
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0300AL316_3
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL316_3.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K       8      D       7           -
LGA    -       -      K       8           -
LGA    -       -      T       9           -
LGA    -       -      Y      10           -
LGA    -       -      E      11           -
LGA    -       -      E      12           -
LGA    -       -      M      13           -
LGA    -       -      V      14           -
LGA    -       -      K      15           -
LGA    -       -      E      16           -
LGA    -       -      V      17           -
LGA    -       -      E      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      E      23           -
LGA    -       -      N      24           -
LGA    -       -      K      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      Q      29           -
LGA    -       -      K      30           -
LGA    -       -      V      31           -
LGA    -       -      S      39           -
LGA    -       -      D      40           -
LGA    -       -      D      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    T       9      L      44          4.840
LGA    Y      10      T      45          2.415
LGA    E      11      A      46          2.156
LGA    E      12      A      47          2.402
LGA    -       -      K      48           -
LGA    M      13      R      49          1.108
LGA    V      14      E      50          0.810
LGA    K      15      S      51          0.529
LGA    E      16      I      52          1.036
LGA    V      17      I      53          0.833
LGA    E      18      V      54          1.179
LGA    R      19      S      55          1.671
LGA    L      20      S      56          1.876
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    K      21      A      59          3.013
LGA    L      22      L      60          3.088
LGA    E      23      -       -           -
LGA    N      24      -       -           -
LGA    K      25      -       -           -
LGA    T      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      -       -           -
LGA    Q      29      -       -           -
LGA    K      30      -       -           -
LGA    V      31      -       -           -
LGA    K      32      -       -           -
LGA    S      33      -       -           -
LGA    S      34      -       -           -
LGA    G      35      -       -           -
LGA    A      36      -       -           -
LGA    V      37      -       -           -
LGA    S      38      -       -           -
LGA    S      39      G      61          3.132
LGA    D      40      -       -           -
LGA    D      41      A      62          3.470
LGA    S      42      V      63          3.283
LGA    I      43      A      64          4.608
LGA    L      44      M      65          4.669
LGA    T      45      -       -           -
LGA    A      46      R      66          2.864
LGA    A      47      K      67          4.714
LGA    K      48      I      68          4.815
LGA    R      49      E      69          3.696
LGA    E      50      A      70          4.620
LGA    -       -      K      71           -
LGA    S      51      V      72          2.567
LGA    -       -      R      73           -
LGA    -       -      S      74           -
LGA    I      52      R      75          3.486
LGA    I      53      A      76          2.339
LGA    V      54      A      77          4.244
LGA    -       -      K      78           -
LGA    -       -      A      79           -
LGA    S      55      V      80          4.425
LGA    S      56      T      81           -
LGA    S      57      E      82           -
LGA    R      58      Q      83           -
LGA    A      59      E      84           -
LGA    L      60      L      85           -
LGA    G      61      T      86           -
LGA    A      62      -       -           -
LGA    V      63      -       -           -
LGA    A      64      -       -           -
LGA    M      65      -       -           -
LGA    R      66      -       -           -
LGA    K      67      -       -           -
LGA    I      68      S      87          3.119
LGA    E      69      L      88          2.749
LGA    A      70      -       -           -
LGA    K      71      -       -           -
LGA    V      72      -       -           -
LGA    R      73      -       -           -
LGA    S      74      L      89          3.108
LGA    R      75      Q      90           #
LGA    -       -      S      91           -
LGA    A      76      L      92          1.800
LGA    A      77      T      93          2.857
LGA    K      78      L      94          2.545
LGA    A      79      R      95           #
LGA    V      80      V      96          2.889
LGA    -       -      D      97           -
LGA    T      81      V      98           #
LGA    E      82      S      99           -
LGA    Q      83      M     100           -
LGA    E      84      E     101           -
LGA    L      85      E     102           -
LGA    T      86      -       -           -
LGA    S      87      -       -           -
LGA    L      88      -       -           -
LGA    L      89      -       -           -
LGA    Q      90      -       -           -
LGA    S      91      -       -           -
LGA    L      92      -       -           -
LGA    T      93      -       -           -
LGA    L      94      -       -           -
LGA    R      95      -       -           -
LGA    V      96      -       -           -
LGA    D      97      -       -           -
LGA    V      98      -       -           -
LGA    S      99      -       -           -
LGA    M     100      -       -           -
LGA    E     101      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   89    5.0     36    3.11     5.56     24.570     1.120

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.350163 * X  +  -0.665089 * Y  +   0.659578 * Z  + 104.983871
  Y_new =   0.669641 * X  +  -0.670112 * Y  +  -0.320205 * Z  + -40.207802
  Z_new =   0.654955 * X  +   0.329557 * Y  +   0.680019 * Z  + 106.912880 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.451275   -2.690318  [ DEG:    25.8562   -154.1438 ]
  Theta =  -0.714124   -2.427469  [ DEG:   -40.9163   -139.0837 ]
  Phi   =   2.052605   -1.088988  [ DEG:   117.6056    -62.3944 ]
 
# 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: T0300AL316_3                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL316_3.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   89   5.0   36   3.11    5.56  24.570
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL316_3
REMARK Aligment from pdb entry: 2ftc_E
ATOM      1  CA  LYS     8      52.463 -21.318 -12.572  1.00  0.00              
ATOM      2  CA  THR     9      53.254 -19.040 -15.598  1.00  0.00              
ATOM      3  CA  TYR    10      55.540 -16.264 -16.946  1.00  0.00              
ATOM      4  CA  GLU    11      55.664 -12.893 -15.093  1.00  0.00              
ATOM      5  CA  GLU    12      52.540 -10.976 -14.194  1.00  0.00              
ATOM      6  CA  MET    13      51.417 -14.426 -13.045  1.00  0.00              
ATOM      7  CA  VAL    14      51.540 -12.917  -9.561  1.00  0.00              
ATOM      8  CA  LYS    15      49.162 -10.180 -10.637  1.00  0.00              
ATOM      9  CA  GLU    16      46.793 -12.612 -12.357  1.00  0.00              
ATOM     10  CA  VAL    17      46.984 -14.665  -9.124  1.00  0.00              
ATOM     11  CA  GLU    18      46.632 -11.748  -6.692  1.00  0.00              
ATOM     12  CA  ARG    19      43.155 -10.851  -7.952  1.00  0.00              
ATOM     13  CA  LEU    20      40.375 -13.503  -7.976  1.00  0.00              
ATOM     14  CA  LYS    21      38.651 -13.172  -4.644  1.00  0.00              
ATOM     15  CA  LEU    22      39.569 -16.297  -2.498  1.00  0.00              
ATOM     16  CA  GLU    23      37.310 -18.707  -4.369  1.00  0.00              
ATOM     17  CA  ASN    24      38.555 -19.388  -7.859  1.00  0.00              
ATOM     18  CA  LYS    25      42.104 -28.493  -6.320  1.00  0.00              
ATOM     19  CA  THR    26      42.336 -28.944 -10.006  1.00  0.00              
ATOM     20  CA  LEU    27      46.064 -29.127 -10.137  1.00  0.00              
ATOM     21  CA  LYS    28      45.698 -31.473  -7.082  1.00  0.00              
ATOM     22  CA  GLN    29      43.074 -34.123  -7.752  1.00  0.00              
ATOM     23  CA  LYS    30      44.501 -34.769 -11.191  1.00  0.00              
ATOM     24  CA  VAL    31      47.775 -35.318 -13.023  1.00  0.00              
ATOM     25  CA  LYS    32      49.978 -36.150  -9.915  1.00  0.00              
ATOM     26  CA  SER    33      48.683 -17.546   2.188  1.00  0.00              
ATOM     27  CA  SER    34      47.766 -14.935  -0.412  1.00  0.00              
ATOM     28  CA  GLY    35      44.379 -16.599   0.113  1.00  0.00              
ATOM     29  CA  ALA    36      44.300 -15.457   3.727  1.00  0.00              
ATOM     30  CA  VAL    37      45.050 -11.758   3.208  1.00  0.00              
ATOM     31  CA  SER    38      42.323 -11.658   0.580  1.00  0.00              
ATOM     32  CA  SER    39      40.315 -13.660   3.218  1.00  0.00              
ATOM     33  CA  ASP    40      40.464 -10.471   5.403  1.00  0.00              
ATOM     34  CA  ASP    41      39.487  -8.367   2.747  1.00  0.00              
ATOM     35  CA  SER    42      36.034  -9.761   1.681  1.00  0.00              
ATOM     36  CA  ILE    43      34.961 -10.167   5.272  1.00  0.00              
ATOM     37  CA  LEU    44      34.827  -6.432   4.483  1.00  0.00              
ATOM     38  CA  THR    45      32.070  -5.410   2.071  1.00  0.00              
ATOM     39  CA  ALA    46      30.268  -8.536   3.276  1.00  0.00              
ATOM     40  CA  ALA    47      31.228 -11.270   0.904  1.00  0.00              
ATOM     41  CA  LYS    48      31.291 -13.760   3.755  1.00  0.00              
ATOM     42  CA  ARG    49      30.630 -13.046   7.437  1.00  0.00              
ATOM     43  CA  GLU    50      31.424 -14.512  10.813  1.00  0.00              
ATOM     44  CA  SER    51      29.788 -16.183  13.826  1.00  0.00              
ATOM     45  CA  ILE    52      29.665 -13.878  16.815  1.00  0.00              
ATOM     46  CA  ILE    53      28.450 -15.571  19.968  1.00  0.00              
ATOM     47  CA  VAL    54      27.527 -12.609  22.347  1.00  0.00              
ATOM     48  CA  SER    55      25.041 -14.002  24.843  1.00  0.00              
ATOM     49  CA  SER    56      26.484 -17.242  26.143  1.00  0.00              
ATOM     50  CA  SER    57      34.390 -25.865  13.440  1.00  0.00              
ATOM     51  CA  ARG    58      37.555 -24.413  15.089  1.00  0.00              
ATOM     52  CA  ALA    59      39.150 -27.843  15.820  1.00  0.00              
ATOM     53  CA  LEU    60      39.478 -26.354  19.227  1.00  0.00              
ATOM     54  CA  GLY    61      40.784 -28.027  22.323  1.00  0.00              
ATOM     55  CA  ALA    62      38.586 -27.880  25.417  1.00  0.00              
ATOM     56  CA  VAL    63      40.922 -25.507  27.307  1.00  0.00              
ATOM     57  CA  ALA    64      41.110 -22.755  24.665  1.00  0.00              
ATOM     58  CA  MET    65      37.543 -23.646  23.775  1.00  0.00              
ATOM     59  CA  ARG    66      36.862 -22.338  27.309  1.00  0.00              
ATOM     60  CA  LYS    67      38.035 -18.811  26.697  1.00  0.00              
ATOM     61  CA  ILE    68      36.434 -18.503  23.345  1.00  0.00              
ATOM     62  CA  GLU    69      32.894 -19.268  24.296  1.00  0.00              
ATOM     63  CA  ALA    70      33.534 -17.673  27.699  1.00  0.00              
ATOM     64  CA  LYS    71      34.866 -14.408  26.135  1.00  0.00              
ATOM     65  CA  VAL    72      31.724 -12.689  24.969  1.00  0.00              
ATOM     66  CA  ARG    73      31.070 -10.914  22.671  1.00  0.00              
ATOM     67  CA  SER    74      33.450 -12.986  20.564  1.00  0.00              
ATOM     68  CA  ARG    75      33.681 -14.720  17.261  1.00  0.00              
ATOM     69  CA  ALA    76      33.464 -18.486  16.913  1.00  0.00              
ATOM     70  CA  ALA    77      34.156 -19.463  13.320  1.00  0.00              
ATOM     71  CA  LYS    78      32.453 -18.781  10.204  1.00  0.00              
ATOM     72  CA  ALA    79      34.226 -16.943   7.451  1.00  0.00              
ATOM     73  CA  VAL    80      31.615 -18.164   5.053  1.00  0.00              
ATOM     74  CA  THR    81      28.604 -16.735   3.349  1.00  0.00              
ATOM     75  CA  GLU    82      24.964 -17.611   4.258  1.00  0.00              
ATOM     76  CA  GLN    83      24.884 -21.366   3.770  1.00  0.00              
ATOM     77  CA  GLU    84      27.129 -22.279   6.589  1.00  0.00              
ATOM     78  CA  LEU    85      26.741 -19.558   9.255  1.00  0.00              
ATOM     79  CA  THR    86      23.067 -20.332   8.960  1.00  0.00              
ATOM     80  CA  SER    87      23.765 -23.958   9.724  1.00  0.00              
ATOM     81  CA  LEU    88      25.605 -22.706  12.784  1.00  0.00              
ATOM     82  CA  LEU    89      23.264 -19.849  13.822  1.00  0.00              
ATOM     83  CA  GLN    90      21.046 -22.857  14.073  1.00  0.00              
ATOM     84  CA  SER    91      22.579 -25.753  16.105  1.00  0.00              
ATOM     85  CA  LEU    92      24.698 -23.143  17.891  1.00  0.00              
ATOM     86  CA  THR    93      21.362 -21.409  18.486  1.00  0.00              
ATOM     87  CA  LEU    94      21.686 -24.876  22.356  1.00  0.00              
ATOM     88  CA  ARG    95      20.861 -21.586  24.132  1.00  0.00              
ATOM     89  CA  VAL    96      23.401 -18.974  22.967  1.00  0.00              
ATOM     90  CA  ASP    97      21.893 -16.185  20.791  1.00  0.00              
ATOM     91  CA  VAL    98      24.248 -15.193  17.994  1.00  0.00              
ATOM     92  CA  SER    99      24.173 -12.847  14.986  1.00  0.00              
ATOM     93  CA  MET   100      25.271 -12.959  11.338  1.00  0.00              
ATOM     94  CA  GLU   101      26.771  -9.496  11.419  1.00  0.00              
END
