
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS599_1-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      R       3           -
LGA    Y       4      Y       4           -
LGA    A       5      A       5           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    V       8      -       -           -
LGA    R       9      -       -           -
LGA    G      10      L       6          4.187
LGA    I      11      L       7          3.296
LGA    N      12      V       8           -
LGA    V      13      R       9           -
LGA    G      14      G      10           -
LGA    G      15      I      11           -
LGA    K      16      -       -           -
LGA    N      17      -       -           -
LGA    K      18      -       -           -
LGA    V      19      -       -           -
LGA    V      20      -       -           -
LGA    M      21      -       -           -
LGA    A      22      -       -           -
LGA    E      23      -       -           -
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      N      12          4.266
LGA    V      36      V      13           -
LGA    E      37      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    S      38      V      19          3.524
LGA    Y      39      V      20          4.451
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    I      40      L      24          1.147
LGA    N      41      R      25           #
LGA    S      42      Q      26           -
LGA    G      43      E      27          4.338
LGA    N      44      L      28          3.776
LGA    I      45      T      29          4.813
LGA    F      46      N      30          5.026
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    F      47      L      33          1.547
LGA    T      48      E      34          4.430
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    -       -      T      48           -
LGA    S      49      S      49          1.728
LGA    I      50      I      50          0.760
LGA    D      51      D      51          0.813
LGA    S      52      S      52          0.795
LGA    K      53      K      53          0.755
LGA    A      54      A      54          0.838
LGA    Q      55      Q      55          0.625
LGA    L      56      L      56          1.049
LGA    V      57      V      57          1.330
LGA    E      58      E      58          0.980
LGA    K      59      K      59          0.714
LGA    L      60      L      60          1.052
LGA    E      61      E      61          1.317
LGA    T      62      T      62          0.934
LGA    F      63      F      63          0.790
LGA    F      64      F      64          1.325
LGA    A      65      A      65          1.590
LGA    V      66      V      66          0.551
LGA    H      67      H      67          0.795
LGA    Y      68      Y      68          1.912
LGA    P      69      P      69          1.956
LGA    F      70      F      70          1.825
LGA    I      71      I      71          3.833
LGA    Q      72      Q      72          2.316
LGA    S      73      S      73          1.044
LGA    F      74      F      74          3.081
LGA    S      75      S      75          3.664
LGA    L      76      L      76           #
LGA    L      77      L      77           #
LGA    S      78      S      78           #
LGA    A     168      A     168           -
LGA    K     169      K     169           -
LGA    T     170      T     170           -
LGA    F     171      F     171           -
LGA    D     172      D     172           -
LGA    K     173      K     173           -
LGA    I     174      I     174           -
LGA    G     175      G     175           -
LGA    Q     176      Q     176           -
LGA    M     177      M     177           -
LGA    L     178      L     178           -
LGA    K     179      K     179           -
LGA    K     180      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     39    2.58    69.23     33.080     1.457

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.106320 * X  +  -0.241978 * Y  +   0.964439 * Z  +  -1.012036
  Y_new =  -0.985671 * X  +   0.102095 * Y  +   0.134276 * Z  +  48.123402
  Z_new =  -0.130956 * X  +  -0.964896 * Y  +  -0.227656 * Z  +   6.035668 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.802497    1.339095  [ DEG:  -103.2755     76.7245 ]
  Theta =   0.131333    3.010259  [ DEG:     7.5248    172.4752 ]
  Phi   =  -1.463346    1.678246  [ DEG:   -83.8436     96.1564 ]
 
# 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_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_1-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   39   2.58   69.23  33.080
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_1-D1
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       8.208  48.456 -11.415  1.00  0.00              
ATOM      2  CA  THR     2       7.664  50.538  -7.795  1.00  0.00              
ATOM      3  CA  ARG     3       4.029  50.412  -9.962  1.00  0.00              
ATOM      4  CA  TYR     4       4.736  46.360  -9.716  1.00  0.00              
ATOM      5  CA  ALA     5       5.024  46.609  -5.977  1.00  0.00              
ATOM      6  CA  LEU     6       1.762  48.552  -5.448  1.00  0.00              
ATOM      7  CA  LEU     7      -0.067  46.223  -7.870  1.00  0.00              
ATOM      8  CA  VAL     8       1.260  42.950  -6.484  1.00  0.00              
ATOM      9  CA  ARG     9       0.450  44.061  -2.863  1.00  0.00              
ATOM     10  CA  GLY    10      -3.113  44.687  -3.364  1.00  0.00              
ATOM     11  CA  ILE    11      -4.281  48.138  -3.866  1.00  0.00              
ATOM     12  CA  ASN    12      -7.566  49.077  -2.595  1.00  0.00              
ATOM     13  CA  VAL    13      -9.145  52.371  -3.554  1.00  0.00              
ATOM     14  CA  GLY    14     -12.080  53.371  -1.464  1.00  0.00              
ATOM     15  CA  GLY    15     -14.436  54.919  -3.949  1.00  0.00              
ATOM     16  CA  LYS    16     -17.817  53.540  -3.081  1.00  0.00              
ATOM     17  CA  ASN    17     -18.208  51.007  -5.837  1.00  0.00              
ATOM     18  CA  LYS    18     -19.212  47.608  -4.470  1.00  0.00              
ATOM     19  CA  VAL    19     -17.028  44.674  -5.397  1.00  0.00              
ATOM     20  CA  VAL    20     -18.381  41.146  -5.594  1.00  0.00              
ATOM     21  CA  MET    21     -15.937  38.318  -4.992  1.00  0.00              
ATOM     22  CA  ALA    22     -16.071  37.094  -8.599  1.00  0.00              
ATOM     23  CA  GLU    23     -15.472  40.627  -9.914  1.00  0.00              
ATOM     24  CA  LEU    24     -12.490  41.194  -7.614  1.00  0.00              
ATOM     25  CA  ARG    25     -10.913  37.935  -8.657  1.00  0.00              
ATOM     26  CA  GLN    26     -11.391  38.915 -12.328  1.00  0.00              
ATOM     27  CA  GLU    27      -9.860  42.350 -11.750  1.00  0.00              
ATOM     28  CA  LEU    28      -6.753  40.923 -10.052  1.00  0.00              
ATOM     29  CA  THR    29      -6.343  38.471 -12.982  1.00  0.00              
ATOM     30  CA  ASN    30      -6.660  41.266 -15.499  1.00  0.00              
ATOM     31  CA  LEU    31      -3.887  43.184 -13.686  1.00  0.00              
ATOM     32  CA  GLY    32      -1.558  40.246 -13.870  1.00  0.00              
ATOM     33  CA  LEU    33      -1.689  38.913 -10.367  1.00  0.00              
ATOM     34  CA  GLU    34      -1.390  35.089 -10.262  1.00  0.00              
ATOM     35  CA  LYS    35      -0.226  34.483  -6.645  1.00  0.00              
ATOM     36  CA  VAL    36      -2.677  36.970  -5.098  1.00  0.00              
ATOM     37  CA  GLU    37      -5.556  35.370  -7.066  1.00  0.00              
ATOM     38  CA  SER    38      -4.744  32.020  -5.376  1.00  0.00              
ATOM     39  CA  TYR    39      -4.689  33.686  -1.893  1.00  0.00              
ATOM     40  CA  ILE    40      -8.021  35.479  -2.561  1.00  0.00              
ATOM     41  CA  ASN    41      -9.765  32.262  -3.752  1.00  0.00              
ATOM     42  CA  SER    42      -8.793  30.665  -0.416  1.00  0.00              
ATOM     43  CA  GLY    43     -10.672  32.798   2.025  1.00  0.00              
ATOM     44  CA  ASN    44     -12.777  34.947  -0.210  1.00  0.00              
ATOM     45  CA  ILE    45     -12.918  38.721   0.104  1.00  0.00              
ATOM     46  CA  PHE    46     -16.203  40.357  -0.820  1.00  0.00              
ATOM     47  CA  PHE    47     -16.328  44.169  -0.550  1.00  0.00              
ATOM     48  CA  THR    48     -19.517  45.973  -0.136  1.00  0.00              
ATOM     49  CA  SER    49     -19.445  49.675  -0.830  1.00  0.00              
ATOM     50  CA  ILE    50     -21.211  51.248   2.188  1.00  0.00              
ATOM     51  CA  ASP    51     -19.039  49.359   4.700  1.00  0.00              
ATOM     52  CA  SER    52     -17.159  51.944   6.765  1.00  0.00              
ATOM     53  CA  LYS    53     -13.405  51.991   6.075  1.00  0.00              
ATOM     54  CA  ALA    54     -12.490  50.697   9.471  1.00  0.00              
ATOM     55  CA  GLN    55     -14.921  47.832   9.375  1.00  0.00              
ATOM     56  CA  LEU    56     -13.769  46.755   5.929  1.00  0.00              
ATOM     57  CA  VAL    57     -10.137  46.840   6.944  1.00  0.00              
ATOM     58  CA  GLU    58     -10.737  44.801  10.031  1.00  0.00              
ATOM     59  CA  LYS    59     -12.662  42.154   8.100  1.00  0.00              
ATOM     60  CA  LEU    60      -9.924  41.925   5.467  1.00  0.00              
ATOM     61  CA  GLU    61      -7.189  41.604   8.027  1.00  0.00              
ATOM     62  CA  THR    62      -8.954  38.874   9.854  1.00  0.00              
ATOM     63  CA  PHE    63      -9.585  36.952   6.692  1.00  0.00              
ATOM     64  CA  PHE    64      -6.076  37.112   5.338  1.00  0.00              
ATOM     65  CA  ALA    65      -4.504  36.115   8.576  1.00  0.00              
ATOM     66  CA  VAL    66      -6.649  33.208   9.112  1.00  0.00              
ATOM     67  CA  HIS    67      -6.522  31.678   5.699  1.00  0.00              
ATOM     68  CA  TYR    68      -3.065  32.176   4.652  1.00  0.00              
ATOM     69  CA  PRO    69      -1.085  32.760   7.781  1.00  0.00              
ATOM     70  CA  PHE    70       0.123  36.104   6.382  1.00  0.00              
ATOM     71  CA  ILE    71       0.862  39.086   8.529  1.00  0.00              
ATOM     72  CA  GLN    72      -0.875  42.044   6.965  1.00  0.00              
ATOM     73  CA  SER    73       0.611  45.373   6.807  1.00  0.00              
ATOM     74  CA  PHE    74      -1.591  48.228   5.706  1.00  0.00              
ATOM     75  CA  SER    75      -0.113  51.292   3.976  1.00  0.00              
ATOM     76  CA  LEU    76      -2.143  54.362   3.224  1.00  0.00              
ATOM     77  CA  LEU    77      -1.079  56.279   0.200  1.00  0.00              
ATOM     78  CA  SER    78      -2.729  59.268  -1.384  1.00  0.00              
ATOM    168  CA  ALA   168       8.785  51.076  24.936  1.00  0.00              
ATOM    169  CA  LYS   169       8.180  52.738  28.221  1.00  0.00              
ATOM    170  CA  THR   170      10.958  55.284  27.659  1.00  0.00              
ATOM    171  CA  PHE   171       9.652  56.095  24.189  1.00  0.00              
ATOM    172  CA  ASP   172       6.123  56.601  25.539  1.00  0.00              
ATOM    173  CA  LYS   173       7.385  59.016  28.203  1.00  0.00              
ATOM    174  CA  ILE   174       9.341  61.063  25.633  1.00  0.00              
ATOM    175  CA  GLY   175       6.335  61.214  23.346  1.00  0.00              
ATOM    176  CA  GLN   176       4.127  62.386  26.168  1.00  0.00              
ATOM    177  CA  MET   177       6.526  65.192  27.222  1.00  0.00              
ATOM    178  CA  LEU   178       6.684  66.413  23.200  1.00  0.00              
ATOM    179  CA  LYS   179       2.501  66.040  23.077  1.00  0.00              
ATOM    180  CA  LYS   180       6.335  67.442  23.214  1.00  0.00              
TER                                                                             
END
