
#######################################################
#                                                     #
#                        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   83 (   83),  selected   83 , name T0353TS599_4-D1
# Molecule2: number of CA atoms   83 ( 1315),  selected   83 , name T0353_D1.pdb
# PARAMETERS: T0353TS599_4-D1.T0353_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    Q       2      Q       2           #
LGA    -       -      I       3           -
LGA    I       3      H       4          2.941
LGA    H       4      V       5          2.977
LGA    V       5      Y       6          3.684
LGA    Y       6      D       7          2.873
LGA    D       7      T       8           #
LGA    T       8      -       -           -
LGA    Y       9      Y       9          3.499
LGA    V      10      V      10          2.782
LGA    K      11      K      11          2.665
LGA    A      12      A      12          1.804
LGA    K      13      K      13          1.972
LGA    D      14      D      14          1.409
LGA    G      15      G      15          5.166
LGA    H      16      H      16          0.775
LGA    V      17      V      17          2.482
LGA    M      18      M      18          1.440
LGA    H      19      H      19          3.346
LGA    -       -      F      20           -
LGA    F      20      D      21          3.174
LGA    D      21      V      22          1.582
LGA    V      22      F      23          2.295
LGA    F      23      T      24          2.116
LGA    T      24      D      25          0.949
LGA    D      25      -       -           -
LGA    V      26      V      26          5.372
LGA    R      27      -       -           -
LGA    D      28      -       -           -
LGA    D      29      -       -           -
LGA    K      30      R      27           #
LGA    K      31      D      28           -
LGA    A      32      D      29           -
LGA    -       -      K      30           -
LGA    -       -      K      31           -
LGA    -       -      A      32           -
LGA    -       -      I      33           -
LGA    -       -      E      34           -
LGA    I      33      F      35           #
LGA    E      34      A      36           -
LGA    F      35      K      37           -
LGA    A      36      -       -           -
LGA    K      37      -       -           -
LGA    Q      38      -       -           -
LGA    W      39      -       -           -
LGA    L      40      -       -           -
LGA    S      41      -       -           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      Q      38           #
LGA    A      48      W      39           -
LGA    T      49      L      40           -
LGA    V      50      S      41          4.364
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      S      42          3.490
LGA    C      55      I      43          3.114
LGA    R      56      G      44          2.940
LGA    F      57      -       -           -
LGA    C      58      -       -           -
LGA    H      59      E      45          1.317
LGA    S      60      E      46          4.433
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      G      47          2.610
LGA    P      64      A      48          5.254
LGA    D      65      -       -           -
LGA    E      66      T      49          0.208
LGA    V      67      V      50          2.775
LGA    I      68      -       -           -
LGA    E      69      T      51          1.010
LGA    A      70      -       -           -
LGA    I      71      -       -           -
LGA    K      72      S      52          1.703
LGA    Q      73      E      53          1.736
LGA    N      74      E      54           #
LGA    G      75      C      55           #
LGA    Y      76      R      56          0.928
LGA    F      77      F      57          4.098
LGA    I      78      C      58           -
LGA    Y      79      H      59           -
LGA    -       -      S      60           -
LGA    -       -      E      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    K      80      Y      76          4.526
LGA    M      81      F      77          2.775
LGA    E      82      I      78           #
LGA    G      83      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   83   83    5.0     38    2.99    36.84     27.550     1.229

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.835815 * X  +   0.243799 * Y  +  -0.491910 * Z  +  -5.508498
  Y_new =   0.348327 * X  +   0.928048 * Y  +  -0.131893 * Z  +  -2.858149
  Z_new =   0.424361 * X  +  -0.281583 * Y  +  -0.860598 * Z  +  -0.153733 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.825377    0.316216  [ DEG:  -161.8822     18.1178 ]
  Theta =  -0.438256   -2.703337  [ DEG:   -25.1102   -154.8898 ]
  Phi   =   2.746729   -0.394863  [ DEG:   157.3760    -22.6240 ]
 
# 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: T0353TS599_4-D1                               
REMARK     2: T0353_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_4-D1.T0353_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   83   83   5.0   38   2.99   36.84  27.550
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_4-D1
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       4.371   4.441  -9.341  1.00  0.00              
ATOM      2  CA  GLN     2       5.328   4.999  -5.551  1.00  0.00              
ATOM      3  CA  ILE     3       3.765   3.421  -2.730  1.00  0.00              
ATOM      4  CA  HIS     4       3.285   5.559   0.786  1.00  0.00              
ATOM      5  CA  VAL     5       2.053   3.782   3.741  1.00  0.00              
ATOM      6  CA  TYR     6       0.142   5.391   6.526  1.00  0.00              
ATOM      7  CA  ASP     7      -0.557   3.301   9.670  1.00  0.00              
ATOM      8  CA  THR     8      -1.702   6.079  11.954  1.00  0.00              
ATOM      9  CA  TYR     9      -3.930   7.714   9.311  1.00  0.00              
ATOM     10  CA  VAL    10      -5.828   4.381   9.143  1.00  0.00              
ATOM     11  CA  LYS    11      -7.041   3.808  12.552  1.00  0.00              
ATOM     12  CA  ALA    12      -9.852   1.429  13.110  1.00  0.00              
ATOM     13  CA  LYS    13     -12.361   2.044  15.958  1.00  0.00              
ATOM     14  CA  ASP    14     -10.628  -0.506  18.152  1.00  0.00              
ATOM     15  CA  GLY    15      -7.213   1.158  17.869  1.00  0.00              
ATOM     16  CA  HIS    16      -5.637  -1.163  15.388  1.00  0.00              
ATOM     17  CA  VAL    17      -3.308   0.560  13.031  1.00  0.00              
ATOM     18  CA  MET    18      -3.380  -0.454   9.421  1.00  0.00              
ATOM     19  CA  HIS    19      -0.244  -0.172   7.409  1.00  0.00              
ATOM     20  CA  PHE    20      -0.393   0.091   3.570  1.00  0.00              
ATOM     21  CA  ASP    21       2.654  -0.671   1.547  1.00  0.00              
ATOM     22  CA  VAL    22       3.400   1.082  -1.576  1.00  0.00              
ATOM     23  CA  PHE    23       5.470  -0.786  -4.331  1.00  0.00              
ATOM     24  CA  THR    24       5.088   0.628  -7.779  1.00  0.00              
ATOM     25  CA  ASP    25       7.196  -0.447 -10.733  1.00  0.00              
ATOM     26  CA  VAL    26       4.837   0.340 -13.664  1.00  0.00              
ATOM     27  CA  ARG    27       5.208  -2.908 -15.675  1.00  0.00              
ATOM     28  CA  ASP    28       4.757  -4.994 -12.515  1.00  0.00              
ATOM     29  CA  ASP    29       1.753  -3.074 -11.148  1.00  0.00              
ATOM     30  CA  LYS    30      -0.401  -3.711 -14.160  1.00  0.00              
ATOM     31  CA  LYS    31       0.404  -7.429 -13.970  1.00  0.00              
ATOM     32  CA  ALA    32      -0.416  -7.665 -10.220  1.00  0.00              
ATOM     33  CA  ILE    33      -3.744  -5.934 -10.606  1.00  0.00              
ATOM     34  CA  GLU    34      -4.652  -8.244 -13.452  1.00  0.00              
ATOM     35  CA  PHE    35      -3.736 -11.397 -11.627  1.00  0.00              
ATOM     36  CA  ALA    36      -5.717 -10.445  -8.579  1.00  0.00              
ATOM     37  CA  LYS    37      -8.779  -9.568 -10.641  1.00  0.00              
ATOM     38  CA  GLN    38      -8.536 -12.914 -12.500  1.00  0.00              
ATOM     39  CA  TRP    39      -8.214 -14.954  -9.303  1.00  0.00              
ATOM     40  CA  LEU    40     -11.098 -13.221  -7.622  1.00  0.00              
ATOM     41  CA  SER    41     -13.294 -13.741 -10.637  1.00  0.00              
ATOM     42  CA  SER    42     -12.426 -17.395 -10.894  1.00  0.00              
ATOM     43  CA  ILE    43     -13.324 -18.097  -7.315  1.00  0.00              
ATOM     44  CA  GLY    44     -16.683 -16.260  -7.549  1.00  0.00              
ATOM     45  CA  GLU    45     -15.608 -13.199  -5.644  1.00  0.00              
ATOM     46  CA  GLU    46     -16.564  -9.767  -6.799  1.00  0.00              
ATOM     47  CA  GLY    47     -13.648  -7.572  -5.765  1.00  0.00              
ATOM     48  CA  ALA    48     -15.809  -5.741  -3.205  1.00  0.00              
ATOM     49  CA  THR    49     -16.810  -8.759  -1.250  1.00  0.00              
ATOM     50  CA  VAL    50     -13.485 -10.380  -0.612  1.00  0.00              
ATOM     51  CA  THR    51     -13.404 -14.065   0.081  1.00  0.00              
ATOM     52  CA  SER    52     -12.059 -15.415   3.328  1.00  0.00              
ATOM     53  CA  GLU    53      -8.707 -16.543   1.841  1.00  0.00              
ATOM     54  CA  GLU    54      -7.941 -13.300   0.111  1.00  0.00              
ATOM     55  CA  CYS    55      -8.370 -10.007   1.848  1.00  0.00              
ATOM     56  CA  ARG    56     -11.670  -9.347   3.503  1.00  0.00              
ATOM     57  CA  PHE    57     -11.122 -12.275   5.876  1.00  0.00              
ATOM     58  CA  CYS    58      -8.252 -10.404   7.576  1.00  0.00              
ATOM     59  CA  HIS    59      -9.510  -6.834   7.150  1.00  0.00              
ATOM     60  CA  SER    60     -12.980  -7.172   8.665  1.00  0.00              
ATOM     61  CA  GLN    61     -12.688  -4.208  11.044  1.00  0.00              
ATOM     62  CA  LYS    62     -11.450  -1.535   8.711  1.00  0.00              
ATOM     63  CA  ALA    63     -13.669  -1.534   5.678  1.00  0.00              
ATOM     64  CA  PRO    64     -11.807  -0.780   2.426  1.00  0.00              
ATOM     65  CA  ASP    65     -13.771   2.351   1.601  1.00  0.00              
ATOM     66  CA  GLU    66     -13.282   3.880   5.009  1.00  0.00              
ATOM     67  CA  VAL    67      -9.588   3.260   5.089  1.00  0.00              
ATOM     68  CA  ILE    68      -8.970   4.785   1.656  1.00  0.00              
ATOM     69  CA  GLU    69     -10.990   7.861   2.465  1.00  0.00              
ATOM     70  CA  ALA    70      -9.163   8.518   5.751  1.00  0.00              
ATOM     71  CA  ILE    71      -5.785   8.095   4.028  1.00  0.00              
ATOM     72  CA  LYS    72      -6.722  10.488   1.218  1.00  0.00              
ATOM     73  CA  GLN    73      -7.910  13.201   3.588  1.00  0.00              
ATOM     74  CA  ASN    74      -4.684  12.960   5.631  1.00  0.00              
ATOM     75  CA  GLY    75      -2.353  13.083   2.621  1.00  0.00              
ATOM     76  CA  TYR    76      -1.287   9.395   2.768  1.00  0.00              
ATOM     77  CA  PHE    77      -1.354   7.089  -0.230  1.00  0.00              
ATOM     78  CA  ILE    78      -1.714   3.405   0.358  1.00  0.00              
ATOM     79  CA  TYR    79      -0.759   1.052  -2.292  1.00  0.00              
ATOM     80  CA  LYS    80      -0.733  -2.604  -1.563  1.00  0.00              
ATOM     81  CA  MET    81       1.414  -4.842  -3.709  1.00  0.00              
ATOM     82  CA  GLU    82       0.298  -8.464  -4.032  1.00  0.00              
ATOM     83  CA  GLY    83       3.271 -10.244  -4.983  1.00  0.00              
TER                                                                             
END
