
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0349TS599_5
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS599_5.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    L       5      L       5           -
LGA    R       6      -       -           -
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    D       9      R       6           #
LGA    A      10      T       7          1.716
LGA    V      11      N       8          2.084
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    L      12      L      12          3.402
LGA    L      13      L      13          2.801
LGA    S      14      S      14          1.489
LGA    A      15      A      15          1.826
LGA    V      16      V      16          2.181
LGA    G      17      G      17          1.453
LGA    A      18      A      18          1.012
LGA    L      19      L      19          1.534
LGA    L      20      L      20          1.137
LGA    D      21      D      21          1.386
LGA    G      22      G      22          1.957
LGA    A      23      A      23          2.565
LGA    D      24      D      24          2.421
LGA    I      25      I      25          1.380
LGA    G      26      G      26          2.091
LGA    H      27      H      27          2.419
LGA    L      28      L      28          2.978
LGA    V      29      -       -           -
LGA    L      30      -       -           -
LGA    D      31      -       -           -
LGA    Q      32      -       -           -
LGA    N      33      -       -           -
LGA    M      34      -       -           -
LGA    S      35      -       -           -
LGA    I      36      -       -           -
LGA    L      37      -       -           -
LGA    E      38      -       -           -
LGA    G      39      -       -           -
LGA    S      40      -       -           -
LGA    L      41      V      29          1.716
LGA    G      42      L      30          1.364
LGA    V      43      D      31           -
LGA    I      44      Q      32           -
LGA    P      45      N      33           -
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      I      44           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    R      46      V      50           #
LGA    R      47      H      51          3.977
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    L      55      -       -           -
LGA    A      56      -       -           -
LGA    G      57      -       -           -
LGA    A      58      -       -           -
LGA    R      59      -       -           -
LGA    R      60      -       -           -
LGA    L      61      E      52          2.217
LGA    L      62      -       -           -
LGA    T      63      D      53           #
LGA    D      64      D      54          4.974
LGA    A      65      L      55          3.569
LGA    -       -      A      56           -
LGA    G      66      G      57          1.964
LGA    L      67      A      58          1.436
LGA    A      68      R      59          0.927
LGA    H      69      R      60          1.003
LGA    E      70      L      61          2.369
LGA    L      71      L      62          2.793
LGA    R      72      T      63          2.117
LGA    S      73      D      64          1.660
LGA    D      74      -       -           -
LGA    D      75      A      65          2.491
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     34    2.30    58.82     33.515     1.414

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.774036 * X  +   0.584228 * Y  +  -0.244020 * Z  +   0.236113
  Y_new =   0.375387 * X  +  -0.733833 * Y  +  -0.566192 * Z  +   3.083807
  Z_new =  -0.509855 * X  +   0.346651 * Y  +  -0.787325 * Z  +   0.756373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.726843   -0.414749  [ DEG:   156.2366    -23.7634 ]
  Theta =   0.535016    2.606576  [ DEG:    30.6542    149.3458 ]
  Phi   =   0.451554   -2.690038  [ DEG:    25.8722   -154.1278 ]
 
# 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: T0349TS599_5                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_5.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   75   5.0   34   2.30   58.82  33.515
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_5
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -4.123  -9.700   7.117  1.00  0.00              
ATOM      2  CA  ARG     2      -2.496  -9.806   3.633  1.00  0.00              
ATOM      3  CA  GLU     3      -4.150 -13.129   5.607  1.00  0.00              
ATOM      4  CA  LEU     4      -1.738 -10.849   3.932  1.00  0.00              
ATOM      5  CA  LEU     5       1.303 -12.164   5.873  1.00  0.00              
ATOM      6  CA  ARG     6       0.360 -15.752   5.102  1.00  0.00              
ATOM      7  CA  THR     7      -0.090 -15.258   1.364  1.00  0.00              
ATOM      8  CA  ASN     8       2.901 -12.941   0.762  1.00  0.00              
ATOM      9  CA  ASP     9       0.942 -10.307  -1.166  1.00  0.00              
ATOM     10  CA  ALA    10       1.203  -7.102   0.945  1.00  0.00              
ATOM     11  CA  VAL    11      -2.137  -5.758   1.982  1.00  0.00              
ATOM     12  CA  LEU    12      -3.477  -4.244   5.229  1.00  0.00              
ATOM     13  CA  LEU    13      -6.377  -1.970   4.197  1.00  0.00              
ATOM     14  CA  SER    14      -7.593  -0.938   7.653  1.00  0.00              
ATOM     15  CA  ALA    15      -4.142  -0.420   9.133  1.00  0.00              
ATOM     16  CA  VAL    16      -3.065   1.722   6.216  1.00  0.00              
ATOM     17  CA  GLY    17      -6.335   3.706   6.149  1.00  0.00              
ATOM     18  CA  ALA    18      -6.299   4.431   9.819  1.00  0.00              
ATOM     19  CA  LEU    19      -2.686   5.498   9.931  1.00  0.00              
ATOM     20  CA  LEU    20      -3.031   7.824   7.003  1.00  0.00              
ATOM     21  CA  ASP    21      -6.130   9.503   8.341  1.00  0.00              
ATOM     22  CA  GLY    22      -4.681  10.148  11.752  1.00  0.00              
ATOM     23  CA  ALA    23      -1.616  11.846  10.324  1.00  0.00              
ATOM     24  CA  ASP    24      -3.624  13.907   7.786  1.00  0.00              
ATOM     25  CA  ILE    25      -1.751  12.467   4.850  1.00  0.00              
ATOM     26  CA  GLY    26      -3.547  11.173   1.873  1.00  0.00              
ATOM     27  CA  HIS    27      -0.730   9.402  -0.098  1.00  0.00              
ATOM     28  CA  LEU    28      -1.175   5.903  -1.436  1.00  0.00              
ATOM     29  CA  VAL    29       1.598   4.030  -3.115  1.00  0.00              
ATOM     30  CA  LEU    30       0.697   0.871  -4.778  1.00  0.00              
ATOM     31  CA  ASP    31       3.385  -1.194  -6.592  1.00  0.00              
ATOM     32  CA  GLN    32       1.858  -2.478  -9.824  1.00  0.00              
ATOM     33  CA  ASN    33       1.632  -6.147  -8.714  1.00  0.00              
ATOM     34  CA  MET    34       0.559  -5.654  -5.105  1.00  0.00              
ATOM     35  CA  SER    35      -2.688  -7.649  -4.926  1.00  0.00              
ATOM     36  CA  ILE    36      -4.175  -6.796  -1.528  1.00  0.00              
ATOM     37  CA  LEU    37      -2.630  -3.360  -1.888  1.00  0.00              
ATOM     38  CA  GLU    38      -4.452  -2.551  -5.065  1.00  0.00              
ATOM     39  CA  GLY    39      -7.895  -3.065  -3.616  1.00  0.00              
ATOM     40  CA  SER    40      -7.453  -1.641  -0.135  1.00  0.00              
ATOM     41  CA  LEU    41      -5.375   1.440  -0.799  1.00  0.00              
ATOM     42  CA  GLY    42      -7.888   2.403  -3.546  1.00  0.00              
ATOM     43  CA  VAL    43     -10.429   2.900  -0.691  1.00  0.00              
ATOM     44  CA  ILE    44      -8.117   5.421   1.031  1.00  0.00              
ATOM     45  CA  PRO    45      -6.553   7.505  -1.740  1.00  0.00              
ATOM     46  CA  ARG    46      -5.955  11.210  -1.562  1.00  0.00              
ATOM     47  CA  ARG    47      -2.850  11.083  -3.863  1.00  0.00              
ATOM     48  CA  VAL    48      -2.461   7.657  -5.363  1.00  0.00              
ATOM     49  CA  LEU    49       0.644   6.486  -6.922  1.00  0.00              
ATOM     50  CA  VAL    50       0.505   3.212  -8.769  1.00  0.00              
ATOM     51  CA  HIS    51       2.564   1.523 -11.249  1.00  0.00              
ATOM     52  CA  GLU    52       5.816  -0.339 -10.848  1.00  0.00              
ATOM     53  CA  ASP    53       7.448   1.506 -13.744  1.00  0.00              
ATOM     54  CA  ASP    54       6.521   4.842 -12.192  1.00  0.00              
ATOM     55  CA  LEU    55       7.881   3.999  -8.728  1.00  0.00              
ATOM     56  CA  ALA    56      10.252   6.982  -8.668  1.00  0.00              
ATOM     57  CA  GLY    57       7.467   9.422  -9.506  1.00  0.00              
ATOM     58  CA  ALA    58       5.241   7.994  -6.767  1.00  0.00              
ATOM     59  CA  ARG    59       8.003   8.239  -4.200  1.00  0.00              
ATOM     60  CA  ARG    60       8.648  11.819  -5.232  1.00  0.00              
ATOM     61  CA  LEU    61       5.004  12.794  -4.623  1.00  0.00              
ATOM     62  CA  LEU    62       5.017  11.173  -1.194  1.00  0.00              
ATOM     63  CA  THR    63       8.330  12.948  -0.302  1.00  0.00              
ATOM     64  CA  ASP    64       7.043  16.309  -1.446  1.00  0.00              
ATOM     65  CA  ALA    65       4.004  15.932   0.705  1.00  0.00              
ATOM     66  CA  GLY    66       6.026  14.941   3.779  1.00  0.00              
ATOM     67  CA  LEU    67       4.366  11.634   4.257  1.00  0.00              
ATOM     68  CA  ALA    68       7.040   9.317   5.506  1.00  0.00              
ATOM     69  CA  HIS    69       8.331  11.485   8.264  1.00  0.00              
ATOM     70  CA  GLU    70       4.908  12.176   9.620  1.00  0.00              
ATOM     71  CA  LEU    71       3.544   8.591   9.589  1.00  0.00              
ATOM     72  CA  ARG    72       6.826   7.177  10.867  1.00  0.00              
ATOM     73  CA  SER    73       7.529   9.459  13.751  1.00  0.00              
ATOM     74  CA  ASP    74       6.717  12.208  15.920  1.00  0.00              
ATOM     75  CA  ASP    75       5.502   8.274  16.813  1.00  0.00              
TER                                                                             
END
