
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0343TS393_5
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS393_5.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    W       3      -       -           -
LGA    R       4      -       -           -
LGA    E       5      -       -           -
LGA    I       6      -       -           -
LGA    L       7      -       -           -
LGA    R       8      -       -           -
LGA    K       9      T       2          3.337
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    D      14      -       -           -
LGA    L      15      -       -           -
LGA    G      16      -       -           -
LGA    E      17      -       -           -
LGA    F      18      -       -           -
LGA    I      19      -       -           -
LGA    V      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    Y      24      W       3          4.759
LGA    I      25      R       4          1.733
LGA    D      26      E       5          1.797
LGA    C      27      I       6           -
LGA    P      28      L       7           -
LGA    C      29      -       -           -
LGA    E      30      -       -           -
LGA    P      31      -       -           -
LGA    I      32      -       -           -
LGA    P      33      R       8          4.613
LGA    P      34      K       9          2.590
LGA    -       -      E      10           -
LGA    T      35      G      11          2.518
LGA    L      36      F      12          1.173
LGA    A      37      L      13          1.933
LGA    I      38      D      14          4.811
LGA    Y      39      L      15           -
LGA    D      40      G      16           -
LGA    K      41      E      17           -
LGA    K      42      F      18           -
LGA    G      43      I      19           -
LGA    D      44      V      20           -
LGA    E      45      -       -           -
LGA    W      46      E      21          3.900
LGA    Y      47      L      22          2.971
LGA    K      48      V      23          3.958
LGA    V      49      Y      24          2.957
LGA    E      50      I      25           #
LGA    E      51      -       -           -
LGA    A      52      -       -           -
LGA    P      53      -       -           -
LGA    N      54      -       -           -
LGA    V      55      -       -           -
LGA    Q      56      D      26          1.658
LGA    N      57      C      27          4.921
LGA    Y      58      P      28           -
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    R      59      P      31           #
LGA    E      60      I      32           #
LGA    A      61      P      33           #
LGA    V      62      P      34          1.964
LGA    E      63      T      35          5.046
LGA    W      64      -       -           -
LGA    A      65      L      36          4.205
LGA    I      66      -       -           -
LGA    E      67      -       -           -
LGA    V      68      -       -           -
LGA    L      69      -       -           -
LGA    E      70      -       -           -
LGA    R      71      -       -           -
LGA    I      72      -       -           -
LGA    R      73      -       -           -
LGA    D      74      -       -           -
LGA    G      75      -       -           -
LGA    E      76      -       -           -
LGA    N      77      -       -           -
LGA    V      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      A      37          4.818
LGA    V      81      I      38          2.438
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    S      82      V      49          2.946
LGA    L      83      E      50          2.882
LGA    D      84      E      51          2.627
LGA    G      85      A      52          0.875
LGA    P      86      P      53          1.389
LGA    A      87      N      54          4.746
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    P      88      W      64          3.737
LGA    -       -      A      65           -
LGA    P      89      I      66           #
LGA    K      90      E      67           #
LGA    V      91      V      68           #
LGA    M      92      L      69           #
LGA    K      93      E      70          4.245
LGA    R      94      R      71          4.226
LGA    L      95      I      72          3.995
LGA    S      96      R      73          2.903
LGA    L      97      D      74          2.488
LGA    A      98      G      75          0.823
LGA    L      99      E      76          1.129
LGA    Q     100      N      77          0.365
LGA    K     101      V      78          2.363
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    L     102      V      91           #
LGA    T     103      M      92          2.995
LGA    E     104      K      93          1.523
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     39    3.21     5.13     24.854     1.177

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.790500 * X  +  -0.612383 * Y  +  -0.009857 * Z  +  23.374912
  Y_new =  -0.332672 * X  +   0.415809 * Y  +   0.846423 * Z  +  20.286514
  Z_new =  -0.514237 * X  +   0.672376 * Y  +  -0.532420 * Z  +  15.154983 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.240547   -0.901046  [ DEG:   128.3739    -51.6261 ]
  Theta =   0.540118    2.601475  [ DEG:    30.9465    149.0535 ]
  Phi   =  -2.743253    0.398340  [ DEG:  -157.1768     22.8232 ]
 
# 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: T0343TS393_5                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS393_5.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104   94   5.0   39   3.21    5.13  24.854
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS393_5
PFRMAT TS
TARGET T0343
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      41.220  11.767  28.025  1.00 25.00           C
ATOM      2  CA  THR     2      37.787  10.217  28.089  1.00 25.00           C
ATOM      3  CA  TRP     3      34.967  11.961  26.259  1.00 25.00           C
ATOM      4  CA  ARG     4      34.574  14.922  23.906  1.00 25.00           C
ATOM      5  CA  GLU     5      34.234  18.600  24.921  1.00 25.00           C
ATOM      6  CA  ILE     6      31.097  18.934  22.751  1.00 25.00           C
ATOM      7  CA  LEU     7      29.617  15.791  24.363  1.00 25.00           C
ATOM      8  CA  ARG     8      30.359  17.199  27.846  1.00 25.00           C
ATOM      9  CA  LYS     9      29.083  13.915  29.184  1.00 25.00           C
ATOM     10  CA  GLU    10      26.751  11.191  27.968  1.00 25.00           C
ATOM     11  CA  GLY    11      27.627   7.746  26.700  1.00 25.00           C
ATOM     12  CA  PHE    12      28.196   9.627  23.402  1.00 25.00           C
ATOM     13  CA  LEU    13      30.298  11.700  20.963  1.00 25.00           C
ATOM     14  CA  ASP    14      30.215   8.837  18.419  1.00 25.00           C
ATOM     15  CA  LEU    15      26.412   8.587  18.789  1.00 25.00           C
ATOM     16  CA  GLY    16      26.086  12.364  18.252  1.00 25.00           C
ATOM     17  CA  GLU    17      28.272  12.132  15.116  1.00 25.00           C
ATOM     18  CA  PHE    18      26.108   9.263  13.791  1.00 25.00           C
ATOM     19  CA  ILE    19      22.306   9.710  13.303  1.00 25.00           C
ATOM     20  CA  VAL    20      21.255  13.082  14.820  1.00 25.00           C
ATOM     21  CA  GLU    21      24.284  15.068  13.566  1.00 25.00           C
ATOM     22  CA  LEU    22      24.318  18.779  14.299  1.00 25.00           C
ATOM     23  CA  VAL    23      23.249  17.835  17.831  1.00 25.00           C
ATOM     24  CA  TYR    24      24.759  19.621  20.863  1.00 25.00           C
ATOM     25  CA  ILE    25      25.208  21.671  24.028  1.00 25.00           C
ATOM     26  CA  ASP    26      25.410  24.927  26.056  1.00 25.00           C
ATOM     27  CA  CYS    27      25.323  27.602  28.779  1.00 25.00           C
ATOM     28  CA  PRO    28      26.399  27.241  32.406  1.00 25.00           C
ATOM     29  CA  CYS    29      29.469  25.352  33.464  1.00 25.00           C
ATOM     30  CA  GLU    30      31.392  28.418  34.508  1.00 25.00           C
ATOM     31  CA  PRO    31      32.548  28.542  30.884  1.00 25.00           C
ATOM     32  CA  ILE    32      31.037  28.195  27.409  1.00 25.00           C
ATOM     33  CA  PRO    33      29.561  27.288  24.077  1.00 25.00           C
ATOM     34  CA  PRO    34      29.260  23.960  22.173  1.00 25.00           C
ATOM     35  CA  THR    35      26.951  23.998  19.117  1.00 25.00           C
ATOM     36  CA  LEU    36      28.036  21.461  16.437  1.00 25.00           C
ATOM     37  CA  ALA    37      29.036  17.839  16.807  1.00 25.00           C
ATOM     38  CA  ILE    38      29.335  17.203  13.011  1.00 25.00           C
ATOM     39  CA  TYR    39      31.991  16.645  10.302  1.00 25.00           C
ATOM     40  CA  ASP    40      33.644  16.894   6.947  1.00 25.00           C
ATOM     41  CA  LYS    41      37.136  16.020   5.591  1.00 25.00           C
ATOM     42  CA  LYS    42      39.459  17.676   8.103  1.00 25.00           C
ATOM     43  CA  GLY    43      38.040  21.053   7.075  1.00 25.00           C
ATOM     44  CA  ASP    44      34.718  22.557   7.931  1.00 25.00           C
ATOM     45  CA  GLU    45      31.151  21.297   8.056  1.00 25.00           C
ATOM     46  CA  TRP    46      27.996  21.694  10.192  1.00 25.00           C
ATOM     47  CA  TYR    47      26.028  24.575  11.753  1.00 25.00           C
ATOM     48  CA  LYS    48      27.208  28.050  12.950  1.00 25.00           C
ATOM     49  CA  VAL    49      23.806  28.188  14.664  1.00 25.00           C
ATOM     50  CA  GLU    50      22.214  31.169  16.414  1.00 25.00           C
ATOM     51  CA  GLU    51      22.090  34.823  17.383  1.00 25.00           C
ATOM     52  CA  ALA    52      25.097  37.136  17.820  1.00 25.00           C
ATOM     53  CA  PRO    53      28.300  36.057  16.105  1.00 25.00           C
ATOM     54  CA  ASN    54      27.186  38.031  13.028  1.00 25.00           C
ATOM     55  CA  VAL    55      23.398  37.396  12.744  1.00 25.00           C
ATOM     56  CA  GLN    56      24.161  37.096   9.003  1.00 25.00           C
ATOM     57  CA  ASN    57      26.565  34.198   9.700  1.00 25.00           C
ATOM     58  CA  TYR    58      23.889  32.453  11.811  1.00 25.00           C
ATOM     59  CA  ARG    59      21.335  32.907   8.993  1.00 25.00           C
ATOM     60  CA  GLU    60      23.819  31.444   6.472  1.00 25.00           C
ATOM     61  CA  ALA    61      24.431  28.447   8.779  1.00 25.00           C
ATOM     62  CA  VAL    62      20.655  27.900   9.110  1.00 25.00           C
ATOM     63  CA  GLU    63      20.276  28.036   5.300  1.00 25.00           C
ATOM     64  CA  TRP    64      23.106  25.485   4.904  1.00 25.00           C
ATOM     65  CA  ALA    65      21.423  23.185   7.462  1.00 25.00           C
ATOM     66  CA  ILE    66      18.099  23.484   5.583  1.00 25.00           C
ATOM     67  CA  GLU    67      19.857  22.630   2.289  1.00 25.00           C
ATOM     68  CA  VAL    68      21.490  19.577   3.925  1.00 25.00           C
ATOM     69  CA  LEU    69      18.087  18.441   5.262  1.00 25.00           C
ATOM     70  CA  GLU    70      16.556  18.838   1.774  1.00 25.00           C
ATOM     71  CA  ARG    71      19.413  16.785   0.260  1.00 25.00           C
ATOM     72  CA  ILE    72      18.872  14.050   2.886  1.00 25.00           C
ATOM     73  CA  ARG    73      15.124  14.003   2.100  1.00 25.00           C
ATOM     74  CA  ASP    74      16.065  11.784  -0.888  1.00 25.00           C
ATOM     75  CA  GLY    75      18.902  12.182  -3.407  1.00 25.00           C
ATOM     76  CA  GLU    76      22.410  10.695  -2.913  1.00 25.00           C
ATOM     77  CA  ASN    77      22.909   9.840   0.759  1.00 25.00           C
ATOM     78  CA  VAL    78      21.831  10.221   4.394  1.00 25.00           C
ATOM     79  CA  LYS    79      21.472  11.159   8.034  1.00 25.00           C
ATOM     80  CA  LEU    80      20.224  14.603   8.893  1.00 25.00           C
ATOM     81  CA  VAL    81      20.706  17.849  10.789  1.00 25.00           C
ATOM     82  CA  SER    82      16.938  17.866  10.929  1.00 25.00           C
ATOM     83  CA  LEU    83      15.701  21.187  12.417  1.00 25.00           C
ATOM     84  CA  ASP    84      12.996  23.188  10.569  1.00 25.00           C
ATOM     85  CA  GLY    85      12.337  26.926  10.830  1.00 25.00           C
ATOM     86  CA  PRO    86      11.644  29.387  13.685  1.00 25.00           C
ATOM     87  CA  ALA    87      15.280  28.774  14.647  1.00 25.00           C
ATOM     88  CA  PRO    88      15.167  29.005  18.414  1.00 25.00           C
ATOM     89  CA  PRO    89      11.455  28.396  19.253  1.00 25.00           C
ATOM     90  CA  LYS    90       9.118  26.336  17.025  1.00 25.00           C
ATOM     91  CA  VAL    91      12.135  24.683  15.344  1.00 25.00           C
ATOM     92  CA  MET    92      13.627  23.859  18.773  1.00 25.00           C
ATOM     93  CA  LYS    93      10.291  22.336  19.884  1.00 25.00           C
ATOM     94  CA  ARG    94      10.160  20.230  16.687  1.00 25.00           C
ATOM     95  CA  LEU    95      13.742  19.023  17.306  1.00 25.00           C
ATOM     96  CA  SER    96      12.830  18.088  20.907  1.00 25.00           C
ATOM     97  CA  LEU    97       9.767  16.160  19.656  1.00 25.00           C
ATOM     98  CA  ALA    98      11.944  14.305  17.109  1.00 25.00           C
ATOM     99  CA  LEU    99      14.453  13.416  19.864  1.00 25.00           C
ATOM    100  CA  GLN   100      11.606  12.120  22.073  1.00 25.00           C
ATOM    101  CA  LYS   101      10.287   9.998  19.171  1.00 25.00           C
ATOM    102  CA  LEU   102      13.793   8.572  18.588  1.00 25.00           C
ATOM    103  CA  THR   103      14.045   9.173  14.847  1.00 25.00           C
ATOM    104  CA  GLU   104      16.236   6.040  14.828  1.00 25.00           C
TER
END
