
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0335TS168_3
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS168_3.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    S       3      S       3           #
LGA    N       4      N       4          1.434
LGA    A       5      A       5          1.692
LGA    K       6      K       6          1.740
LGA    I       7      I       7          1.211
LGA    A       8      A       8          1.005
LGA    R       9      R       9          1.929
LGA    I      10      I      10          1.907
LGA    N      11      N      11          1.191
LGA    E      12      E      12          1.609
LGA    L      13      L      13          2.934
LGA    A      14      A      14          2.230
LGA    A      15      A      15          1.221
LGA    K      16      K      16          2.641
LGA    A      17      A      17          3.633
LGA    K      18      K      18          1.906
LGA    A      19      A      19          2.119
LGA    G      20      G      20          1.719
LGA    V      21      V      21          2.627
LGA    I      22      I      22          1.609
LGA    T      23      T      23          1.771
LGA    E      24      E      24          1.070
LGA    E      25      E      25          0.362
LGA    E      26      E      26          0.861
LGA    K      27      K      27          1.043
LGA    A      28      A      28          0.596
LGA    E      29      E      29          0.946
LGA    Q      30      Q      30          1.536
LGA    Q      31      Q      31          1.130
LGA    K      32      K      32          1.516
LGA    L      33      L      33          1.498
LGA    R      34      R      34          1.082
LGA    Q      35      Q      35          0.837
LGA    E      36      E      36          1.966
LGA    Y      37      Y      37          1.920
LGA    L      38      L      38          0.921
LGA    K      39      K      39          2.444
LGA    G      40      G      40          3.303
LGA    F      41      F      41          0.919
LGA    R      42      -       -           -
LGA    S      43      -       -           -
LGA    S      44      -       -           -
LGA    M      45      R      42          2.296
LGA    K      46      -       -           -
LGA    N      47      -       -           -
LGA    T      48      -       -           -
LGA    L      49      -       -           -
LGA    K      50      -       -           -
LGA    S      51      -       -           -
LGA    V      52      -       -           -
LGA    K      53      -       -           -
LGA    I      54      -       -           -
LGA    I      55      -       -           -
LGA    D      56      -       -           -
LGA    P      57      -       -           -
LGA    E      58      -       -           -
LGA    G      59      -       -           -
LGA    N      60      -       -           -
LGA    D      61      -       -           -
LGA    V      62      -       -           -
LGA    T      63      -       -           -
LGA    P      64      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -
LGA    K      75      -       -           -
LGA    L      76      -       -           -
LGA    H      77      -       -           -
LGA    L      78      -       -           -
LGA    E      79      -       -           -
LGA    H      80      -       -           -
LGA    H      81      -       -           -
LGA    H      82      -       -           -
LGA    H      83      -       -           -
LGA    H      84      -       -           -
LGA    H      85      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   42    5.0     39    1.80    97.44     84.076     2.051

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.294344 * X  +   0.282190 * Y  +   0.913088 * Z  +   4.962316
  Y_new =   0.951187 * X  +  -0.179234 * Y  +  -0.251233 * Z  +   1.698758
  Z_new =   0.092761 * X  +   0.942467 * Y  +  -0.321172 * Z  +  -6.741787 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.899233   -1.242360  [ DEG:   108.8180    -71.1820 ]
  Theta =  -0.092895   -3.048698  [ DEG:    -5.3225   -174.6775 ]
  Phi   =   1.270694   -1.870899  [ DEG:    72.8054   -107.1946 ]
 
# 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: T0335TS168_3                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_3.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   42   5.0   39   1.80   97.44  84.076
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_3
PFRMAT TS
TARGET T0335
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -7.481 -17.534 -14.231  1.00 25.00           C
ATOM      2  CA  ILE     2      -6.107 -15.244 -11.564  1.00 25.00           C
ATOM      3  CA  SER     3      -3.220 -12.896 -11.127  1.00 25.00           C
ATOM      4  CA  ASN     4      -0.976  -9.964 -10.042  1.00 25.00           C
ATOM      5  CA  ALA     5       0.404 -10.452  -6.504  1.00 25.00           C
ATOM      6  CA  LYS     6       1.665  -6.837  -6.471  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.771  -5.601  -7.622  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.459  -7.641  -4.856  1.00 25.00           C
ATOM      9  CA  ARG     9      -1.055  -6.164  -2.265  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.823  -2.632  -3.532  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.580  -3.332  -3.283  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.128  -4.616   0.297  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.147  -1.467   1.203  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.907   0.728  -0.292  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.548  -1.180   1.721  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.491  -0.708   4.917  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.183   3.040   4.194  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.967   3.271   3.649  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.581   1.446   6.959  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.294   0.505  10.633  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.851   2.123  10.597  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.980   5.308   9.970  1.00 25.00           C
ATOM     23  CA  THR    23      -2.222   5.093  12.555  1.00 25.00           C
ATOM     24  CA  GLU    24       1.058   6.445  11.110  1.00 25.00           C
ATOM     25  CA  GLU    25       2.982   3.166  10.649  1.00 25.00           C
ATOM     26  CA  GLU    26       0.151   1.783   8.471  1.00 25.00           C
ATOM     27  CA  LYS    27       0.187   4.974   6.354  1.00 25.00           C
ATOM     28  CA  ALA    28       3.983   4.681   5.931  1.00 25.00           C
ATOM     29  CA  GLU    29       3.605   1.024   4.861  1.00 25.00           C
ATOM     30  CA  GLN    30       0.918   2.019   2.320  1.00 25.00           C
ATOM     31  CA  GLN    31       3.205   4.763   0.939  1.00 25.00           C
ATOM     32  CA  LYS    32       6.075   2.247   0.624  1.00 25.00           C
ATOM     33  CA  LEU    33       3.768  -0.191  -1.221  1.00 25.00           C
ATOM     34  CA  ARG    34       2.676   2.604  -3.600  1.00 25.00           C
ATOM     35  CA  GLN    35       6.339   3.504  -4.263  1.00 25.00           C
ATOM     36  CA  GLU    36       7.135  -0.172  -4.988  1.00 25.00           C
ATOM     37  CA  TYR    37       4.173  -0.362  -7.408  1.00 25.00           C
ATOM     38  CA  LEU    38       5.382   2.811  -9.177  1.00 25.00           C
ATOM     39  CA  LYS    39       8.902   1.332  -9.479  1.00 25.00           C
ATOM     40  CA  GLY    40       7.446  -1.896 -10.938  1.00 25.00           C
ATOM     41  CA  PHE    41       5.409   0.138 -13.466  1.00 25.00           C
ATOM     42  CA  ARG    42       8.549   2.091 -14.463  1.00 25.00           C
ATOM     43  CA  SER    43      10.473  -1.188 -14.924  1.00 25.00           C
ATOM     44  CA  SER    44       7.642  -2.571 -17.101  1.00 25.00           C
ATOM     45  CA  MET    45       7.678   0.621 -19.218  1.00 25.00           C
ATOM     46  CA  LYS    46      11.473   0.328 -19.641  1.00 25.00           C
ATOM     47  CA  ASN    47      11.096  -3.329 -20.711  1.00 25.00           C
ATOM     48  CA  THR    48       8.408  -2.334 -23.252  1.00 25.00           C
ATOM     49  CA  LEU    49      10.696   0.410 -24.633  1.00 25.00           C
ATOM     50  CA  LYS    50       7.472   2.423 -24.236  1.00 25.00           C
ATOM     51  CA  SER    51       4.096   1.552 -22.575  1.00 25.00           C
ATOM     52  CA  VAL    52       1.473  -0.841 -21.189  1.00 25.00           C
ATOM     53  CA  LYS    53      -1.994  -0.566 -19.643  1.00 25.00           C
ATOM     54  CA  ILE    54      -1.765   1.582 -16.537  1.00 25.00           C
ATOM     55  CA  ILE    55      -2.546   4.917 -14.850  1.00 25.00           C
ATOM     56  CA  ASP    56      -3.737   8.437 -15.591  1.00 25.00           C
ATOM     57  CA  PRO    57      -3.569   9.743 -19.178  1.00 25.00           C
ATOM     58  CA  GLU    58      -1.495  12.246 -21.245  1.00 25.00           C
ATOM     59  CA  GLY    59      -0.506  15.184 -18.981  1.00 25.00           C
ATOM     60  CA  ASN    60      -1.542  14.144 -15.461  1.00 25.00           C
ATOM     61  CA  ASP    61       0.124  11.386 -13.366  1.00 25.00           C
ATOM     62  CA  VAL    62       1.456   7.973 -14.389  1.00 25.00           C
ATOM     63  CA  THR    63       4.437   9.392 -16.294  1.00 25.00           C
ATOM     64  CA  PRO    64       7.873  10.952 -16.183  1.00 25.00           C
ATOM     65  CA  GLU    65      10.226  13.733 -15.002  1.00 25.00           C
ATOM     66  CA  LYS    66      10.096  12.360 -11.429  1.00 25.00           C
ATOM     67  CA  LEU    67      10.897   8.846 -12.725  1.00 25.00           C
ATOM     68  CA  LYS    68      13.858  10.229 -14.721  1.00 25.00           C
ATOM     69  CA  ARG    69      15.137  12.052 -11.606  1.00 25.00           C
ATOM     70  CA  GLU    70      14.841   8.826  -9.565  1.00 25.00           C
ATOM     71  CA  GLN    71      16.773   6.913 -12.263  1.00 25.00           C
ATOM     72  CA  ARG    72      19.507   9.594 -12.241  1.00 25.00           C
ATOM     73  CA  ASN    73      19.735   9.366  -8.425  1.00 25.00           C
ATOM     74  CA  ASN    74      20.030   5.554  -8.646  1.00 25.00           C
ATOM     75  CA  LYS    75      23.587   4.766  -9.586  1.00 25.00           C
ATOM     76  CA  LEU    76      24.113   4.862  -5.835  1.00 25.00           C
ATOM     77  CA  HIS    77      21.708   3.447  -3.299  1.00 25.00           C
ATOM     78  CA  LEU    78      24.554   1.160  -2.097  1.00 25.00           C
ATOM     79  CA  GLU    79      24.490  -2.675  -1.953  1.00 25.00           C
ATOM     80  CA  HIS    80      20.784  -3.344  -2.488  1.00 25.00           C
ATOM     81  CA  HIS    81      18.470  -1.044  -0.477  1.00 25.00           C
ATOM     82  CA  HIS    82      18.376  -2.488   3.049  1.00 25.00           C
ATOM     83  CA  HIS    83      15.489  -4.388   4.570  1.00 25.00           C
ATOM     84  CA  HIS    84      15.354  -8.238   4.663  1.00 25.00           C
ATOM     85  CA  HIS    85      14.208  -8.014   8.323  1.00 25.00           C
TER
END
