
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS599_4.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    I       2      M       1          4.959
LGA    S       3      I       2          2.319
LGA    N       4      S       3          2.438
LGA    A       5      N       4          2.349
LGA    K       6      A       5           #
LGA    -       -      K       6           -
LGA    I       7      I       7          2.930
LGA    A       8      A       8          2.436
LGA    R       9      R       9          2.532
LGA    I      10      I      10          1.852
LGA    N      11      N      11          1.131
LGA    E      12      E      12          1.127
LGA    L      13      L      13          1.572
LGA    A      14      A      14          1.068
LGA    A      15      A      15          1.738
LGA    K      16      K      16          2.011
LGA    A      17      A      17          1.092
LGA    K      18      K      18          2.001
LGA    A      19      A      19          3.990
LGA    G      20      G      20          3.376
LGA    V      21      V      21          1.047
LGA    I      22      I      22          1.141
LGA    T      23      T      23          0.948
LGA    E      24      E      24          2.182
LGA    E      25      E      25          2.767
LGA    E      26      E      26          1.703
LGA    K      27      K      27          1.179
LGA    A      28      A      28          2.324
LGA    E      29      E      29          2.116
LGA    Q      30      Q      30          0.957
LGA    Q      31      Q      31          1.451
LGA    K      32      K      32          1.695
LGA    L      33      L      33          1.467
LGA    R      34      R      34          0.879
LGA    Q      35      Q      35          0.878
LGA    E      36      E      36          1.080
LGA    Y      37      Y      37          2.481
LGA    L      38      L      38          2.827
LGA    K      39      K      39          2.280
LGA    G      40      G      40          3.603
LGA    F      41      F      41          4.182
LGA    R      42      R      42          3.394
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     40    2.31    90.00     81.203     1.660

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.180682 * X  +  -0.983351 * Y  +  -0.019366 * Z  +   5.349023
  Y_new =   0.774133 * X  +   0.154330 * Y  +  -0.613923 * Z  +  -3.241628
  Z_new =   0.606690 * X  +   0.095933 * Y  +   0.789129 * Z  + -18.817156 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.120974   -3.020618  [ DEG:     6.9313   -173.0687 ]
  Theta =  -0.651890   -2.489702  [ DEG:   -37.3506   -142.6494 ]
  Phi   =   1.341502   -1.800090  [ DEG:    76.8624   -103.1376 ]
 
# 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_4                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS599_4.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   40   2.31   90.00  81.203
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS599_4
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -0.785   0.144 -10.431  1.00  0.00              
ATOM      2  CA  ILE     2       0.939  -1.067 -13.346  1.00  0.00              
ATOM      3  CA  SER     3       0.931  -5.267 -13.240  1.00  0.00              
ATOM      4  CA  ASN     4      -2.486  -6.369 -12.434  1.00  0.00              
ATOM      5  CA  ALA     5      -1.465  -8.525  -9.449  1.00  0.00              
ATOM      6  CA  LYS     6       0.286  -5.521  -7.933  1.00  0.00              
ATOM      7  CA  ILE     7      -2.761  -3.356  -8.509  1.00  0.00              
ATOM      8  CA  ALA     8      -5.020  -5.937  -6.844  1.00  0.00              
ATOM      9  CA  ARG     9      -2.681  -6.250  -3.874  1.00  0.00              
ATOM     10  CA  ILE    10      -2.489  -2.525  -3.346  1.00  0.00              
ATOM     11  CA  ASN    11      -6.228  -2.274  -3.439  1.00  0.00              
ATOM     12  CA  GLU    12      -6.631  -5.001  -0.888  1.00  0.00              
ATOM     13  CA  LEU    13      -4.132  -3.338   1.471  1.00  0.00              
ATOM     14  CA  ALA    14      -5.891   0.016   1.106  1.00  0.00              
ATOM     15  CA  ALA    15      -9.190  -1.627   2.056  1.00  0.00              
ATOM     16  CA  LYS    16      -7.531  -3.341   5.070  1.00  0.00              
ATOM     17  CA  ALA    17      -6.068  -0.014   6.140  1.00  0.00              
ATOM     18  CA  LYS    18      -9.417   1.735   5.828  1.00  0.00              
ATOM     19  CA  ALA    19     -11.087  -0.871   8.004  1.00  0.00              
ATOM     20  CA  GLY    20      -8.421  -0.598  10.661  1.00  0.00              
ATOM     21  CA  VAL    21      -8.064   3.183  10.565  1.00  0.00              
ATOM     22  CA  ILE    22      -4.546   3.330   9.330  1.00  0.00              
ATOM     23  CA  THR    23      -2.131   5.522  11.180  1.00  0.00              
ATOM     24  CA  GLU    24       0.046   8.088   9.526  1.00  0.00              
ATOM     25  CA  GLU    25       3.022   5.661   9.762  1.00  0.00              
ATOM     26  CA  GLU    26       1.031   2.926   8.049  1.00  0.00              
ATOM     27  CA  LYS    27       0.058   5.379   5.257  1.00  0.00              
ATOM     28  CA  ALA    28       3.693   6.418   4.724  1.00  0.00              
ATOM     29  CA  GLU    29       4.793   2.761   4.535  1.00  0.00              
ATOM     30  CA  GLN    30       2.044   2.013   1.995  1.00  0.00              
ATOM     31  CA  GLN    31       3.080   4.925  -0.157  1.00  0.00              
ATOM     32  CA  LYS    32       6.750   3.797  -0.096  1.00  0.00              
ATOM     33  CA  LEU    33       5.791   0.235  -1.003  1.00  0.00              
ATOM     34  CA  ARG    34       3.655   1.398  -3.893  1.00  0.00              
ATOM     35  CA  GLN    35       6.438   3.566  -5.248  1.00  0.00              
ATOM     36  CA  GLU    36       8.967   0.706  -5.059  1.00  0.00              
ATOM     37  CA  TYR    37       6.634  -1.745  -6.802  1.00  0.00              
ATOM     38  CA  LEU    38       5.885   0.746  -9.515  1.00  0.00              
ATOM     39  CA  LYS    39       9.624   1.424 -10.087  1.00  0.00              
ATOM     40  CA  GLY    40      10.321  -2.317 -10.212  1.00  0.00              
ATOM     41  CA  PHE    41       7.491  -2.809 -12.778  1.00  0.00              
ATOM     42  CA  ARG    42       8.805   0.069 -14.888  1.00  0.00              
ATOM     43  CA  SER    43      12.272  -1.515 -14.868  1.00  0.00              
ATOM     44  CA  SER    44      10.807  -4.927 -15.873  1.00  0.00              
ATOM     45  CA  MET    45       8.818  -3.269 -18.683  1.00  0.00              
ATOM     46  CA  LYS    46      11.939  -1.410 -19.907  1.00  0.00              
ATOM     47  CA  ASN    47      13.883  -4.685 -19.988  1.00  0.00              
ATOM     48  CA  THR    48      11.092  -6.349 -21.980  1.00  0.00              
ATOM     49  CA  LEU    49      10.968  -3.442 -24.428  1.00  0.00              
ATOM     50  CA  LYS    50      14.736  -3.518 -25.041  1.00  0.00              
ATOM     51  CA  SER    51      14.653  -7.307 -25.626  1.00  0.00              
ATOM     52  CA  VAL    52      11.698  -7.484 -27.925  1.00  0.00              
ATOM     53  CA  LYS    53      11.862  -9.865 -30.906  1.00  0.00              
ATOM     54  CA  ILE    54       9.558  -9.618 -33.834  1.00  0.00              
ATOM     55  CA  ILE    55       8.129 -12.711 -35.400  1.00  0.00              
ATOM     56  CA  ASP    56       6.627 -12.165 -38.796  1.00  0.00              
ATOM     57  CA  PRO    57       3.419 -13.484 -40.257  1.00  0.00              
ATOM     58  CA  GLU    58       5.117 -16.751 -41.335  1.00  0.00              
ATOM     59  CA  GLY    59       6.567 -17.419 -37.908  1.00  0.00              
ATOM     60  CA  ASN    60      10.159 -16.511 -38.491  1.00  0.00              
ATOM     61  CA  ASP    61      11.846 -14.693 -35.671  1.00  0.00              
ATOM     62  CA  VAL    62      12.911 -11.247 -36.632  1.00  0.00              
ATOM     63  CA  THR    63      15.620  -9.734 -34.485  1.00  0.00              
ATOM     64  CA  PRO    64      15.401  -5.962 -33.852  1.00  0.00              
ATOM     65  CA  GLU    65      18.510  -5.353 -35.873  1.00  0.00              
ATOM     66  CA  LYS    66      17.352  -7.330 -38.859  1.00  0.00              
ATOM     67  CA  LEU    67      13.989  -5.660 -38.979  1.00  0.00              
ATOM     68  CA  LYS    68      15.351  -2.175 -38.841  1.00  0.00              
ATOM     69  CA  ARG    69      17.888  -2.849 -41.551  1.00  0.00              
ATOM     70  CA  GLU    70      15.394  -4.435 -43.876  1.00  0.00              
ATOM     71  CA  GLN    71      12.905  -1.585 -43.427  1.00  0.00              
ATOM     72  CA  ARG    72      15.515   1.028 -44.099  1.00  0.00              
ATOM     73  CA  ASN    73      16.751  -0.636 -47.257  1.00  0.00              
ATOM     74  CA  ASN    74      13.379  -1.132 -48.844  1.00  0.00              
ATOM     75  CA  LYS    75      11.424   1.786 -47.225  1.00  0.00              
ATOM     76  CA  LEU    76       9.046  -0.499 -45.419  1.00  0.00              
ATOM     77  CA  HIS    77       7.749  -0.101 -41.910  1.00  0.00              
ATOM     78  CA  LEU    78       7.564  -3.601 -40.558  1.00  0.00              
ATOM     79  CA  GLU    79       4.853  -4.270 -37.901  1.00  0.00              
ATOM     80  CA  HIS    80       3.769  -7.901 -38.340  1.00  0.00              
ATOM     81  CA  HIS    81       0.105  -7.151 -39.250  1.00  0.00              
ATOM     82  CA  HIS    82       1.254  -4.944 -42.155  1.00  0.00              
ATOM     83  CA  HIS    83       4.672  -7.318 -42.761  1.00  0.00              
ATOM     84  CA  HIS    84       7.800  -7.812 -44.647  1.00  0.00              
ATOM     85  CA  HIS    85       8.053  -4.823 -47.594  1.00  0.00              
TER                                                                             
END
