
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0306TS599_5
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS599_5.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    L       3      -       -           -
LGA    A       4      -       -           -
LGA    V       5      -       -           -
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    I      10      -       -           -
LGA    V      11      M       1           #
LGA    C      12      K       2          4.364
LGA    T      13      L       3          3.137
LGA    V      14      A       4          1.649
LGA    R      15      V       5          3.533
LGA    H      16      V       6          5.173
LGA    H      17      T       7           #
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    G      18      Q      39          4.044
LGA    L      19      C      40          4.803
LGA    A      20      A      41          4.157
LGA    H      21      V      42          2.968
LGA    D      22      A      43          3.029
LGA    K      23      -       -           -
LGA    L      24      I      44          1.474
LGA    L      25      D      45          2.756
LGA    M      26      N      46          1.371
LGA    V      27      -       -           -
LGA    E      28      -       -           -
LGA    M      29      -       -           -
LGA    I      30      -       -           -
LGA    D      31      -       -           -
LGA    P      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    D      37      -       -           -
LGA    G      38      -       -           -
LGA    Q      39      -       -           -
LGA    C      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      I      47          1.805
LGA    A      43      G      48          3.783
LGA    I      44      A      49          3.726
LGA    D      45      -       -           -
LGA    N      46      G      50           #
LGA    I      47      T      51          3.744
LGA    G      48      G      52          4.383
LGA    A      49      E      53          2.541
LGA    G      50      W      54          2.442
LGA    T      51      -       -           -
LGA    G      52      -       -           -
LGA    E      53      V      55          3.866
LGA    W      54      L      56          3.955
LGA    V      55      L      57           #
LGA    L      56      V      58           -
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    L      57      A      66           #
LGA    V      58      H      67          4.634
LGA    S      59      -       -           -
LGA    G      60      -       -           -
LGA    S      61      -       -           -
LGA    S      62      -       -           -
LGA    A      63      -       -           -
LGA    R      64      K      68           #
LGA    Q      65      S      69          1.517
LGA    A      66      -       -           -
LGA    H      67      -       -           -
LGA    K      68      E      70          1.536
LGA    S      69      T      71          3.852
LGA    E      70      S      72          1.797
LGA    T      71      P      73          2.247
LGA    S      72      V      74          1.475
LGA    P      73      D      75          3.945
LGA    V      74      L      76          3.011
LGA    D      75      C      77          3.729
LGA    L      76      V      78          2.083
LGA    C      77      I      79          2.652
LGA    V      78      G      80          4.520
LGA    I      79      I      81           -
LGA    G      80      V      82           -
LGA    I      81      D      83           -
LGA    V      82      E      84           -
LGA    D      83      V      85           -
LGA    E      84      V      86           -
LGA    V      85      S      87           -
LGA    V      86      G      88           -
LGA    S      87      G      89           -
LGA    G      88      Q      90           -
LGA    G      89      V      91           -
LGA    Q      90      I      92           -
LGA    V      91      F      93           -
LGA    I      92      H      94           -
LGA    F      93      K      95           -
LGA    H      94      -       -           -
LGA    K      95      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     35    3.32     5.71     20.834     1.022

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.871001 * X  +  -0.468801 * Y  +   0.146912 * Z  +  35.814030
  Y_new =  -0.488495 * X  +  -0.794623 * Y  +   0.360482 * Z  +  28.752398
  Z_new =  -0.052255 * X  +  -0.385745 * Y  +  -0.921124 * Z  +  57.537971 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.745005    0.396588  [ DEG:  -157.2772     22.7228 ]
  Theta =   0.052278    3.089314  [ DEG:     2.9953    177.0047 ]
  Phi   =  -0.511130    2.630463  [ DEG:   -29.2856    150.7144 ]
 
# 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: T0306TS599_5                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS599_5.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   35   3.32    5.71  20.834
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS599_5
PFRMAT TS                                                                       
TARGET T0306                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      46.216  47.679  55.447  1.00  0.00              
ATOM      2  CA  LYS     2      49.727  46.974  55.101  1.00  0.00              
ATOM      3  CA  LEU     3      45.569  46.421  55.386  1.00  0.00              
ATOM      4  CA  ALA     4      45.593  44.114  51.878  1.00  0.00              
ATOM      5  CA  VAL     5      48.706  42.413  53.157  1.00  0.00              
ATOM      6  CA  VAL     6      46.800  41.410  56.320  1.00  0.00              
ATOM      7  CA  THR     7      43.515  40.442  54.671  1.00  0.00              
ATOM      8  CA  GLY     8      45.228  38.259  52.022  1.00  0.00              
ATOM      9  CA  GLN     9      47.270  36.386  54.525  1.00  0.00              
ATOM     10  CA  ILE    10      44.984  35.824  57.403  1.00  0.00              
ATOM     11  CA  VAL    11      45.124  32.335  58.851  1.00  0.00              
ATOM     12  CA  CYS    12      43.480  31.554  62.165  1.00  0.00              
ATOM     13  CA  THR    13      45.022  28.841  64.411  1.00  0.00              
ATOM     14  CA  VAL    14      43.671  28.255  67.821  1.00  0.00              
ATOM     15  CA  ARG    15      46.427  27.902  70.490  1.00  0.00              
ATOM     16  CA  HIS    16      45.112  24.997  72.468  1.00  0.00              
ATOM     17  CA  HIS    17      43.743  26.914  75.508  1.00  0.00              
ATOM     18  CA  GLY    18      42.025  29.531  73.377  1.00  0.00              
ATOM     19  CA  LEU    19      40.264  27.041  71.057  1.00  0.00              
ATOM     20  CA  ALA    20      39.182  24.659  73.833  1.00  0.00              
ATOM     21  CA  HIS    21      35.462  25.240  74.060  1.00  0.00              
ATOM     22  CA  ASP    22      35.227  26.822  70.587  1.00  0.00              
ATOM     23  CA  LYS    23      32.996  25.130  68.186  1.00  0.00              
ATOM     24  CA  LEU    24      34.296  24.479  64.679  1.00  0.00              
ATOM     25  CA  LEU    25      32.259  22.561  62.239  1.00  0.00              
ATOM     26  CA  MET    26      33.924  21.278  59.214  1.00  0.00              
ATOM     27  CA  VAL    27      31.698  20.429  56.111  1.00  0.00              
ATOM     28  CA  GLU    28      33.463  19.027  53.201  1.00  0.00              
ATOM     29  CA  MET    29      31.442  19.055  50.036  1.00  0.00              
ATOM     30  CA  ILE    30      27.932  18.861  51.630  1.00  0.00              
ATOM     31  CA  ASP    31      25.487  21.399  50.302  1.00  0.00              
ATOM     32  CA  PRO    32      21.986  21.377  51.625  1.00  0.00              
ATOM     33  CA  GLN    33      20.596  19.192  48.879  1.00  0.00              
ATOM     34  CA  GLY    34      23.547  16.802  48.716  1.00  0.00              
ATOM     35  CA  ASN    35      24.850  18.204  45.484  1.00  0.00              
ATOM     36  CA  PRO    36      28.562  18.767  44.989  1.00  0.00              
ATOM     37  CA  ASP    37      28.819  22.518  44.353  1.00  0.00              
ATOM     38  CA  GLY    38      32.569  22.802  43.382  1.00  0.00              
ATOM     39  CA  GLN    39      33.445  24.609  46.616  1.00  0.00              
ATOM     40  CA  CYS    40      35.721  22.976  49.122  1.00  0.00              
ATOM     41  CA  ALA    41      34.832  23.182  52.748  1.00  0.00              
ATOM     42  CA  VAL    42      37.370  22.471  55.431  1.00  0.00              
ATOM     43  CA  ALA    43      36.103  21.790  58.794  1.00  0.00              
ATOM     44  CA  ILE    44      38.413  22.358  61.910  1.00  0.00              
ATOM     45  CA  ASP    45      37.052  21.308  65.232  1.00  0.00              
ATOM     46  CA  ASN    46      38.880  22.631  68.234  1.00  0.00              
ATOM     47  CA  ILE    47      42.066  20.662  68.074  1.00  0.00              
ATOM     48  CA  GLY    48      45.163  22.599  69.035  1.00  0.00              
ATOM     49  CA  ALA    49      46.542  23.211  65.528  1.00  0.00              
ATOM     50  CA  GLY    50      48.965  25.922  65.559  1.00  0.00              
ATOM     51  CA  THR    51      49.667  29.421  64.790  1.00  0.00              
ATOM     52  CA  GLY    52      49.656  30.066  61.055  1.00  0.00              
ATOM     53  CA  GLU    53      47.359  27.240  60.111  1.00  0.00              
ATOM     54  CA  TRP    54      44.146  28.195  58.275  1.00  0.00              
ATOM     55  CA  VAL    55      41.004  26.272  58.996  1.00  0.00              
ATOM     56  CA  LEU    56      37.845  26.959  56.994  1.00  0.00              
ATOM     57  CA  LEU    57      34.466  26.141  58.513  1.00  0.00              
ATOM     58  CA  VAL    58      31.490  25.354  56.392  1.00  0.00              
ATOM     59  CA  SER    59      28.237  24.264  58.141  1.00  0.00              
ATOM     60  CA  GLY    60      25.508  22.785  56.018  1.00  0.00              
ATOM     61  CA  SER    61      22.733  25.074  57.116  1.00  0.00              
ATOM     62  CA  SER    62      22.293  26.979  53.834  1.00  0.00              
ATOM     63  CA  ALA    63      19.550  29.251  55.042  1.00  0.00              
ATOM     64  CA  ARG    64      21.256  30.404  58.270  1.00  0.00              
ATOM     65  CA  GLN    65      24.527  30.961  56.426  1.00  0.00              
ATOM     66  CA  ALA    66      23.318  33.089  53.484  1.00  0.00              
ATOM     67  CA  HIS    67      21.633  35.663  55.743  1.00  0.00              
ATOM     68  CA  LYS    68      24.662  35.846  58.045  1.00  0.00              
ATOM     69  CA  SER    69      23.351  35.648  61.544  1.00  0.00              
ATOM     70  CA  GLU    70      23.694  32.116  62.700  1.00  0.00              
ATOM     71  CA  THR    71      25.952  32.583  65.743  1.00  0.00              
ATOM     72  CA  SER    72      28.177  29.548  65.792  1.00  0.00              
ATOM     73  CA  PRO    73      31.683  29.516  67.088  1.00  0.00              
ATOM     74  CA  VAL    74      34.170  29.234  64.286  1.00  0.00              
ATOM     75  CA  ASP    75      37.377  27.664  65.090  1.00  0.00              
ATOM     76  CA  LEU    76      39.827  28.929  62.475  1.00  0.00              
ATOM     77  CA  CYS    77      38.875  31.324  59.796  1.00  0.00              
ATOM     78  CA  VAL    78      40.840  31.574  56.588  1.00  0.00              
ATOM     79  CA  ILE    79      41.000  34.915  54.968  1.00  0.00              
ATOM     80  CA  GLY    80      42.437  35.170  51.541  1.00  0.00              
ATOM     81  CA  ILE    81      40.448  32.116  50.435  1.00  0.00              
ATOM     82  CA  VAL    82      37.178  33.447  51.934  1.00  0.00              
ATOM     83  CA  ASP    83      37.448  36.792  50.307  1.00  0.00              
ATOM     84  CA  GLU    84      38.136  35.310  46.921  1.00  0.00              
ATOM     85  CA  VAL    85      35.091  33.267  46.812  1.00  0.00              
ATOM     86  CA  VAL    86      32.230  34.779  48.510  1.00  0.00              
ATOM     87  CA  SER    87      28.849  33.601  47.818  1.00  0.00              
ATOM     88  CA  GLY    88      26.128  35.148  49.804  1.00  0.00              
ATOM     89  CA  GLY    89      28.379  35.012  52.955  1.00  0.00              
ATOM     90  CA  GLN    90      29.152  31.461  52.321  1.00  0.00              
ATOM     91  CA  VAL    91      32.675  31.051  51.955  1.00  0.00              
ATOM     92  CA  ILE    92      33.966  28.822  49.372  1.00  0.00              
ATOM     93  CA  PHE    93      37.341  27.653  49.601  1.00  0.00              
ATOM     94  CA  HIS    94      39.087  26.531  46.238  1.00  0.00              
ATOM     95  CA  LYS    95      42.169  24.687  46.426  1.00  0.00              
TER                                                                             
END
