
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0299TS599_5-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS599_5-D1.T0299_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    T       2      T       2           -
LGA    R       3      -       -           -
LGA    Y       4      -       -           -
LGA    A       5      -       -           -
LGA    L       6      R       3           #
LGA    L       7      -       -           -
LGA    V       8      -       -           -
LGA    R       9      -       -           -
LGA    G      10      -       -           -
LGA    I      11      Y       4           #
LGA    N      12      A       5           -
LGA    V      13      L       6           -
LGA    G      14      L       7           -
LGA    G      15      V       8           -
LGA    K      16      R       9           -
LGA    N      17      G      10           -
LGA    K      18      I      11           -
LGA    V      19      N      12           -
LGA    V      20      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    M      21      V      20           #
LGA    A      22      M      21          6.675
LGA    E      23      -       -           -
LGA    L      24      -       -           -
LGA    R      25      A      22          0.856
LGA    Q      26      E      23          4.900
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    E      27      V      36           #
LGA    L      28      E      37           #
LGA    T      29      -       -           -
LGA    N      30      -       -           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      S      38          4.578
LGA    E      37      Y      39           -
LGA    S      38      I      40          3.714
LGA    Y      39      N      41          3.690
LGA    I      40      -       -           -
LGA    N      41      -       -           -
LGA    S      42      S      42          2.641
LGA    G      43      G      43          2.834
LGA    N      44      N      44          3.312
LGA    I      45      I      45          3.128
LGA    F      46      F      46          2.587
LGA    F      47      F      47          3.321
LGA    T      48      T      48          2.773
LGA    S      49      S      49          3.561
LGA    I      50      I      50          1.585
LGA    D      51      D      51          1.317
LGA    S      52      S      52          1.921
LGA    K      53      K      53          2.382
LGA    A      54      A      54          2.963
LGA    Q      55      Q      55          2.307
LGA    L      56      L      56          1.059
LGA    V      57      V      57          1.423
LGA    E      58      E      58          1.479
LGA    K      59      K      59          1.229
LGA    L      60      L      60          0.860
LGA    E      61      E      61          0.634
LGA    T      62      T      62          1.592
LGA    F      63      F      63          1.938
LGA    F      64      F      64          2.114
LGA    A      65      A      65          2.244
LGA    V      66      V      66          2.747
LGA    H      67      H      67          3.144
LGA    Y      68      Y      68          2.657
LGA    P      69      P      69          1.717
LGA    F      70      F      70          3.038
LGA    -       -      I      71           -
LGA    I      71      Q      72          1.339
LGA    Q      72      S      73          1.649
LGA    S      73      F      74          2.355
LGA    F      74      S      75          2.242
LGA    S      75      L      76          3.599
LGA    L      76      L      77          2.034
LGA    L      77      S      78          3.389
LGA    S      78      A     168           -
LGA    A     168      K     169           -
LGA    K     169      T     170           -
LGA    T     170      F     171           -
LGA    F     171      D     172           -
LGA    D     172      K     173           -
LGA    K     173      I     174           -
LGA    I     174      G     175           -
LGA    G     175      Q     176           -
LGA    Q     176      M     177           -
LGA    M     177      L     178           -
LGA    L     178      K     179           -
LGA    K     179      K     180           -
LGA    K     180      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     42    2.77    71.43     35.466     1.461

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.500489 * X  +  -0.651658 * Y  +  -0.569959 * Z  +  -1.530183
  Y_new =   0.788510 * X  +   0.071305 * Y  +   0.610875 * Z  +  46.704624
  Z_new =  -0.357440 * X  +  -0.755154 * Y  +   0.549526 * Z  +   1.882763 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.941721    2.199872  [ DEG:   -53.9566    126.0434 ]
  Theta =   0.365526    2.776067  [ DEG:    20.9431    159.0569 ]
  Phi   =   1.005233   -2.136360  [ DEG:    57.5956   -122.4044 ]
 
# 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: T0299TS599_5-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_5-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   42   2.77   71.43  35.466
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_5-D1
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1     -14.870  42.129 -16.012  1.00  0.00              
ATOM      2  CA  THR     2     -15.498  45.823 -17.910  1.00  0.00              
ATOM      3  CA  ARG     3     -14.747  49.334 -17.649  1.00  0.00              
ATOM      4  CA  TYR     4     -14.129  45.216 -17.019  1.00  0.00              
ATOM      5  CA  ALA     5     -10.658  46.267 -15.740  1.00  0.00              
ATOM      6  CA  LEU     6     -11.932  48.953 -13.398  1.00  0.00              
ATOM      7  CA  LEU     7     -14.488  46.702 -11.822  1.00  0.00              
ATOM      8  CA  VAL     8     -12.113  43.756 -11.213  1.00  0.00              
ATOM      9  CA  ARG     9      -9.408  45.895  -9.591  1.00  0.00              
ATOM     10  CA  GLY    10     -11.844  47.436  -7.362  1.00  0.00              
ATOM     11  CA  ILE    11     -14.041  45.103  -5.601  1.00  0.00              
ATOM     12  CA  ASN    12     -17.281  46.447  -4.248  1.00  0.00              
ATOM     13  CA  VAL    13     -18.770  45.081  -1.084  1.00  0.00              
ATOM     14  CA  GLY    14     -22.146  46.601  -0.407  1.00  0.00              
ATOM     15  CA  GLY    15     -23.207  44.712   2.677  1.00  0.00              
ATOM     16  CA  LYS    16     -20.052  43.527   4.333  1.00  0.00              
ATOM     17  CA  ASN    17     -20.102  39.926   3.167  1.00  0.00              
ATOM     18  CA  LYS    18     -16.433  39.179   2.918  1.00  0.00              
ATOM     19  CA  VAL    19     -15.117  37.209   0.018  1.00  0.00              
ATOM     20  CA  VAL    20     -11.863  35.171   0.366  1.00  0.00              
ATOM     21  CA  MET    21      -9.096  35.385  -2.127  1.00  0.00              
ATOM     22  CA  ALA    22      -9.773  31.801  -3.156  1.00  0.00              
ATOM     23  CA  GLU    23     -13.399  32.703  -4.039  1.00  0.00              
ATOM     24  CA  LEU    24     -12.343  35.676  -6.056  1.00  0.00              
ATOM     25  CA  ARG    25      -9.891  33.471  -7.879  1.00  0.00              
ATOM     26  CA  GLN    26     -12.522  30.950  -8.710  1.00  0.00              
ATOM     27  CA  GLU    27     -14.871  33.671 -10.071  1.00  0.00              
ATOM     28  CA  LEU    28     -12.144  35.220 -12.197  1.00  0.00              
ATOM     29  CA  THR    29     -11.174  31.881 -13.643  1.00  0.00              
ATOM     30  CA  ASN    30     -14.750  31.084 -14.458  1.00  0.00              
ATOM     31  CA  LEU    31     -15.336  34.381 -16.140  1.00  0.00              
ATOM     32  CA  GLY    32     -12.259  34.066 -18.414  1.00  0.00              
ATOM     33  CA  LEU    33     -10.004  36.469 -16.581  1.00  0.00              
ATOM     34  CA  GLU    34      -6.332  35.683 -16.762  1.00  0.00              
ATOM     35  CA  LYS    35      -4.922  39.202 -15.916  1.00  0.00              
ATOM     36  CA  VAL    36      -7.275  39.370 -12.875  1.00  0.00              
ATOM     37  CA  GLU    37      -5.983  35.888 -11.848  1.00  0.00              
ATOM     38  CA  SER    38      -2.454  37.259 -11.701  1.00  0.00              
ATOM     39  CA  TYR    39      -3.710  40.116  -9.452  1.00  0.00              
ATOM     40  CA  ILE    40      -5.574  37.770  -7.037  1.00  0.00              
ATOM     41  CA  ASN    41      -2.384  35.639  -6.712  1.00  0.00              
ATOM     42  CA  SER    42      -0.203  38.746  -6.009  1.00  0.00              
ATOM     43  CA  GLY    43      -1.831  39.521  -2.697  1.00  0.00              
ATOM     44  CA  ASN    44      -3.241  42.978  -3.247  1.00  0.00              
ATOM     45  CA  ILE    45      -6.793  43.627  -2.193  1.00  0.00              
ATOM     46  CA  PHE    46      -8.950  46.402  -3.609  1.00  0.00              
ATOM     47  CA  PHE    47     -12.071  47.338  -1.561  1.00  0.00              
ATOM     48  CA  THR    48     -14.466  49.948  -2.549  1.00  0.00              
ATOM     49  CA  SER    49     -16.347  51.660   0.219  1.00  0.00              
ATOM     50  CA  ILE    50     -19.869  50.418   0.817  1.00  0.00              
ATOM     51  CA  ASP    51     -19.308  49.157   4.320  1.00  0.00              
ATOM     52  CA  SER    52     -18.224  51.367   7.086  1.00  0.00              
ATOM     53  CA  LYS    53     -14.641  51.892   8.013  1.00  0.00              
ATOM     54  CA  ALA    54     -14.585  49.711  11.081  1.00  0.00              
ATOM     55  CA  GLN    55     -16.321  46.716   9.414  1.00  0.00              
ATOM     56  CA  LEU    56     -14.011  46.920   6.441  1.00  0.00              
ATOM     57  CA  VAL    57     -10.891  47.118   8.489  1.00  0.00              
ATOM     58  CA  GLU    58     -11.798  44.119  10.568  1.00  0.00              
ATOM     59  CA  LYS    59     -12.664  42.001   7.561  1.00  0.00              
ATOM     60  CA  LEU    60      -9.477  42.853   5.740  1.00  0.00              
ATOM     61  CA  GLU    61      -7.322  42.097   8.742  1.00  0.00              
ATOM     62  CA  THR    62      -8.914  38.736   9.196  1.00  0.00              
ATOM     63  CA  PHE    63      -8.549  37.624   5.682  1.00  0.00              
ATOM     64  CA  PHE    64      -4.928  38.792   5.196  1.00  0.00              
ATOM     65  CA  ALA    65      -3.713  37.191   8.349  1.00  0.00              
ATOM     66  CA  VAL    66      -5.320  34.045   7.515  1.00  0.00              
ATOM     67  CA  HIS    67      -4.350  33.552   3.956  1.00  0.00              
ATOM     68  CA  TYR    68      -0.980  34.832   3.705  1.00  0.00              
ATOM     69  CA  PRO    69       0.286  35.092   7.238  1.00  0.00              
ATOM     70  CA  PHE    70       1.107  38.609   6.508  1.00  0.00              
ATOM     71  CA  ILE    71       1.515  42.130   7.380  1.00  0.00              
ATOM     72  CA  GLN    72      -0.974  44.451   5.873  1.00  0.00              
ATOM     73  CA  SER    73      -0.252  47.718   4.455  1.00  0.00              
ATOM     74  CA  PHE    74      -3.221  50.013   3.935  1.00  0.00              
ATOM     75  CA  SER    75      -3.430  52.567   1.140  1.00  0.00              
ATOM     76  CA  LEU    76      -6.281  54.999   0.937  1.00  0.00              
ATOM     77  CA  LEU    77      -7.132  56.335  -2.450  1.00  0.00              
ATOM     78  CA  SER    78      -9.684  59.076  -3.385  1.00  0.00              
ATOM    168  CA  ALA   168      16.018  54.453  16.566  1.00  0.00              
ATOM    169  CA  LYS   169      18.461  53.941  19.390  1.00  0.00              
ATOM    170  CA  THR   170      16.928  50.517  20.175  1.00  0.00              
ATOM    171  CA  PHE   171      17.128  49.524  16.501  1.00  0.00              
ATOM    172  CA  ASP   172      20.716  50.567  16.156  1.00  0.00              
ATOM    173  CA  LYS   173      21.606  48.535  19.284  1.00  0.00              
ATOM    174  CA  ILE   174      19.771  45.481  17.935  1.00  0.00              
ATOM    175  CA  GLY   175      21.620  45.757  14.577  1.00  0.00              
ATOM    176  CA  GLN   176      24.868  46.006  16.395  1.00  0.00              
ATOM    177  CA  MET   177      24.309  42.975  18.551  1.00  0.00              
ATOM    178  CA  LEU   178      23.373  40.934  15.598  1.00  0.00              
ATOM    179  CA  LYS   179      26.293  42.028  13.626  1.00  0.00              
ATOM    180  CA  LYS   180      25.851  44.554  10.298  1.00  0.00              
TER                                                                             
END
