
#######################################################
#                                                     #
#                        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  103 (  103),  selected  103 , name T0314TS168_1-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS168_1-D1.T0314_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    S       2      S       2           -
LGA    I       3      I       3           -
LGA    T       4      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      C       9           -
LGA    -       -      Q      10           -
LGA    S       5      A      11           #
LGA    T       6      A      12           -
LGA    D       7      D      13           #
LGA    I       8      A      14          1.320
LGA    C       9      -       -           -
LGA    Q      10      -       -           -
LGA    A      11      L      15          2.491
LGA    A      12      K      16          2.716
LGA    D      13      G      17          0.246
LGA    A      14      F      18          4.820
LGA    L      15      V      19          3.905
LGA    K      16      G      20           -
LGA    G      17      F      21           -
LGA    F      18      N      22           -
LGA    -       -      R      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    V      19      R      27           #
LGA    G      20      Y      28          1.058
LGA    F      21      -       -           -
LGA    N      22      -       -           -
LGA    R      23      -       -           -
LGA    K      24      -       -           -
LGA    T      25      -       -           -
LGA    G      26      -       -           -
LGA    R      27      -       -           -
LGA    Y      28      -       -           -
LGA    I      29      I      29          4.300
LGA    V      30      V      30          4.632
LGA    R      31      R      31           -
LGA    F      32      -       -           -
LGA    S      33      -       -           -
LGA    E      34      -       -           -
LGA    D      35      -       -           -
LGA    S      36      -       -           -
LGA    F      37      -       -           -
LGA    G      38      F      32           #
LGA    M      39      S      33          3.506
LGA    D      40      E      34          4.018
LGA    V      41      D      35          1.124
LGA    A      42      S      36          2.809
LGA    D      43      F      37           #
LGA    D      44      G      38          4.212
LGA    S      45      M      39          1.390
LGA    I      46      D      40          2.080
LGA    T      47      V      41          2.367
LGA    P      48      A      42          3.636
LGA    T      49      D      43           #
LGA    S      50      D      44          2.540
LGA    E      51      S      45          4.954
LGA    F      52      I      46          2.891
LGA    V      53      T      47           #
LGA    W      54      P      48           -
LGA    S      55      T      49           -
LGA    S      56      S      50           -
LGA    V      57      E      51           -
LGA    R      58      F      52           -
LGA    D      59      V      53           -
LGA    D      60      W      54           -
LGA    V      61      S      55           -
LGA    M      62      S      56           -
LGA    -       -      V      57           -
LGA    -       -      R      58           -
LGA    -       -      D      59           -
LGA    -       -      D      60           -
LGA    -       -      V      61           -
LGA    -       -      M      62           -
LGA    -       -      R      63           -
LGA    -       -      L      64           -
LGA    -       -      G      65           -
LGA    -       -      R      66           -
LGA    -       -      E      67           -
LGA    -       -      Q      68           -
LGA    -       -      L      69           -
LGA    -       -      Q      70           -
LGA    -       -      I      71           -
LGA    -       -      L      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    R      63      Q      75           #
LGA    L      64      N      76          4.880
LGA    G      65      I      77          3.673
LGA    R      66      N      78          3.523
LGA    E      67      E      79           #
LGA    Q      68      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    L      69      I      83          3.399
LGA    Q      70      G      84          4.292
LGA    I      71      -       -           -
LGA    L      72      E      85          4.789
LGA    L      73      P      86          3.128
LGA    E      74      L      87          3.086
LGA    Q      75      L      88          3.903
LGA    N      76      V      89          2.302
LGA    I      77      Y      90          3.681
LGA    N      78      L      91           #
LGA    E      79      R      92           #
LGA    R      80      R      93           #
LGA    L      81      -       -           -
LGA    N      82      Q      94          1.314
LGA    I      83      D      95          1.744
LGA    G      84      L      96          3.499
LGA    E      85      P      97          4.708
LGA    P      86      E      98           #
LGA    L      87      I      99          1.302
LGA    L      88      T     100          2.331
LGA    V      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    R      92      A     101          3.872
LGA    R      93      Q     102          2.108
LGA    Q      94      R     103          2.274
LGA    D      95      -       -           -
LGA    L      96      -       -           -
LGA    P      97      -       -           -
LGA    E      98      -       -           -
LGA    I      99      -       -           -
LGA    T     100      -       -           -
LGA    A     101      -       -           -
LGA    Q     102      -       -           -
LGA    R     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  103  103    5.0     41    3.28     4.88     22.612     1.212

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.196216 * X  +   0.815872 * Y  +  -0.543923 * Z  +  18.628490
  Y_new =  -0.854647 * X  +   0.414233 * Y  +   0.313033 * Z  +   7.331252
  Z_new =   0.480706 * X  +   0.403440 * Y  +   0.778562 * Z  + -13.675757 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.478091   -2.663502  [ DEG:    27.3926   -152.6074 ]
  Theta =  -0.501459   -2.640133  [ DEG:   -28.7315   -151.2685 ]
  Phi   =  -1.345120    1.796473  [ DEG:   -77.0697    102.9303 ]
 
# 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: T0314TS168_1-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS168_1-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  103  103   5.0   41   3.28    4.88  22.612
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS168_1-D1
PFRMAT TS
TARGET T0314
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      29.036  13.511  -0.461  1.00 25.00           C
ATOM      2  CA  SER     2      25.770  15.099  -1.587  1.00 25.00           C
ATOM      3  CA  ILE     3      23.627  14.131  -4.632  1.00 25.00           C
ATOM      4  CA  THR     4      22.174  11.667  -2.167  1.00 25.00           C
ATOM      5  CA  SER     5      18.646  10.105  -2.259  1.00 25.00           C
ATOM      6  CA  THR     6      20.633   6.837  -2.464  1.00 25.00           C
ATOM      7  CA  ASP     7      17.744   5.169  -4.346  1.00 25.00           C
ATOM      8  CA  ILE     8      17.599   8.117  -6.787  1.00 25.00           C
ATOM      9  CA  CYS     9      21.379   7.863  -7.357  1.00 25.00           C
ATOM     10  CA  GLN    10      21.050   4.104  -8.017  1.00 25.00           C
ATOM     11  CA  ALA    11      18.225   4.765 -10.516  1.00 25.00           C
ATOM     12  CA  ALA    12      20.373   7.394 -12.287  1.00 25.00           C
ATOM     13  CA  ASP    13      23.291   4.922 -12.472  1.00 25.00           C
ATOM     14  CA  ALA    14      20.969   2.252 -13.937  1.00 25.00           C
ATOM     15  CA  LEU    15      19.697   4.753 -16.542  1.00 25.00           C
ATOM     16  CA  LYS    16      16.731   6.621 -18.102  1.00 25.00           C
ATOM     17  CA  GLY    17      14.603   3.872 -19.502  1.00 25.00           C
ATOM     18  CA  PHE    18      17.314   1.143 -19.476  1.00 25.00           C
ATOM     19  CA  VAL    19      18.583   0.405 -22.983  1.00 25.00           C
ATOM     20  CA  GLY    20      20.035  -3.095 -22.650  1.00 25.00           C
ATOM     21  CA  PHE    21      20.736  -6.457 -24.148  1.00 25.00           C
ATOM     22  CA  ASN    22      19.251  -8.739 -21.520  1.00 25.00           C
ATOM     23  CA  ARG    23      21.976 -11.427 -21.674  1.00 25.00           C
ATOM     24  CA  LYS    24      25.553 -11.834 -20.392  1.00 25.00           C
ATOM     25  CA  THR    25      24.126 -11.560 -16.815  1.00 25.00           C
ATOM     26  CA  GLY    26      21.297  -9.009 -16.952  1.00 25.00           C
ATOM     27  CA  ARG    27      23.875  -6.215 -17.120  1.00 25.00           C
ATOM     28  CA  TYR    28      26.148  -3.631 -18.692  1.00 25.00           C
ATOM     29  CA  ILE    29      25.657  -0.944 -21.360  1.00 25.00           C
ATOM     30  CA  VAL    30      22.700   1.288 -20.561  1.00 25.00           C
ATOM     31  CA  ARG    31      21.123   4.646 -21.474  1.00 25.00           C
ATOM     32  CA  PHE    32      21.904   7.974 -19.698  1.00 25.00           C
ATOM     33  CA  SER    33      20.693   9.768 -22.868  1.00 25.00           C
ATOM     34  CA  GLU    34      23.571  11.754 -24.392  1.00 25.00           C
ATOM     35  CA  ASP    35      24.931  12.795 -20.952  1.00 25.00           C
ATOM     36  CA  SER    36      27.552  10.063 -20.584  1.00 25.00           C
ATOM     37  CA  PHE    37      27.615  11.121 -16.924  1.00 25.00           C
ATOM     38  CA  GLY    38      31.191  10.061 -16.343  1.00 25.00           C
ATOM     39  CA  MET    39      30.959   6.314 -16.592  1.00 25.00           C
ATOM     40  CA  ASP    40      34.433   5.189 -15.578  1.00 25.00           C
ATOM     41  CA  VAL    41      34.579   3.696 -19.037  1.00 25.00           C
ATOM     42  CA  ALA    42      36.089   0.425 -20.379  1.00 25.00           C
ATOM     43  CA  ASP    43      38.577   0.548 -23.299  1.00 25.00           C
ATOM     44  CA  ASP    44      38.373   0.025 -27.061  1.00 25.00           C
ATOM     45  CA  SER    45      35.157   0.732 -29.020  1.00 25.00           C
ATOM     46  CA  ILE    46      31.894   0.474 -27.067  1.00 25.00           C
ATOM     47  CA  THR    47      29.233   2.205 -29.111  1.00 25.00           C
ATOM     48  CA  PRO    48      25.405   2.095 -29.550  1.00 25.00           C
ATOM     49  CA  THR    49      23.860   4.299 -26.871  1.00 25.00           C
ATOM     50  CA  SER    50      25.463   7.154 -24.926  1.00 25.00           C
ATOM     51  CA  GLU    51      27.336   4.328 -23.092  1.00 25.00           C
ATOM     52  CA  PHE    52      25.874   5.121 -19.664  1.00 25.00           C
ATOM     53  CA  VAL    53      27.295   2.182 -17.746  1.00 25.00           C
ATOM     54  CA  TRP    54      28.218  -0.575 -15.314  1.00 25.00           C
ATOM     55  CA  SER    55      30.785  -1.511 -12.685  1.00 25.00           C
ATOM     56  CA  SER    56      31.184  -4.937 -11.135  1.00 25.00           C
ATOM     57  CA  VAL    57      28.704  -7.650 -10.119  1.00 25.00           C
ATOM     58  CA  ARG    58      28.051  -5.710  -6.882  1.00 25.00           C
ATOM     59  CA  ASP    59      27.382  -2.523  -8.898  1.00 25.00           C
ATOM     60  CA  ASP    60      24.948  -4.431 -11.155  1.00 25.00           C
ATOM     61  CA  VAL    61      23.141  -5.817  -8.077  1.00 25.00           C
ATOM     62  CA  MET    62      22.883  -2.289  -6.609  1.00 25.00           C
ATOM     63  CA  ARG    63      21.460  -0.990  -9.919  1.00 25.00           C
ATOM     64  CA  LEU    64      18.892  -3.831  -9.958  1.00 25.00           C
ATOM     65  CA  GLY    65      17.887  -3.005  -6.357  1.00 25.00           C
ATOM     66  CA  ARG    66      17.484   0.687  -7.289  1.00 25.00           C
ATOM     67  CA  GLU    67      15.308  -0.282 -10.288  1.00 25.00           C
ATOM     68  CA  GLN    68      13.147  -2.500  -8.035  1.00 25.00           C
ATOM     69  CA  LEU    69      12.752   0.379  -5.540  1.00 25.00           C
ATOM     70  CA  GLN    70      11.731   2.735  -8.381  1.00 25.00           C
ATOM     71  CA  ILE    71       9.160   0.176  -9.611  1.00 25.00           C
ATOM     72  CA  LEU    72       7.755  -0.153  -6.064  1.00 25.00           C
ATOM     73  CA  LEU    73       7.493   3.658  -5.787  1.00 25.00           C
ATOM     74  CA  GLU    74       5.670   3.802  -9.152  1.00 25.00           C
ATOM     75  CA  GLN    75       3.244   1.080  -7.981  1.00 25.00           C
ATOM     76  CA  ASN    76       2.590   3.020  -4.744  1.00 25.00           C
ATOM     77  CA  ILE    77       1.922   6.207  -6.760  1.00 25.00           C
ATOM     78  CA  ASN    78      -0.512   4.299  -9.018  1.00 25.00           C
ATOM     79  CA  GLU    79      -2.319   2.913  -5.939  1.00 25.00           C
ATOM     80  CA  ARG    80      -2.577   6.440  -4.472  1.00 25.00           C
ATOM     81  CA  LEU    81      -4.000   7.740  -7.782  1.00 25.00           C
ATOM     82  CA  ASN    82      -1.197   9.186  -9.859  1.00 25.00           C
ATOM     83  CA  ILE    83       0.150  12.361  -8.145  1.00 25.00           C
ATOM     84  CA  GLY    84      -2.009  15.456  -8.512  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.351  16.036 -11.928  1.00 25.00           C
ATOM     86  CA  PRO    86       2.744  16.521  -9.724  1.00 25.00           C
ATOM     87  CA  LEU    87       4.926  14.823 -12.375  1.00 25.00           C
ATOM     88  CA  LEU    88       3.454  17.099 -15.080  1.00 25.00           C
ATOM     89  CA  VAL    89       4.163  20.176 -12.912  1.00 25.00           C
ATOM     90  CA  TYR    90       7.770  19.002 -12.382  1.00 25.00           C
ATOM     91  CA  LEU    91       8.188  18.503 -16.156  1.00 25.00           C
ATOM     92  CA  ARG    92       6.816  22.021 -16.798  1.00 25.00           C
ATOM     93  CA  ARG    93       9.254  23.468 -14.223  1.00 25.00           C
ATOM     94  CA  GLN    94      10.607  25.269 -17.339  1.00 25.00           C
ATOM     95  CA  ASP    95       9.800  28.642 -15.858  1.00 25.00           C
ATOM     96  CA  LEU    96      11.661  28.597 -12.510  1.00 25.00           C
ATOM     97  CA  PRO    97      12.216  31.372 -10.019  1.00 25.00           C
ATOM     98  CA  GLU    98      14.623  30.300  -7.240  1.00 25.00           C
ATOM     99  CA  ILE    99      16.256  27.763  -9.599  1.00 25.00           C
ATOM    100  CA  THR   100      16.646  30.471 -12.279  1.00 25.00           C
ATOM    101  CA  ALA   101      18.240  32.821  -9.709  1.00 25.00           C
ATOM    102  CA  GLN   102      20.660  30.051  -8.641  1.00 25.00           C
ATOM    103  CA  ARG   103      21.588  29.418 -12.303  1.00 25.00           C
TER
END
