
#######################################################
#                                                     #
#                        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 T0309TS168_5
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS168_5.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      K       5           -
LGA    K       5      V       6           -
LGA    V       6      H       7           -
LGA    H       7      Q       8           -
LGA    Q       8      I       9           -
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      -       -           -
LGA    E      28      -       -           -
LGA    A      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      N      10          4.460
LGA    T      32      V      11          3.634
LGA    Y      33      K      12          2.376
LGA    D      34      G      13          3.883
LGA    F      35      F      14          4.896
LGA    K      36      F      15          4.360
LGA    E      37      -       -           -
LGA    I      38      D      16          2.532
LGA    L      39      M      17          2.652
LGA    S      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      -       -           -
LGA    G      44      -       -           -
LGA    K      45      -       -           -
LGA    N      46      D      18          1.846
LGA    V      47      V      19          1.460
LGA    S      48      M      20          1.901
LGA    I      49      E      21          1.542
LGA    T      50      V      22          1.622
LGA    V      51      T      23          2.798
LGA    K      52      E      24          4.120
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    N      55      -       -           -
LGA    E      56      -       -           -
LGA    L      57      Q      25           #
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    P      58      E      28          1.322
LGA    V      59      A      29          0.749
LGA    K      60      E      30          3.287
LGA    G      61      Y      31          2.658
LGA    V      62      T      32          2.584
LGA    E      63      Y      33          1.868
LGA    M      64      D      34          0.629
LGA    A      65      F      35          3.462
LGA    G      66      K      36          4.329
LGA    D      67      E      37          4.283
LGA    -       -      I      38           -
LGA    -       -      L      39           -
LGA    P      68      S      40          2.095
LGA    L      69      E      41          2.192
LGA    E      70      F      42          3.158
LGA    H      71      N      43           #
LGA    H      72      G      44           -
LGA    H      73      -       -           -
LGA    H      74      K      45          4.053
LGA    H      75      N      46          3.398
LGA    H      76      V      47           #
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    -       -      T      50           -
LGA    -       -      V      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      N      55           -
LGA    -       -      E      56           -
LGA    -       -      L      57           -
LGA    -       -      P      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     30    3.03     6.67     31.152     0.957

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.890849 * X  +  -0.338063 * Y  +   0.303483 * Z  +   1.425521
  Y_new =   0.415946 * X  +  -0.338304 * Y  +   0.844121 * Z  +  -9.239018
  Z_new =  -0.182697 * X  +   0.878216 * Y  +   0.441993 * Z  + -10.912411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.104524   -2.037069  [ DEG:    63.2846   -116.7154 ]
  Theta =   0.183729    2.957864  [ DEG:    10.5269    169.4731 ]
  Phi   =   2.704766   -0.436826  [ DEG:   154.9717    -25.0283 ]
 
# 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: T0309TS168_5                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS168_5.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   30   3.03    6.67  31.152
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS168_5
PFRMAT TS
TARGET T0309
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      18.343  -9.499 -29.601  1.00 25.00           C
ATOM      2  CA  ALA     2      18.403 -10.768 -25.995  1.00 25.00           C
ATOM      3  CA  SER     3      15.896 -11.408 -23.131  1.00 25.00           C
ATOM      4  CA  LYS     4      13.908  -9.085 -20.817  1.00 25.00           C
ATOM      5  CA  LYS     5      12.294 -10.870 -17.943  1.00 25.00           C
ATOM      6  CA  VAL     6       8.826 -12.442 -17.397  1.00 25.00           C
ATOM      7  CA  HIS     7       8.387  -9.641 -14.862  1.00 25.00           C
ATOM      8  CA  GLN     8       6.528  -6.323 -14.785  1.00 25.00           C
ATOM      9  CA  ILE     9       3.069  -5.619 -13.530  1.00 25.00           C
ATOM     10  CA  ASN    10      -0.298  -3.938 -13.952  1.00 25.00           C
ATOM     11  CA  VAL    11      -2.566  -1.472 -12.095  1.00 25.00           C
ATOM     12  CA  LYS    12      -3.388  -0.260 -15.625  1.00 25.00           C
ATOM     13  CA  GLY    13      -6.452   1.373 -17.313  1.00 25.00           C
ATOM     14  CA  PHE    14      -4.794   4.649 -16.286  1.00 25.00           C
ATOM     15  CA  PHE    15      -1.017   4.188 -16.217  1.00 25.00           C
ATOM     16  CA  ASP    16      -0.526   3.893 -19.956  1.00 25.00           C
ATOM     17  CA  MET    17      -1.228   0.165 -20.395  1.00 25.00           C
ATOM     18  CA  ASP    18       1.320  -0.498 -17.669  1.00 25.00           C
ATOM     19  CA  VAL    19       3.406  -3.679 -18.028  1.00 25.00           C
ATOM     20  CA  MET    20       1.891  -7.218 -18.132  1.00 25.00           C
ATOM     21  CA  GLU    21       3.415 -10.216 -16.281  1.00 25.00           C
ATOM     22  CA  VAL    22       4.717 -13.400 -14.633  1.00 25.00           C
ATOM     23  CA  THR    23       7.720 -15.112 -12.956  1.00 25.00           C
ATOM     24  CA  GLU    24       8.992 -18.313 -11.342  1.00 25.00           C
ATOM     25  CA  GLN    25       7.230 -21.670 -10.951  1.00 25.00           C
ATOM     26  CA  THR    26       5.971 -22.857  -7.596  1.00 25.00           C
ATOM     27  CA  LYS    27       9.332 -21.734  -6.329  1.00 25.00           C
ATOM     28  CA  GLU    28      10.000 -18.275  -4.932  1.00 25.00           C
ATOM     29  CA  ALA    29       6.633 -18.110  -3.241  1.00 25.00           C
ATOM     30  CA  GLU    30       4.108 -17.599  -6.094  1.00 25.00           C
ATOM     31  CA  TYR    31       0.358 -16.894  -5.758  1.00 25.00           C
ATOM     32  CA  THR    32       0.849 -13.421  -7.295  1.00 25.00           C
ATOM     33  CA  TYR    33       2.812 -14.958 -10.203  1.00 25.00           C
ATOM     34  CA  ASP    34       5.706 -12.845  -8.829  1.00 25.00           C
ATOM     35  CA  PHE    35       4.472  -9.596  -7.284  1.00 25.00           C
ATOM     36  CA  LYS    36       6.912  -8.548  -4.525  1.00 25.00           C
ATOM     37  CA  GLU    37       9.791  -8.512  -7.051  1.00 25.00           C
ATOM     38  CA  ILE    38       7.704  -6.362  -9.436  1.00 25.00           C
ATOM     39  CA  LEU    39       6.904  -3.933  -6.584  1.00 25.00           C
ATOM     40  CA  SER    40      10.622  -3.716  -5.693  1.00 25.00           C
ATOM     41  CA  GLU    41      11.485  -3.008  -9.356  1.00 25.00           C
ATOM     42  CA  PHE    42       8.821  -0.260  -9.478  1.00 25.00           C
ATOM     43  CA  ASN    43      11.814   2.074  -8.946  1.00 25.00           C
ATOM     44  CA  GLY    44      11.070   1.363  -5.277  1.00 25.00           C
ATOM     45  CA  LYS    45       7.432   0.783  -4.446  1.00 25.00           C
ATOM     46  CA  ASN    46       3.746  -0.148  -5.070  1.00 25.00           C
ATOM     47  CA  VAL    47       3.389  -0.651  -8.817  1.00 25.00           C
ATOM     48  CA  SER    48       1.965  -4.023  -7.765  1.00 25.00           C
ATOM     49  CA  ILE    49       0.451  -7.371  -8.928  1.00 25.00           C
ATOM     50  CA  THR    50       0.948 -10.000 -11.643  1.00 25.00           C
ATOM     51  CA  VAL    51      -0.835 -12.055 -14.276  1.00 25.00           C
ATOM     52  CA  LYS    52      -1.832 -14.597 -16.904  1.00 25.00           C
ATOM     53  CA  GLU    53      -5.451 -15.656 -16.497  1.00 25.00           C
ATOM     54  CA  GLU    54      -8.607 -17.355 -17.704  1.00 25.00           C
ATOM     55  CA  ASN    55      -7.280 -17.702 -21.263  1.00 25.00           C
ATOM     56  CA  GLU    56      -4.668 -20.095 -19.953  1.00 25.00           C
ATOM     57  CA  LEU    57      -1.303 -18.259 -20.333  1.00 25.00           C
ATOM     58  CA  PRO    58      -1.990 -17.542 -23.991  1.00 25.00           C
ATOM     59  CA  VAL    59      -0.709 -14.061 -22.992  1.00 25.00           C
ATOM     60  CA  LYS    60      -3.152 -11.787 -21.085  1.00 25.00           C
ATOM     61  CA  GLY    61      -5.098 -10.755 -18.023  1.00 25.00           C
ATOM     62  CA  VAL    62      -3.671  -7.440 -16.735  1.00 25.00           C
ATOM     63  CA  GLU    63      -3.661  -7.724 -12.974  1.00 25.00           C
ATOM     64  CA  MET    64      -4.388  -6.261  -9.558  1.00 25.00           C
ATOM     65  CA  ALA    65      -4.048  -9.816  -8.201  1.00 25.00           C
ATOM     66  CA  GLY    66      -5.482  -8.746  -4.807  1.00 25.00           C
ATOM     67  CA  ASP    67      -4.202  -5.552  -3.126  1.00 25.00           C
ATOM     68  CA  PRO    68      -7.512  -5.181  -1.281  1.00 25.00           C
ATOM     69  CA  LEU    69     -10.861  -6.848  -0.509  1.00 25.00           C
ATOM     70  CA  GLU    70     -12.372  -9.745   1.549  1.00 25.00           C
ATOM     71  CA  HIS    71     -14.978  -9.695   4.342  1.00 25.00           C
ATOM     72  CA  HIS    72     -15.432 -13.487   4.174  1.00 25.00           C
ATOM     73  CA  HIS    73     -12.289 -14.870   5.809  1.00 25.00           C
ATOM     74  CA  HIS    74     -12.152 -14.902   9.610  1.00 25.00           C
ATOM     75  CA  HIS    75     -10.182 -14.222  12.756  1.00 25.00           C
ATOM     76  CA  HIS    76      -7.314 -11.955  11.758  1.00 25.00           C
TER
END
