
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0309TS599_4
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_4.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      A       2           -
LGA    A       2      S       3           -
LGA    S       3      K       4           -
LGA    K       4      -       -           -
LGA    K       5      -       -           -
LGA    V       6      -       -           -
LGA    H       7      -       -           -
LGA    Q       8      -       -           -
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      -       -           -
LGA    M      17      -       -           -
LGA    D      18      -       -           -
LGA    V      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    V      22      -       -           -
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    Q      25      -       -           -
LGA    T      26      -       -           -
LGA    K      27      K       5          4.141
LGA    E      28      V       6          1.024
LGA    A      29      H       7          3.603
LGA    E      30      Q       8          1.526
LGA    Y      31      I       9          2.270
LGA    T      32      N      10          3.225
LGA    Y      33      V      11          2.042
LGA    D      34      K      12          3.503
LGA    F      35      G      13          2.785
LGA    K      36      F      14          3.486
LGA    E      37      F      15           -
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    I      38      V      22          5.329
LGA    L      39      T      23          2.669
LGA    S      40      E      24          2.726
LGA    -       -      Q      25           -
LGA    E      41      T      26          5.302
LGA    F      42      K      27           -
LGA    N      43      E      28          5.403
LGA    -       -      A      29           -
LGA    G      44      E      30          1.238
LGA    K      45      Y      31          2.823
LGA    N      46      T      32          1.695
LGA    V      47      Y      33          1.127
LGA    S      48      D      34          1.475
LGA    I      49      F      35          3.090
LGA    -       -      K      36           -
LGA    -       -      E      37           -
LGA    T      50      I      38          1.305
LGA    V      51      L      39          1.834
LGA    -       -      S      40           -
LGA    -       -      E      41           -
LGA    K      52      F      42          0.820
LGA    E      53      N      43          2.926
LGA    E      54      G      44          2.421
LGA    N      55      K      45          3.667
LGA    E      56      N      46          3.594
LGA    L      57      V      47          3.950
LGA    P      58      S      48          3.375
LGA    V      59      I      49          1.967
LGA    K      60      T      50          3.407
LGA    G      61      V      51           #
LGA    V      62      K      52           -
LGA    E      63      E      53           -
LGA    M      64      E      54           -
LGA    A      65      N      55           -
LGA    G      66      E      56           -
LGA    D      67      L      57           -
LGA    P      68      P      58           -
LGA    L      69      V      59           -
LGA    E      70      K      60           -
LGA    H      71      G      61           -
LGA    H      72      V      62           -
LGA    H      73      E      63           -
LGA    H      74      -       -           -
LGA    H      75      -       -           -
LGA    H      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     32    3.06     3.12     32.059     1.012

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.824434 * X  +   0.038319 * Y  +  -0.564660 * Z  + -10.587246
  Y_new =   0.561756 * X  +  -0.065953 * Y  +  -0.824670 * Z  + -10.283123
  Z_new =  -0.068842 * X  +  -0.997087 * Y  +   0.032848 * Z  +  -6.071732 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.537864    1.603729  [ DEG:   -88.1131     91.8869 ]
  Theta =   0.068896    3.072696  [ DEG:     3.9475    176.0525 ]
  Phi   =   2.543470   -0.598122  [ DEG:   145.7301    -34.2699 ]
 
# 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: T0309TS599_4                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_4.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76   62   5.0   32   3.06    3.12  32.059
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_4
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1     -25.509 -17.470  -0.637  1.00  0.00              
ATOM      2  CA  ALA     2     -27.187 -16.801   3.170  1.00  0.00              
ATOM      3  CA  SER     3     -29.272 -13.235   4.029  1.00  0.00              
ATOM      4  CA  LYS     4     -26.066 -10.892   5.464  1.00  0.00              
ATOM      5  CA  LYS     5     -24.079 -12.549   2.659  1.00  0.00              
ATOM      6  CA  VAL     6     -26.699 -11.439   0.060  1.00  0.00              
ATOM      7  CA  HIS     7     -26.726  -7.846   1.214  1.00  0.00              
ATOM      8  CA  GLN     8     -22.966  -7.516   1.701  1.00  0.00              
ATOM      9  CA  ILE     9     -21.703  -8.446  -1.706  1.00  0.00              
ATOM     10  CA  ASN    10     -18.909  -6.104  -2.534  1.00  0.00              
ATOM     11  CA  VAL    11     -18.226  -5.479  -6.261  1.00  0.00              
ATOM     12  CA  LYS    12     -14.863  -3.818  -6.373  1.00  0.00              
ATOM     13  CA  GLY    13     -14.783  -2.053  -9.750  1.00  0.00              
ATOM     14  CA  PHE    14     -12.170  -4.350 -11.359  1.00  0.00              
ATOM     15  CA  PHE    15     -13.866  -7.529 -10.099  1.00  0.00              
ATOM     16  CA  ASP    16     -17.641  -7.360  -9.989  1.00  0.00              
ATOM     17  CA  MET    17     -18.157  -9.587  -6.947  1.00  0.00              
ATOM     18  CA  ASP    18     -21.512 -11.047  -6.518  1.00  0.00              
ATOM     19  CA  VAL    19     -22.573 -12.266  -3.200  1.00  0.00              
ATOM     20  CA  MET    20     -22.382 -16.049  -3.584  1.00  0.00              
ATOM     21  CA  GLU    21     -18.830 -15.790  -5.012  1.00  0.00              
ATOM     22  CA  VAL    22     -17.527 -13.535  -2.250  1.00  0.00              
ATOM     23  CA  THR    23     -18.881 -15.742   0.568  1.00  0.00              
ATOM     24  CA  GLU    24     -17.507 -18.972  -0.755  1.00  0.00              
ATOM     25  CA  GLN    25     -14.019 -17.682  -1.299  1.00  0.00              
ATOM     26  CA  THR    26     -13.988 -16.013   2.162  1.00  0.00              
ATOM     27  CA  LYS    27     -15.166 -19.022   4.075  1.00  0.00              
ATOM     28  CA  GLU    28     -12.534 -21.261   2.671  1.00  0.00              
ATOM     29  CA  ALA    29      -9.599 -18.792   2.983  1.00  0.00              
ATOM     30  CA  GLU    30      -7.762 -19.696  -0.144  1.00  0.00              
ATOM     31  CA  TYR    31      -5.800 -16.965  -1.813  1.00  0.00              
ATOM     32  CA  THR    32      -2.191 -17.529  -3.006  1.00  0.00              
ATOM     33  CA  TYR    33      -0.685 -15.833  -6.023  1.00  0.00              
ATOM     34  CA  ASP    34       3.049 -15.480  -6.869  1.00  0.00              
ATOM     35  CA  PHE    35       3.786 -12.594  -9.317  1.00  0.00              
ATOM     36  CA  LYS    36       5.257 -14.714 -12.146  1.00  0.00              
ATOM     37  CA  GLU    37       2.262 -17.053 -11.833  1.00  0.00              
ATOM     38  CA  ILE    38      -0.313 -14.290 -11.931  1.00  0.00              
ATOM     39  CA  LEU    39       1.342 -12.766 -15.031  1.00  0.00              
ATOM     40  CA  SER    40       1.419 -16.213 -16.631  1.00  0.00              
ATOM     41  CA  GLU    41      -2.256 -16.867 -15.843  1.00  0.00              
ATOM     42  CA  PHE    42      -3.302 -13.569 -17.328  1.00  0.00              
ATOM     43  CA  ASN    43      -1.252 -13.978 -20.564  1.00  0.00              
ATOM     44  CA  GLY    44       0.724 -10.783 -19.962  1.00  0.00              
ATOM     45  CA  LYS    45      -2.269  -8.748 -18.700  1.00  0.00              
ATOM     46  CA  ASN    46      -1.897  -7.088 -15.355  1.00  0.00              
ATOM     47  CA  VAL    47      -4.024  -8.646 -12.697  1.00  0.00              
ATOM     48  CA  SER    48      -5.049  -7.192  -9.400  1.00  0.00              
ATOM     49  CA  ILE    49      -5.295  -9.527  -6.366  1.00  0.00              
ATOM     50  CA  THR    50      -7.147  -8.457  -3.259  1.00  0.00              
ATOM     51  CA  VAL    51      -6.115  -9.918   0.142  1.00  0.00              
ATOM     52  CA  LYS    52      -8.803 -10.056   2.774  1.00  0.00              
ATOM     53  CA  GLU    53      -7.796  -9.414   6.341  1.00  0.00              
ATOM     54  CA  GLU    54     -11.124  -9.992   8.022  1.00  0.00              
ATOM     55  CA  ASN    55     -12.151 -13.017   5.950  1.00  0.00              
ATOM     56  CA  GLU    56      -8.742 -14.652   6.517  1.00  0.00              
ATOM     57  CA  LEU    57      -6.913 -14.563   3.237  1.00  0.00              
ATOM     58  CA  PRO    58      -3.950 -16.824   2.775  1.00  0.00              
ATOM     59  CA  VAL    59      -0.793 -14.761   1.969  1.00  0.00              
ATOM     60  CA  LYS    60       1.097 -15.847  -1.105  1.00  0.00              
ATOM     61  CA  GLY    61       2.044 -12.612  -2.884  1.00  0.00              
ATOM     62  CA  VAL    62      -0.974 -10.474  -2.123  1.00  0.00              
ATOM     63  CA  GLU    63      -1.654  -7.450  -4.375  1.00  0.00              
ATOM     64  CA  MET    64      -4.029  -4.886  -3.254  1.00  0.00              
ATOM     65  CA  ALA    65      -5.869  -3.031  -5.831  1.00  0.00              
ATOM     66  CA  GLY    66      -7.398   0.274  -4.955  1.00  0.00              
ATOM     67  CA  ASP    67      -7.690   1.389  -8.626  1.00  0.00              
ATOM     68  CA  PRO    68     -10.387  -0.815  -9.995  1.00  0.00              
ATOM     69  CA  LEU    69     -12.385   1.640 -12.200  1.00  0.00              
ATOM     70  CA  GLU    70     -13.361  -0.223 -15.364  1.00  0.00              
ATOM     71  CA  HIS    71     -14.531   2.385 -17.907  1.00  0.00              
ATOM     72  CA  HIS    72     -16.672   0.249 -20.144  1.00  0.00              
ATOM     73  CA  HIS    73     -16.828   1.175 -23.699  1.00  0.00              
ATOM     74  CA  HIS    74     -13.678   2.898 -22.550  1.00  0.00              
ATOM     75  CA  HIS    75     -11.026   3.428 -25.279  1.00  0.00              
ATOM     76  CA  HIS    76     -10.166   0.211 -27.154  1.00  0.00              
TER                                                                             
END
