
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS599_3.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    M       1      D       9          3.807
LGA    R       2      A      10           #
LGA    E       3      V      11           #
LGA    L       4      -       -           -
LGA    L       5      -       -           -
LGA    R       6      -       -           -
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      -       -           -
LGA    V      11      -       -           -
LGA    L      12      L      12          3.661
LGA    L      13      L      13          2.327
LGA    S      14      S      14          2.209
LGA    A      15      A      15          2.103
LGA    V      16      V      16          1.572
LGA    G      17      G      17          0.840
LGA    A      18      A      18          1.248
LGA    L      19      L      19          0.810
LGA    L      20      L      20          0.677
LGA    D      21      D      21          1.067
LGA    G      22      G      22          1.189
LGA    A      23      A      23          1.191
LGA    D      24      D      24          1.380
LGA    I      25      I      25          1.073
LGA    G      26      G      26          1.545
LGA    H      27      H      27          2.467
LGA    L      28      L      28          3.343
LGA    V      29      -       -           -
LGA    L      30      -       -           -
LGA    D      31      -       -           -
LGA    Q      32      -       -           -
LGA    N      33      -       -           -
LGA    M      34      -       -           -
LGA    S      35      -       -           -
LGA    I      36      V      29           #
LGA    L      37      L      30           #
LGA    E      38      D      31          3.160
LGA    G      39      Q      32          4.874
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           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      I      44           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    S      40      V      48           #
LGA    L      41      L      49          5.553
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    I      44      -       -           -
LGA    P      45      -       -           -
LGA    R      46      V      50           #
LGA    R      47      -       -           -
LGA    V      48      H      51          2.330
LGA    L      49      E      52          4.276
LGA    V      50      D      53           -
LGA    H      51      D      54           -
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      L      55          2.881
LGA    L      62      A      56          3.352
LGA    T      63      -       -           -
LGA    D      64      -       -           -
LGA    A      65      G      57          1.811
LGA    G      66      A      58          3.473
LGA    L      67      R      59          2.202
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    A      68      L      62          3.299
LGA    H      69      T      63          2.307
LGA    E      70      D      64          5.042
LGA    L      71      A      65           #
LGA    R      72      G      66          3.095
LGA    S      73      L      67          4.017
LGA    D      74      -       -           -
LGA    D      75      A      68          4.860
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    2.94    55.88     30.724     1.118

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.402180 * X  +   0.890374 * Y  +   0.213271 * Z  +   1.416521
  Y_new =  -0.126409 * X  +  -0.284710 * Y  +   0.950243 * Z  +   4.470840
  Z_new =   0.906792 * X  +   0.355209 * Y  +   0.227056 * Z  +   2.529123 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.002038   -2.139555  [ DEG:    57.4126   -122.5874 ]
  Theta =  -1.135611   -2.005981  [ DEG:   -65.0657   -114.9343 ]
  Phi   =  -2.837059    0.304533  [ DEG:  -162.5515     17.4485 ]
 
# 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_3                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_3.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   2.94   55.88  30.724
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_3
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.951  -5.965   8.187  1.00  0.00              
ATOM      2  CA  ARG     2      -1.743  -8.544  10.167  1.00  0.00              
ATOM      3  CA  GLU     3      -2.059 -11.094  12.680  1.00  0.00              
ATOM      4  CA  LEU     4      -0.227  -8.158  11.729  1.00  0.00              
ATOM      5  CA  LEU     5      -1.875  -5.785  14.270  1.00  0.00              
ATOM      6  CA  ARG     6      -1.569  -8.211  17.125  1.00  0.00              
ATOM      7  CA  THR     7       2.058  -9.066  16.691  1.00  0.00              
ATOM      8  CA  ASN     8       3.396  -5.568  15.896  1.00  0.00              
ATOM      9  CA  ASP     9       4.490  -6.710  12.421  1.00  0.00              
ATOM     10  CA  ALA    10       2.961  -4.045  10.141  1.00  0.00              
ATOM     11  CA  VAL    11       0.133  -5.287   7.892  1.00  0.00              
ATOM     12  CA  LEU    12       0.010  -2.975   5.060  1.00  0.00              
ATOM     13  CA  LEU    13      -3.062  -1.760   3.235  1.00  0.00              
ATOM     14  CA  SER    14      -5.143  -1.400   6.426  1.00  0.00              
ATOM     15  CA  ALA    15      -2.433   0.130   8.556  1.00  0.00              
ATOM     16  CA  VAL    16      -1.561   2.685   5.965  1.00  0.00              
ATOM     17  CA  GLY    17      -5.115   3.786   5.482  1.00  0.00              
ATOM     18  CA  ALA    18      -5.791   4.236   9.149  1.00  0.00              
ATOM     19  CA  LEU    19      -2.621   6.288   9.719  1.00  0.00              
ATOM     20  CA  LEU    20      -3.273   8.579   6.797  1.00  0.00              
ATOM     21  CA  ASP    21      -6.941   9.160   7.798  1.00  0.00              
ATOM     22  CA  GLY    22      -5.973   9.983  11.341  1.00  0.00              
ATOM     23  CA  ALA    23      -3.496  12.644  10.337  1.00  0.00              
ATOM     24  CA  ASP    24      -5.829  14.102   7.632  1.00  0.00              
ATOM     25  CA  ILE    25      -3.255  13.481   4.946  1.00  0.00              
ATOM     26  CA  GLY    26      -4.381  11.969   1.677  1.00  0.00              
ATOM     27  CA  HIS    27      -1.148  10.458   0.392  1.00  0.00              
ATOM     28  CA  LEU    28      -1.198   8.228  -2.648  1.00  0.00              
ATOM     29  CA  VAL    29       1.880   6.280  -3.572  1.00  0.00              
ATOM     30  CA  LEU    30       2.262   4.659  -6.931  1.00  0.00              
ATOM     31  CA  ASP    31       5.367   2.383  -7.123  1.00  0.00              
ATOM     32  CA  GLN    32       4.890   0.011 -10.004  1.00  0.00              
ATOM     33  CA  ASN    33       4.059  -3.033  -7.961  1.00  0.00              
ATOM     34  CA  MET    34       1.966  -1.602  -5.201  1.00  0.00              
ATOM     35  CA  SER    35      -1.412  -3.304  -5.732  1.00  0.00              
ATOM     36  CA  ILE    36      -2.733  -3.408  -2.111  1.00  0.00              
ATOM     37  CA  LEU    37      -1.399   0.089  -1.402  1.00  0.00              
ATOM     38  CA  GLU    38      -3.126   1.526  -4.524  1.00  0.00              
ATOM     39  CA  GLY    39      -6.693   0.581  -3.585  1.00  0.00              
ATOM     40  CA  SER    40      -6.331   2.353  -0.188  1.00  0.00              
ATOM     41  CA  LEU    41      -4.540   5.427  -1.596  1.00  0.00              
ATOM     42  CA  GLY    42      -7.209   6.099  -4.253  1.00  0.00              
ATOM     43  CA  VAL    43      -9.694   6.975  -1.472  1.00  0.00              
ATOM     44  CA  ILE    44      -7.181   9.669  -0.371  1.00  0.00              
ATOM     45  CA  PRO    45      -5.574  11.247  -3.501  1.00  0.00              
ATOM     46  CA  ARG    46      -4.408  14.555  -2.024  1.00  0.00              
ATOM     47  CA  ARG    47      -0.705  14.212  -2.405  1.00  0.00              
ATOM     48  CA  VAL    48       0.525  11.823  -5.001  1.00  0.00              
ATOM     49  CA  LEU    49       4.006  10.271  -4.639  1.00  0.00              
ATOM     50  CA  VAL    50       5.502   8.361  -7.382  1.00  0.00              
ATOM     51  CA  HIS    51       5.725   6.347 -10.522  1.00  0.00              
ATOM     52  CA  GLU    52       7.947   3.316 -10.318  1.00  0.00              
ATOM     53  CA  ASP    53      10.649   4.764 -12.642  1.00  0.00              
ATOM     54  CA  ASP    54      10.791   7.847 -10.428  1.00  0.00              
ATOM     55  CA  LEU    55      11.107   5.859  -7.177  1.00  0.00              
ATOM     56  CA  ALA    56      13.831   8.141  -5.710  1.00  0.00              
ATOM     57  CA  GLY    57      11.427  11.126  -6.227  1.00  0.00              
ATOM     58  CA  ALA    58       8.580   9.146  -4.614  1.00  0.00              
ATOM     59  CA  ARG    59      10.731   8.491  -1.517  1.00  0.00              
ATOM     60  CA  ARG    60      11.436  12.221  -1.281  1.00  0.00              
ATOM     61  CA  LEU    61       7.721  13.053  -1.532  1.00  0.00              
ATOM     62  CA  LEU    62       6.857  10.499   1.217  1.00  0.00              
ATOM     63  CA  THR    63       9.557  11.919   3.408  1.00  0.00              
ATOM     64  CA  ASP    64       8.344  15.462   2.937  1.00  0.00              
ATOM     65  CA  ALA    65       4.795  14.371   3.818  1.00  0.00              
ATOM     66  CA  GLY    66       5.771  12.534   7.028  1.00  0.00              
ATOM     67  CA  LEU    67       4.771   9.059   6.006  1.00  0.00              
ATOM     68  CA  ALA    68       7.432   6.614   7.222  1.00  0.00              
ATOM     69  CA  HIS    69       7.458   7.909  10.758  1.00  0.00              
ATOM     70  CA  GLU    70       3.728   7.753  11.092  1.00  0.00              
ATOM     71  CA  LEU    71       3.265   4.260   9.633  1.00  0.00              
ATOM     72  CA  ARG    72       6.200   2.826  11.546  1.00  0.00              
ATOM     73  CA  SER    73       5.630   3.925  15.138  1.00  0.00              
ATOM     74  CA  ASP    74       7.059   2.590  11.406  1.00  0.00              
ATOM     75  CA  ASP    75       5.572  -1.053  12.350  1.00  0.00              
TER                                                                             
END
