
#######################################################
#                                                     #
#                        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   68 (   68),  selected   68 , name T0348TS168_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_1.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D       2           -
LGA    D       2      A       3           -
LGA    A       3      K       4           -
LGA    K       4      F       5           -
LGA    F       5      L       6           -
LGA    L       6      E       7           -
LGA    E       7      -       -           -
LGA    I       8      -       -           -
LGA    L       9      -       -           -
LGA    V      10      -       -           -
LGA    C      11      -       -           -
LGA    P      12      I       8           #
LGA    L      13      L       9          0.763
LGA    C      14      V      10          0.478
LGA    K      15      C      11          3.321
LGA    G      16      P      12          1.806
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    P      17      K      15          3.680
LGA    L      18      G      16          2.843
LGA    V      19      P      17          0.836
LGA    F      20      L      18          1.704
LGA    D      21      V      19          2.057
LGA    K      22      F      20          3.488
LGA    S      23      -       -           -
LGA    K      24      D      21          2.691
LGA    D      25      K      22           #
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    E      26      D      25          1.918
LGA    L      27      E      26          3.337
LGA    I      28      L      27           #
LGA    -       -      I      28           -
LGA    -       -      C      29           -
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    C      29      A      35          2.646
LGA    K      30      F      36          3.026
LGA    G      31      P      37          1.916
LGA    D      32      I      38          2.168
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    R      33      M      44          2.309
LGA    L      34      M      45          3.436
LGA    A      35      L      46           #
LGA    F      36      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    P      37      R      51          5.173
LGA    I      38      E      52          0.755
LGA    K      39      L      53          4.836
LGA    D      40      A      54           -
LGA    G      41      P      55           -
LGA    I      42      E      56           -
LGA    P      43      E      57           -
LGA    M      44      E      58           -
LGA    M      45      V      59           -
LGA    L      46      K      60           -
LGA    E      47      L      61           -
LGA    S      48      E      62           -
LGA    E      49      -       -           -
LGA    A      50      -       -           -
LGA    R      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    A      54      -       -           -
LGA    P      55      -       -           -
LGA    E      56      -       -           -
LGA    E      57      -       -           -
LGA    E      58      -       -           -
LGA    V      59      -       -           -
LGA    K      60      -       -           -
LGA    L      61      -       -           -
LGA    E      62      -       -           -
LGA    H      63      -       -           -
LGA    H      64      -       -           -
LGA    H      65      -       -           -
LGA    H      66      -       -           -
LGA    H      67      -       -           -
LGA    H      68      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   68   61    5.0     22    2.79     4.55     24.282     0.761

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.497829 * X  +  -0.460738 * Y  +   0.734770 * Z  +  10.555997
  Y_new =   0.832039 * X  +  -0.492765 * Y  +   0.254743 * Z  +  17.430660
  Z_new =   0.244699 * X  +   0.738176 * Y  +   0.628664 * Z  +  62.972126 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.865348   -2.276245  [ DEG:    49.5808   -130.4192 ]
  Theta =  -0.247210   -2.894383  [ DEG:   -14.1641   -165.8359 ]
  Phi   =   2.109982   -1.031610  [ DEG:   120.8931    -59.1069 ]
 
# 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: T0348TS168_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   68   61   5.0   22   2.79    4.55  24.282
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_1
PFRMAT TS
TARGET T0348
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      17.363  13.923  55.677  1.00 25.00           C
ATOM      2  CA  ASP     2      19.066  16.789  53.736  1.00 25.00           C
ATOM      3  CA  ALA     3      19.505  18.317  57.197  1.00 25.00           C
ATOM      4  CA  LYS     4      20.187  22.085  57.120  1.00 25.00           C
ATOM      5  CA  PHE     5      16.635  22.725  55.839  1.00 25.00           C
ATOM      6  CA  LEU     6      15.204  20.542  58.642  1.00 25.00           C
ATOM      7  CA  GLU     7      17.271  22.467  61.229  1.00 25.00           C
ATOM      8  CA  ILE     8      16.000  25.789  59.808  1.00 25.00           C
ATOM      9  CA  LEU     9      12.392  24.517  59.996  1.00 25.00           C
ATOM     10  CA  VAL    10      11.622  26.863  57.069  1.00 25.00           C
ATOM     11  CA  CYS    11       9.706  29.677  55.383  1.00 25.00           C
ATOM     12  CA  PRO    12       9.793  32.844  53.214  1.00 25.00           C
ATOM     13  CA  LEU    13       9.505  34.518  56.633  1.00 25.00           C
ATOM     14  CA  CYS    14       8.375  33.375  60.078  1.00 25.00           C
ATOM     15  CA  LYS    15       5.731  31.488  58.191  1.00 25.00           C
ATOM     16  CA  GLY    16       4.289  30.879  61.618  1.00 25.00           C
ATOM     17  CA  PRO    17       7.498  28.909  62.175  1.00 25.00           C
ATOM     18  CA  LEU    18      10.999  28.009  63.361  1.00 25.00           C
ATOM     19  CA  VAL    19      12.543  31.144  61.986  1.00 25.00           C
ATOM     20  CA  PHE    20      13.966  31.140  58.413  1.00 25.00           C
ATOM     21  CA  ASP    21      16.790  30.124  56.033  1.00 25.00           C
ATOM     22  CA  LYS    22      15.198  32.195  53.207  1.00 25.00           C
ATOM     23  CA  SER    23      15.034  31.226  49.506  1.00 25.00           C
ATOM     24  CA  LYS    24      17.592  28.437  50.098  1.00 25.00           C
ATOM     25  CA  ASP    25      14.806  26.498  51.750  1.00 25.00           C
ATOM     26  CA  GLU    26      13.685  25.681  48.149  1.00 25.00           C
ATOM     27  CA  LEU    27      12.012  22.709  49.904  1.00 25.00           C
ATOM     28  CA  ILE    28      10.955  22.099  53.534  1.00 25.00           C
ATOM     29  CA  CYS    29       8.616  25.128  53.388  1.00 25.00           C
ATOM     30  CA  LYS    30       6.806  24.028  50.296  1.00 25.00           C
ATOM     31  CA  GLY    31       8.471  26.662  48.041  1.00 25.00           C
ATOM     32  CA  ASP    32       7.731  30.236  49.109  1.00 25.00           C
ATOM     33  CA  ARG    33       5.301  28.944  51.735  1.00 25.00           C
ATOM     34  CA  LEU    34       4.502  27.552  55.121  1.00 25.00           C
ATOM     35  CA  ALA    35       6.552  26.063  57.933  1.00 25.00           C
ATOM     36  CA  PHE    36       7.681  22.429  57.501  1.00 25.00           C
ATOM     37  CA  PRO    37       4.852  20.150  58.689  1.00 25.00           C
ATOM     38  CA  ILE    38       6.993  17.429  56.979  1.00 25.00           C
ATOM     39  CA  LYS    39       6.408  14.974  54.122  1.00 25.00           C
ATOM     40  CA  ASP    40       3.845  13.517  56.528  1.00 25.00           C
ATOM     41  CA  GLY    41       1.583  12.584  59.414  1.00 25.00           C
ATOM     42  CA  ILE    42       4.175  10.165  60.830  1.00 25.00           C
ATOM     43  CA  PRO    43       4.511   6.591  59.614  1.00 25.00           C
ATOM     44  CA  MET    44       6.949   3.826  60.617  1.00 25.00           C
ATOM     45  CA  MET    45       5.496   4.400  64.138  1.00 25.00           C
ATOM     46  CA  LEU    46       8.958   5.678  65.193  1.00 25.00           C
ATOM     47  CA  GLU    47      12.172   3.645  64.902  1.00 25.00           C
ATOM     48  CA  SER    48      14.648   3.769  67.839  1.00 25.00           C
ATOM     49  CA  GLU    49      16.385   0.832  66.156  1.00 25.00           C
ATOM     50  CA  ALA    50      13.465  -1.585  65.756  1.00 25.00           C
ATOM     51  CA  ARG    51      12.785  -3.963  68.608  1.00 25.00           C
ATOM     52  CA  GLU    52      15.616  -4.443  71.040  1.00 25.00           C
ATOM     53  CA  LEU    53      15.930  -1.985  73.908  1.00 25.00           C
ATOM     54  CA  ALA    54      14.357  -4.548  76.183  1.00 25.00           C
ATOM     55  CA  PRO    55      11.279  -3.077  77.953  1.00 25.00           C
ATOM     56  CA  GLU    56      13.920  -2.231  80.606  1.00 25.00           C
ATOM     57  CA  GLU    57      14.790   1.469  80.784  1.00 25.00           C
ATOM     58  CA  GLU    58      14.525   3.841  83.783  1.00 25.00           C
ATOM     59  CA  VAL    59      10.756   4.395  83.867  1.00 25.00           C
ATOM     60  CA  LYS    60      10.306   7.974  82.753  1.00 25.00           C
ATOM     61  CA  LEU    61       7.478   8.178  85.363  1.00 25.00           C
ATOM     62  CA  GLU    62       6.175  11.020  83.208  1.00 25.00           C
ATOM     63  CA  HIS    63       2.717  11.178  81.621  1.00 25.00           C
ATOM     64  CA  HIS    64       0.253  12.203  78.839  1.00 25.00           C
ATOM     65  CA  HIS    65       1.841  15.610  78.215  1.00 25.00           C
ATOM     66  CA  HIS    66       4.835  17.815  77.499  1.00 25.00           C
ATOM     67  CA  HIS    67       7.687  20.260  78.003  1.00 25.00           C
ATOM     68  CA  HIS    68      11.381  19.797  77.062  1.00 25.00           C
TER
END
