
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS168_1.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       2           -
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    M       1      K       5          3.006
LGA    A       2      V       6          3.308
LGA    S       3      H       7          4.350
LGA    K       4      Q       8          1.935
LGA    K       5      I       9          2.759
LGA    V       6      N      10          1.877
LGA    H       7      V      11          1.955
LGA    Q       8      K      12          1.669
LGA    I       9      G      13          1.478
LGA    N      10      F      14          3.637
LGA    V      11      F      15          2.839
LGA    K      12      D      16          4.322
LGA    G      13      M      17           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      D      18          3.762
LGA    M      17      V      19           #
LGA    D      18      M      20           #
LGA    V      19      E      21           #
LGA    M      20      V      22           #
LGA    E      21      T      23           #
LGA    V      22      E      24          5.175
LGA    T      23      Q      25          2.737
LGA    E      24      T      26          3.428
LGA    Q      25      K      27          2.374
LGA    T      26      E      28          2.724
LGA    K      27      A      29          3.883
LGA    E      28      -       -           -
LGA    A      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      E      30           #
LGA    D      34      Y      31          3.748
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      T      32          1.504
LGA    I      38      Y      33          1.415
LGA    L      39      D      34          2.762
LGA    S      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      F      35          3.647
LGA    N      43      K      36          4.109
LGA    G      44      E      37          1.002
LGA    K      45      I      38          2.789
LGA    N      46      L      39          4.266
LGA    V      47      S      40           -
LGA    S      48      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    I      49      T      50           #
LGA    T      50      V      51           #
LGA    V      51      K      52          4.593
LGA    K      52      E      53          4.364
LGA    E      53      E      54          1.036
LGA    E      54      N      55          3.426
LGA    N      55      E      56          3.464
LGA    E      56      L      57           -
LGA    L      57      P      58           -
LGA    P      58      V      59           -
LGA    V      59      K      60           -
LGA    K      60      G      61           -
LGA    G      61      V      62           -
LGA    V      62      E      63           -
LGA    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     33    3.20     9.09     32.468     0.999

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.170431 * X  +  -0.111905 * Y  +   0.978995 * Z  +   1.619017
  Y_new =   0.509308 * X  +  -0.860530 * Y  +  -0.009699 * Z  + -14.575653
  Z_new =   0.843539 * X  +   0.496957 * Y  +   0.203655 * Z  +  -6.101893 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.181866   -1.959727  [ DEG:    67.7159   -112.2841 ]
  Theta =  -1.003840   -2.137753  [ DEG:   -57.5158   -122.4842 ]
  Phi   =   1.893716   -1.247876  [ DEG:   108.5020    -71.4980 ]
 
# 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_1                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS168_1.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   33   3.20    9.09  32.468
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS168_1
PFRMAT TS
TARGET T0309
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1     -16.732 -22.490   1.739  1.00 25.00           C
ATOM      2  CA  ALA     2     -13.925 -25.033   1.619  1.00 25.00           C
ATOM      3  CA  SER     3     -11.236 -23.424  -0.520  1.00 25.00           C
ATOM      4  CA  LYS     4      -8.692 -20.950  -1.789  1.00 25.00           C
ATOM      5  CA  LYS     5      -5.690 -19.469  -3.574  1.00 25.00           C
ATOM      6  CA  VAL     6      -2.295 -19.248  -5.390  1.00 25.00           C
ATOM      7  CA  HIS     7      -2.276 -15.436  -5.805  1.00 25.00           C
ATOM      8  CA  GLN     8       0.210 -15.834  -8.610  1.00 25.00           C
ATOM      9  CA  ILE     9       2.268 -13.456 -10.768  1.00 25.00           C
ATOM     10  CA  ASN    10       3.073  -9.870  -9.813  1.00 25.00           C
ATOM     11  CA  VAL    11       5.196  -6.687  -9.841  1.00 25.00           C
ATOM     12  CA  LYS    12       8.279  -5.956 -11.830  1.00 25.00           C
ATOM     13  CA  GLY    13      11.886  -4.931 -11.997  1.00 25.00           C
ATOM     14  CA  PHE    14      12.147  -1.305 -10.936  1.00 25.00           C
ATOM     15  CA  PHE    15       8.455  -0.869 -11.730  1.00 25.00           C
ATOM     16  CA  ASP    16       8.282   0.399  -8.137  1.00 25.00           C
ATOM     17  CA  MET    17       9.100  -3.108  -6.964  1.00 25.00           C
ATOM     18  CA  ASP    18       7.468  -5.991  -5.097  1.00 25.00           C
ATOM     19  CA  VAL    19       8.288  -9.341  -6.616  1.00 25.00           C
ATOM     20  CA  MET    20       7.932 -11.077  -9.963  1.00 25.00           C
ATOM     21  CA  GLU    21       6.854 -13.356 -12.772  1.00 25.00           C
ATOM     22  CA  VAL    22       5.449 -16.922 -12.989  1.00 25.00           C
ATOM     23  CA  THR    23       4.280 -15.761 -16.479  1.00 25.00           C
ATOM     24  CA  GLU    24       3.470 -15.411 -20.220  1.00 25.00           C
ATOM     25  CA  GLN    25       1.110 -18.203 -21.372  1.00 25.00           C
ATOM     26  CA  THR    26      -1.114 -15.488 -22.782  1.00 25.00           C
ATOM     27  CA  LYS    27      -4.833 -15.264 -21.985  1.00 25.00           C
ATOM     28  CA  GLU    28      -4.389 -18.981 -21.185  1.00 25.00           C
ATOM     29  CA  ALA    29      -6.933 -18.817 -18.368  1.00 25.00           C
ATOM     30  CA  GLU    30      -4.767 -19.427 -15.256  1.00 25.00           C
ATOM     31  CA  TYR    31      -4.071 -18.948 -11.520  1.00 25.00           C
ATOM     32  CA  THR    32      -0.339 -19.573 -12.111  1.00 25.00           C
ATOM     33  CA  TYR    33      -0.336 -17.014 -14.959  1.00 25.00           C
ATOM     34  CA  ASP    34      -3.130 -14.537 -15.758  1.00 25.00           C
ATOM     35  CA  PHE    35      -3.272 -13.147 -12.223  1.00 25.00           C
ATOM     36  CA  LYS    36      -0.696 -10.510 -13.265  1.00 25.00           C
ATOM     37  CA  GLU    37      -3.515  -8.119 -14.269  1.00 25.00           C
ATOM     38  CA  ILE    38      -5.229  -8.681 -10.891  1.00 25.00           C
ATOM     39  CA  LEU    39      -1.935  -7.974  -9.073  1.00 25.00           C
ATOM     40  CA  SER    40      -1.482  -4.753 -11.094  1.00 25.00           C
ATOM     41  CA  GLU    41      -5.053  -3.676 -10.225  1.00 25.00           C
ATOM     42  CA  PHE    42      -4.384  -4.366  -6.517  1.00 25.00           C
ATOM     43  CA  ASN    43      -7.375  -2.240  -5.712  1.00 25.00           C
ATOM     44  CA  GLY    44      -8.934  -5.448  -4.502  1.00 25.00           C
ATOM     45  CA  LYS    45      -6.091  -7.284  -2.761  1.00 25.00           C
ATOM     46  CA  ASN    46      -2.554  -6.033  -2.126  1.00 25.00           C
ATOM     47  CA  VAL    47       0.276  -5.370  -4.505  1.00 25.00           C
ATOM     48  CA  SER    48       2.638  -8.354  -5.061  1.00 25.00           C
ATOM     49  CA  ILE    49       1.285 -11.905  -5.532  1.00 25.00           C
ATOM     50  CA  THR    50       4.881 -12.998  -6.355  1.00 25.00           C
ATOM     51  CA  VAL    51       7.392 -15.813  -6.214  1.00 25.00           C
ATOM     52  CA  LYS    52       9.081 -17.637  -9.167  1.00 25.00           C
ATOM     53  CA  GLU    53      10.926 -19.494  -6.364  1.00 25.00           C
ATOM     54  CA  GLU    54      13.737 -21.960  -6.110  1.00 25.00           C
ATOM     55  CA  ASN    55      14.219 -23.454  -9.623  1.00 25.00           C
ATOM     56  CA  GLU    56      11.456 -25.468 -11.286  1.00 25.00           C
ATOM     57  CA  LEU    57       9.371 -24.162  -8.383  1.00 25.00           C
ATOM     58  CA  PRO    58       8.601 -26.225  -5.352  1.00 25.00           C
ATOM     59  CA  VAL    59       7.840 -22.937  -3.640  1.00 25.00           C
ATOM     60  CA  LYS    60       4.220 -24.186  -3.751  1.00 25.00           C
ATOM     61  CA  GLY    61       1.877 -22.742  -6.403  1.00 25.00           C
ATOM     62  CA  VAL    62       3.543 -19.631  -7.967  1.00 25.00           C
ATOM     63  CA  GLU    63       2.780 -17.848  -4.685  1.00 25.00           C
ATOM     64  CA  MET    64       4.069 -15.073  -2.422  1.00 25.00           C
ATOM     65  CA  ALA    65       1.392 -12.920  -0.839  1.00 25.00           C
ATOM     66  CA  GLY    66       4.026 -12.036   1.779  1.00 25.00           C
ATOM     67  CA  ASP    67       1.027 -11.349   3.990  1.00 25.00           C
ATOM     68  CA  PRO    68      -0.091 -13.687   6.797  1.00 25.00           C
ATOM     69  CA  LEU    69       2.323 -14.305   9.734  1.00 25.00           C
ATOM     70  CA  GLU    70       0.662 -16.180  12.643  1.00 25.00           C
ATOM     71  CA  HIS    71      -1.480 -18.086  15.158  1.00 25.00           C
ATOM     72  CA  HIS    72       0.329 -21.458  14.799  1.00 25.00           C
ATOM     73  CA  HIS    73       3.976 -22.413  15.304  1.00 25.00           C
ATOM     74  CA  HIS    74       7.618 -22.433  16.424  1.00 25.00           C
ATOM     75  CA  HIS    75       8.133 -26.013  15.344  1.00 25.00           C
ATOM     76  CA  HIS    76       4.766 -27.740  14.765  1.00 25.00           C
TER
END
