
#######################################################
#                                                     #
#                        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 T0335TS599_5
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS599_5.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          4.695
LGA    S       3      S       3          2.172
LGA    N       4      N       4          4.756
LGA    A       5      A       5          3.549
LGA    K       6      K       6          2.787
LGA    I       7      I       7          2.212
LGA    A       8      A       8          1.538
LGA    R       9      R       9          1.728
LGA    I      10      I      10          1.298
LGA    N      11      N      11          0.866
LGA    E      12      E      12          0.705
LGA    L      13      L      13          1.055
LGA    A      14      A      14          1.011
LGA    A      15      A      15          2.152
LGA    K      16      K      16          2.193
LGA    A      17      A      17          0.896
LGA    K      18      K      18          2.194
LGA    A      19      A      19          4.240
LGA    G      20      G      20          3.493
LGA    V      21      V      21          0.799
LGA    I      22      I      22          1.025
LGA    T      23      T      23          1.395
LGA    E      24      E      24          2.640
LGA    E      25      E      25          3.267
LGA    E      26      E      26          2.050
LGA    K      27      K      27          1.384
LGA    A      28      A      28          2.605
LGA    E      29      E      29          2.355
LGA    Q      30      Q      30          1.078
LGA    Q      31      Q      31          1.581
LGA    K      32      K      32          1.784
LGA    L      33      L      33          1.561
LGA    R      34      R      34          1.121
LGA    Q      35      Q      35          1.061
LGA    E      36      E      36          1.196
LGA    Y      37      Y      37          2.899
LGA    L      38      L      38          3.357
LGA    K      39      K      39          2.700
LGA    G      40      G      40          4.059
LGA    F      41      F      41          4.817
LGA    R      42      R      42          3.430
LGA    S      43      -       -           -
LGA    S      44      -       -           -
LGA    M      45      -       -           -
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     41    2.53   100.00     80.607     1.562

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.153772 * X  +   0.988065 * Y  +  -0.009008 * Z  +   4.071041
  Y_new =  -0.505307 * X  +   0.070800 * Y  +  -0.860030 * Z  +  -3.670383
  Z_new =  -0.849129 * X  +   0.136800 * Y  +   0.510163 * Z  + -16.981709 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.261986   -2.879606  [ DEG:    15.0107   -164.9893 ]
  Theta =   1.014333    2.127259  [ DEG:    58.1170    121.8830 ]
  Phi   =  -1.275387    1.866205  [ DEG:   -73.0743    106.9257 ]
 
# 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: T0335TS599_5                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS599_5.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   41   2.53  100.00  80.607
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS599_5
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -1.007  -0.607 -10.087  1.00  0.00              
ATOM      2  CA  ILE     2       0.733  -1.963 -12.930  1.00  0.00              
ATOM      3  CA  SER     3       0.827  -6.150 -12.599  1.00  0.00              
ATOM      4  CA  ASN     4      -2.556  -7.278 -11.694  1.00  0.00              
ATOM      5  CA  ALA     5      -1.433  -9.248  -8.586  1.00  0.00              
ATOM      6  CA  LYS     6       0.265  -6.118  -7.288  1.00  0.00              
ATOM      7  CA  ILE     7      -2.852  -4.042  -7.939  1.00  0.00              
ATOM      8  CA  ALA     8      -5.035  -6.592  -6.092  1.00  0.00              
ATOM      9  CA  ARG     9      -2.642  -6.666  -3.146  1.00  0.00              
ATOM     10  CA  ILE    10      -2.520  -2.913  -2.839  1.00  0.00              
ATOM     11  CA  ASN    11      -6.276  -2.747  -2.899  1.00  0.00              
ATOM     12  CA  GLU    12      -6.594  -5.340  -0.192  1.00  0.00              
ATOM     13  CA  LEU    13      -4.087  -3.476   2.052  1.00  0.00              
ATOM     14  CA  ALA    14      -5.927  -0.193   1.510  1.00  0.00              
ATOM     15  CA  ALA    15      -9.176  -1.853   2.600  1.00  0.00              
ATOM     16  CA  LYS    16      -7.466  -3.343   5.673  1.00  0.00              
ATOM     17  CA  ALA    17      -6.024   0.052   6.524  1.00  0.00              
ATOM     18  CA  LYS    18      -9.463   1.727   6.159  1.00  0.00              
ATOM     19  CA  ALA    19     -11.047  -0.787   8.501  1.00  0.00              
ATOM     20  CA  GLY    20      -8.356  -0.311  11.104  1.00  0.00              
ATOM     21  CA  VAL    21      -8.090   3.464  10.804  1.00  0.00              
ATOM     22  CA  ILE    22      -4.566   3.642   9.505  1.00  0.00              
ATOM     23  CA  THR    23      -2.196   5.980  11.200  1.00  0.00              
ATOM     24  CA  GLU    24      -0.100   8.507   9.359  1.00  0.00              
ATOM     25  CA  GLU    25       2.943   6.161   9.702  1.00  0.00              
ATOM     26  CA  GLU    26       0.997   3.280   8.169  1.00  0.00              
ATOM     27  CA  LYS    27      -0.087   5.552   5.264  1.00  0.00              
ATOM     28  CA  ALA    28       3.515   6.635   4.613  1.00  0.00              
ATOM     29  CA  GLU    29       4.688   3.017   4.608  1.00  0.00              
ATOM     30  CA  GLN    30       1.939   2.046   2.162  1.00  0.00              
ATOM     31  CA  GLN    31       2.873   4.852  -0.170  1.00  0.00              
ATOM     32  CA  LYS    32       6.561   3.828  -0.092  1.00  0.00              
ATOM     33  CA  LEU    33       5.708   0.206  -0.806  1.00  0.00              
ATOM     34  CA  ARG    34       3.476   1.139  -3.677  1.00  0.00              
ATOM     35  CA  GLN    35       6.170   3.311  -5.228  1.00  0.00              
ATOM     36  CA  GLU    36       8.813   0.525  -4.910  1.00  0.00              
ATOM     37  CA  TYR    37       6.512  -2.084  -6.471  1.00  0.00              
ATOM     38  CA  LEU    38       5.658   0.210  -9.331  1.00  0.00              
ATOM     39  CA  LYS    39       9.353   0.982  -9.957  1.00  0.00              
ATOM     40  CA  GLY    40      10.189  -2.739  -9.934  1.00  0.00              
ATOM     41  CA  PHE    41       7.342  -3.459 -12.371  1.00  0.00              
ATOM     42  CA  ARG    42       8.526  -0.690 -14.689  1.00  0.00              
ATOM     43  CA  SER    43      12.046  -2.124 -14.625  1.00  0.00              
ATOM     44  CA  SER    44      10.715  -5.633 -15.435  1.00  0.00              
ATOM     45  CA  MET    45       8.602  -4.258 -18.266  1.00  0.00              
ATOM     46  CA  LYS    46      11.609  -2.371 -19.679  1.00  0.00              
ATOM     47  CA  ASN    47      13.718  -5.495 -19.620  1.00  0.00              
ATOM     48  CA  THR    48      10.946  -7.395 -21.420  1.00  0.00              
ATOM     49  CA  LEU    49      10.674  -4.660 -24.066  1.00  0.00              
ATOM     50  CA  LYS    50      14.423  -4.547 -24.653  1.00  0.00              
ATOM     51  CA  SER    51      14.495  -8.368 -25.039  1.00  0.00              
ATOM     52  CA  VAL    52      11.589  -8.602 -27.410  1.00  0.00              
ATOM     53  CA  LYS    53      11.864 -11.141 -30.255  1.00  0.00              
ATOM     54  CA  ILE    54       9.701 -10.802 -33.279  1.00  0.00              
ATOM     55  CA  ILE    55       8.241 -13.938 -34.726  1.00  0.00              
ATOM     56  CA  ASP    56       6.318 -13.373 -37.979  1.00  0.00              
ATOM     57  CA  PRO    57       3.241 -15.414 -38.884  1.00  0.00              
ATOM     58  CA  GLU    58       5.424 -18.038 -40.615  1.00  0.00              
ATOM     59  CA  GLY    59       7.806 -18.491 -37.682  1.00  0.00              
ATOM     60  CA  ASN    60      10.718 -16.519 -38.964  1.00  0.00              
ATOM     61  CA  ASP    61      12.766 -14.537 -36.536  1.00  0.00              
ATOM     62  CA  VAL    62      12.515 -10.916 -36.890  1.00  0.00              
ATOM     63  CA  THR    63      15.485  -8.676 -36.379  1.00  0.00              
ATOM     64  CA  PRO    64      15.421  -5.367 -34.601  1.00  0.00              
ATOM     65  CA  GLU    65      15.544  -3.402 -37.806  1.00  0.00              
ATOM     66  CA  LYS    66      12.706  -5.308 -39.419  1.00  0.00              
ATOM     67  CA  LEU    67      10.515  -4.882 -36.411  1.00  0.00              
ATOM     68  CA  LYS    68      11.125  -1.137 -36.276  1.00  0.00              
ATOM     69  CA  ARG    69      10.329  -0.749 -40.011  1.00  0.00              
ATOM     70  CA  GLU    70       7.125  -2.736 -39.792  1.00  0.00              
ATOM     71  CA  GLN    71       5.896  -0.934 -36.721  1.00  0.00              
ATOM     72  CA  ARG    72       6.532   2.378 -38.333  1.00  0.00              
ATOM     73  CA  ASN    73       4.780   1.459 -41.603  1.00  0.00              
ATOM     74  CA  ASN    74       1.638  -0.024 -40.160  1.00  0.00              
ATOM     75  CA  LYS    75       1.554   1.769 -36.764  1.00  0.00              
ATOM     76  CA  LEU    76       1.973  -1.388 -34.781  1.00  0.00              
ATOM     77  CA  HIS    77       4.116  -2.017 -31.780  1.00  0.00              
ATOM     78  CA  LEU    78       5.358  -5.567 -32.460  1.00  0.00              
ATOM     79  CA  GLU    79       6.093  -7.929 -29.530  1.00  0.00              
ATOM     80  CA  HIS    80       4.875 -11.347 -30.470  1.00  0.00              
ATOM     81  CA  HIS    81       1.621 -11.439 -28.509  1.00  0.00              
ATOM     82  CA  HIS    82      -0.054 -10.459 -31.825  1.00  0.00              
ATOM     83  CA  HIS    83       1.644  -7.429 -32.681  1.00  0.00              
ATOM     84  CA  HIS    84       2.538  -6.912 -36.800  1.00  0.00              
ATOM     85  CA  HIS    85       2.225  -9.781 -39.890  1.00  0.00              
TER                                                                             
END
