
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS168_3.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      -       -           -
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      V       6           #
LGA    D      16      H       7           -
LGA    M      17      -       -           -
LGA    D      18      -       -           -
LGA    V      19      Q       8          4.113
LGA    M      20      I       9          3.758
LGA    E      21      N      10          2.860
LGA    V      22      V      11          0.971
LGA    T      23      K      12          4.459
LGA    E      24      G      13          3.413
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    Q      25      E      30          3.890
LGA    T      26      Y      31          2.393
LGA    K      27      T      32          2.033
LGA    E      28      Y      33          3.453
LGA    A      29      D      34           #
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      -       -           -
LGA    D      34      -       -           -
LGA    F      35      F      35          3.074
LGA    K      36      K      36          1.531
LGA    E      37      E      37          1.716
LGA    I      38      I      38          1.865
LGA    L      39      L      39          1.722
LGA    S      40      S      40          1.943
LGA    E      41      E      41          2.393
LGA    F      42      F      42          2.376
LGA    N      43      -       -           -
LGA    G      44      N      43          3.250
LGA    K      45      G      44          3.440
LGA    N      46      K      45          4.190
LGA    V      47      N      46           -
LGA    -       -      V      47           -
LGA    S      48      S      48          3.490
LGA    I      49      I      49          1.823
LGA    T      50      T      50          1.473
LGA    V      51      V      51          2.727
LGA    K      52      K      52          2.718
LGA    E      53      E      53          0.760
LGA    E      54      E      54          2.613
LGA    N      55      N      55          3.056
LGA    E      56      E      56           -
LGA    L      57      L      57           -
LGA    P      58      P      58           -
LGA    V      59      V      59           -
LGA    K      60      K      60           -
LGA    G      61      G      61           -
LGA    V      62      V      62           -
LGA    E      63      E      63           -
LGA    M      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    D      67      -       -           -
LGA    P      68      -       -           -
LGA    L      69      -       -           -
LGA    E      70      -       -           -
LGA    H      71      -       -           -
LGA    H      72      -       -           -
LGA    H      73      -       -           -
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     29    2.84    58.62     29.274     0.986

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.008166 * X  +   0.828285 * Y  +   0.560247 * Z  +   1.378961
  Y_new =  -0.967138 * X  +   0.135838 * Y  +  -0.214924 * Z  + -12.065509
  Z_new =  -0.254121 * X  +  -0.543591 * Y  +   0.799957 * Z  +   0.272424 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.596853    2.544740  [ DEG:   -34.1971    145.8029 ]
  Theta =   0.256939    2.884654  [ DEG:    14.7215    165.2785 ]
  Phi   =  -1.579240    1.562353  [ DEG:   -90.4838     89.5162 ]
 
# 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_3                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS168_3.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   29   2.84   58.62  29.274
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS168_3
PFRMAT TS
TARGET T0309
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       6.574   9.454   3.510  1.00 25.00           C
ATOM      2  CA  ALA     2       7.940   6.155   4.861  1.00 25.00           C
ATOM      3  CA  SER     3       7.126   2.703   3.468  1.00 25.00           C
ATOM      4  CA  LYS     4       5.168  -0.550   2.981  1.00 25.00           C
ATOM      5  CA  LYS     5       3.742  -4.035   2.478  1.00 25.00           C
ATOM      6  CA  VAL     6       1.551  -6.715   0.813  1.00 25.00           C
ATOM      7  CA  HIS     7       1.899 -10.198  -0.710  1.00 25.00           C
ATOM      8  CA  GLN     8      -1.353 -12.127  -0.327  1.00 25.00           C
ATOM      9  CA  ILE     9       0.469 -14.792  -2.249  1.00 25.00           C
ATOM     10  CA  ASN    10       0.783 -18.350  -3.445  1.00 25.00           C
ATOM     11  CA  VAL    11      -1.199 -21.290  -2.062  1.00 25.00           C
ATOM     12  CA  LYS    12      -3.502 -24.298  -2.417  1.00 25.00           C
ATOM     13  CA  GLY    13      -4.958 -27.457  -3.834  1.00 25.00           C
ATOM     14  CA  PHE    14      -8.306 -26.382  -2.278  1.00 25.00           C
ATOM     15  CA  PHE    15      -6.620 -26.411   1.161  1.00 25.00           C
ATOM     16  CA  ASP    16      -4.622 -26.401   4.449  1.00 25.00           C
ATOM     17  CA  MET    17      -2.625 -23.739   2.666  1.00 25.00           C
ATOM     18  CA  ASP    18      -4.030 -20.633   4.475  1.00 25.00           C
ATOM     19  CA  VAL    19      -5.358 -19.303   1.131  1.00 25.00           C
ATOM     20  CA  MET    20      -4.086 -16.810  -1.360  1.00 25.00           C
ATOM     21  CA  GLU    21      -3.934 -15.498  -4.973  1.00 25.00           C
ATOM     22  CA  VAL    22      -0.974 -15.635  -7.356  1.00 25.00           C
ATOM     23  CA  THR    23      -1.981 -13.684 -10.462  1.00 25.00           C
ATOM     24  CA  GLU    24       0.388 -13.874 -13.359  1.00 25.00           C
ATOM     25  CA  GLN    25      -0.085 -11.858 -16.527  1.00 25.00           C
ATOM     26  CA  THR    26      -3.807 -12.648 -16.079  1.00 25.00           C
ATOM     27  CA  LYS    27      -4.228  -8.892 -15.518  1.00 25.00           C
ATOM     28  CA  GLU    28      -2.844  -6.123 -13.208  1.00 25.00           C
ATOM     29  CA  ALA    29       0.897  -6.701 -13.660  1.00 25.00           C
ATOM     30  CA  GLU    30       3.521  -7.930 -11.194  1.00 25.00           C
ATOM     31  CA  TYR    31       5.680  -7.912  -8.030  1.00 25.00           C
ATOM     32  CA  THR    32       2.535  -7.678  -5.856  1.00 25.00           C
ATOM     33  CA  TYR    33       0.976 -10.617  -7.753  1.00 25.00           C
ATOM     34  CA  ASP    34      -2.259  -9.486  -6.150  1.00 25.00           C
ATOM     35  CA  PHE    35      -1.681  -7.470  -2.959  1.00 25.00           C
ATOM     36  CA  LYS    36      -4.246  -4.661  -2.507  1.00 25.00           C
ATOM     37  CA  GLU    37      -6.625  -6.408  -4.947  1.00 25.00           C
ATOM     38  CA  ILE    38      -6.217  -9.697  -3.028  1.00 25.00           C
ATOM     39  CA  LEU    39      -6.961  -7.895   0.267  1.00 25.00           C
ATOM     40  CA  SER    40     -10.093  -6.318  -1.272  1.00 25.00           C
ATOM     41  CA  GLU    41     -11.244  -9.755  -2.511  1.00 25.00           C
ATOM     42  CA  PHE    42     -10.695 -11.226   0.983  1.00 25.00           C
ATOM     43  CA  ASN    43     -14.028  -9.691   1.931  1.00 25.00           C
ATOM     44  CA  GLY    44     -12.158  -7.996   4.800  1.00 25.00           C
ATOM     45  CA  LYS    45      -8.400  -8.024   5.642  1.00 25.00           C
ATOM     46  CA  ASN    46      -7.989 -11.810   5.153  1.00 25.00           C
ATOM     47  CA  VAL    47      -5.678 -12.564   2.215  1.00 25.00           C
ATOM     48  CA  SER    48      -3.053 -14.894   3.780  1.00 25.00           C
ATOM     49  CA  ILE    49      -0.500 -17.285   2.286  1.00 25.00           C
ATOM     50  CA  THR    50       2.802 -18.926   1.325  1.00 25.00           C
ATOM     51  CA  VAL    51       5.711 -18.486  -1.040  1.00 25.00           C
ATOM     52  CA  LYS    52       5.545 -17.335  -4.620  1.00 25.00           C
ATOM     53  CA  GLU    53       9.229 -18.187  -4.876  1.00 25.00           C
ATOM     54  CA  GLU    54      10.606 -21.679  -4.510  1.00 25.00           C
ATOM     55  CA  ASN    55      13.900 -20.085  -5.687  1.00 25.00           C
ATOM     56  CA  GLU    56      14.408 -19.385  -1.947  1.00 25.00           C
ATOM     57  CA  LEU    57      12.241 -16.331  -1.281  1.00 25.00           C
ATOM     58  CA  PRO    58      13.616 -14.667  -4.447  1.00 25.00           C
ATOM     59  CA  VAL    59      10.697 -13.331  -6.499  1.00 25.00           C
ATOM     60  CA  LYS    60      10.967 -10.311  -4.247  1.00 25.00           C
ATOM     61  CA  GLY    61       7.535 -10.160  -2.503  1.00 25.00           C
ATOM     62  CA  VAL    62       7.808 -13.878  -1.781  1.00 25.00           C
ATOM     63  CA  GLU    63       5.685 -13.143   1.295  1.00 25.00           C
ATOM     64  CA  MET    64       3.597 -14.651   4.162  1.00 25.00           C
ATOM     65  CA  ALA    65       1.141 -11.752   4.441  1.00 25.00           C
ATOM     66  CA  GLY    66      -0.015 -12.216   8.016  1.00 25.00           C
ATOM     67  CA  ASP    67       3.088 -11.068   9.866  1.00 25.00           C
ATOM     68  CA  PRO    68       3.980 -11.758  13.485  1.00 25.00           C
ATOM     69  CA  LEU    69       7.626 -10.758  13.590  1.00 25.00           C
ATOM     70  CA  GLU    70       8.985  -9.884  17.044  1.00 25.00           C
ATOM     71  CA  HIS    71       7.150  -8.992  20.222  1.00 25.00           C
ATOM     72  CA  HIS    72       7.235  -5.372  21.538  1.00 25.00           C
ATOM     73  CA  HIS    73      10.185  -3.198  20.572  1.00 25.00           C
ATOM     74  CA  HIS    74      13.746  -4.325  19.672  1.00 25.00           C
ATOM     75  CA  HIS    75      17.500  -5.103  19.372  1.00 25.00           C
ATOM     76  CA  HIS    76      16.869  -7.118  16.243  1.00 25.00           C
TER
END
