM     94  CA  HIS    94      45.069  20.486  56.070  1.00 25.00           C
ATOM     95  CA  LYS    95      46.725  19.443  52.846  1.00 25.00           C
TER
END
