
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS393_3.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      T       2           -
LGA    -       -      W       3           -
LGA    -       -      R       4           -
LGA    T       2      E       5          3.846
LGA    W       3      I       6          4.045
LGA    R       4      L       7          4.578
LGA    E       5      R       8          3.552
LGA    I       6      K       9           #
LGA    L       7      E      10          4.410
LGA    R       8      G      11          5.510
LGA    K       9      -       -           -
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    D      14      -       -           -
LGA    L      15      -       -           -
LGA    G      16      F      12          4.032
LGA    E      17      L      13           #
LGA    F      18      -       -           -
LGA    I      19      D      14          3.799
LGA    V      20      L      15          4.471
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    E      21      I      19          2.790
LGA    L      22      V      20          1.403
LGA    V      23      E      21           #
LGA    Y      24      L      22          1.330
LGA    I      25      V      23          3.244
LGA    D      26      Y      24          3.448
LGA    C      27      I      25           #
LGA    P      28      D      26          4.308
LGA    C      29      C      27          2.460
LGA    E      30      P      28          3.205
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    P      31      P      31           #
LGA    I      32      I      32          4.907
LGA    -       -      P      33           -
LGA    P      33      P      34          3.466
LGA    P      34      T      35          2.462
LGA    T      35      L      36           #
LGA    L      36      A      37          2.278
LGA    A      37      I      38          4.698
LGA    I      38      Y      39          3.505
LGA    Y      39      D      40          5.132
LGA    D      40      -       -           -
LGA    K      41      -       -           -
LGA    K      42      -       -           -
LGA    G      43      K      41          4.111
LGA    D      44      K      42          2.480
LGA    E      45      G      43           #
LGA    W      46      D      44           #
LGA    Y      47      -       -           -
LGA    K      48      -       -           -
LGA    V      49      -       -           -
LGA    E      50      -       -           -
LGA    E      51      -       -           -
LGA    A      52      -       -           -
LGA    P      53      -       -           -
LGA    N      54      -       -           -
LGA    V      55      -       -           -
LGA    Q      56      -       -           -
LGA    N      57      -       -           -
LGA    Y      58      -       -           -
LGA    R      59      -       -           -
LGA    E      60      -       -           -
LGA    A      61      -       -           -
LGA    V      62      -       -           -
LGA    E      63      -       -           -
LGA    W      64      -       -           -
LGA    A      65      -       -           -
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      -       -           -
LGA    V      81      -       -           -
LGA    S      82      E      45          1.182
LGA    L      83      W      46           -
LGA    D      84      Y      47           -
LGA    G      85      K      48           -
LGA    P      86      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    -       -      N      54           -
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    -       -      W      64           -
LGA    -       -      A      65           -
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           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    A      87      A      87          3.760
LGA    P      88      P      88          3.772
LGA    P      89      P      89          4.082
LGA    K      90      K      90          2.018
LGA    V      91      V      91          2.034
LGA    M      92      M      92          1.806
LGA    K      93      K      93          2.119
LGA    R      94      R      94          1.222
LGA    L      95      L      95          1.582
LGA    S      96      S      96          1.352
LGA    L      97      L      97          0.567
LGA    A      98      A      98          1.754
LGA    L      99      L      99          1.263
LGA    Q     100      Q     100          0.694
LGA    K     101      K     101          2.298
LGA    L     102      -       -           -
LGA    T     103      -       -           -
LGA    E     104      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     42    3.25    42.86     27.460     1.253

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.840671 * X  +  -0.263900 * Y  +   0.472894 * Z  +  21.395090
  Y_new =  -0.372256 * X  +  -0.915815 * Y  +   0.150692 * Z  +  18.211042
  Z_new =   0.393316 * X  +  -0.302719 * Y  +  -0.868138 * Z  +  10.448607 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.806077    0.335516  [ DEG:  -160.7764     19.2236 ]
  Theta =  -0.404235   -2.737357  [ DEG:   -23.1610   -156.8390 ]
  Phi   =  -0.416856    2.724736  [ DEG:   -23.8841    156.1159 ]
 
# 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_3                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS393_3.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   42   3.25   42.86  27.460
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS393_3
PFRMAT TS
TARGET T0343
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      25.478  28.066  30.525  1.00 25.00           C
ATOM      2  CA  THR     2      27.548  25.747  28.348  1.00 25.00           C
ATOM      3  CA  TRP     3      26.552  24.699  24.842  1.00 25.00           C
ATOM      4  CA  ARG     4      26.088  26.701  21.578  1.00 25.00           C
ATOM      5  CA  GLU     5      29.337  24.916  20.615  1.00 25.00           C
ATOM      6  CA  ILE     6      28.027  24.401  17.054  1.00 25.00           C
ATOM      7  CA  LEU     7      27.101  28.111  16.832  1.00 25.00           C
ATOM      8  CA  ARG     8      30.600  29.082  18.050  1.00 25.00           C
ATOM      9  CA  LYS     9      34.226  29.740  16.996  1.00 25.00           C
ATOM     10  CA  GLU    10      35.938  27.388  14.600  1.00 25.00           C
ATOM     11  CA  GLY    11      37.773  25.675  17.471  1.00 25.00           C
ATOM     12  CA  PHE    12      36.125  22.289  16.989  1.00 25.00           C
ATOM     13  CA  LEU    13      33.006  23.296  15.008  1.00 25.00           C
ATOM     14  CA  ASP    14      34.196  21.208  12.026  1.00 25.00           C
ATOM     15  CA  LEU    15      34.782  18.205  14.331  1.00 25.00           C
ATOM     16  CA  GLY    16      31.270  18.616  15.800  1.00 25.00           C
ATOM     17  CA  GLU    17      29.784  18.756  12.273  1.00 25.00           C
ATOM     18  CA  PHE    18      31.694  15.577  11.317  1.00 25.00           C
ATOM     19  CA  ILE    19      29.618  12.956  13.179  1.00 25.00           C
ATOM     20  CA  VAL    20      25.880  13.068  13.132  1.00 25.00           C
ATOM     21  CA  GLU    21      25.847  16.219  15.174  1.00 25.00           C
ATOM     22  CA  LEU    22      22.943  17.547  13.138  1.00 25.00           C
ATOM     23  CA  VAL    23      20.414  20.320  13.741  1.00 25.00           C
ATOM     24  CA  TYR    24      23.011  23.100  13.460  1.00 25.00           C
ATOM     25  CA  ILE    25      22.624  26.862  13.287  1.00 25.00           C
ATOM     26  CA  ASP    26      20.741  30.161  13.500  1.00 25.00           C
ATOM     27  CA  CYS    27      18.872  33.400  13.956  1.00 25.00           C
ATOM     28  CA  PRO    28      21.674  35.809  13.128  1.00 25.00           C
ATOM     29  CA  CYS    29      24.127  38.010  11.288  1.00 25.00           C
ATOM     30  CA  GLU    30      24.829  39.501   7.821  1.00 25.00           C
ATOM     31  CA  PRO    31      24.325  35.949   6.400  1.00 25.00           C
ATOM     32  CA  ILE    32      23.624  32.980   8.739  1.00 25.00           C
ATOM     33  CA  PRO    33      23.027  29.194   8.729  1.00 25.00           C
ATOM     34  CA  PRO    34      22.016  25.559   8.443  1.00 25.00           C
ATOM     35  CA  THR    35      25.236  23.586   8.949  1.00 25.00           C
ATOM     36  CA  LEU    36      22.909  20.546   8.996  1.00 25.00           C
ATOM     37  CA  ALA    37      25.892  18.196   9.072  1.00 25.00           C
ATOM     38  CA  ILE    38      27.556  14.767   8.601  1.00 25.00           C
ATOM     39  CA  TYR    39      29.408  11.433   8.416  1.00 25.00           C
ATOM     40  CA  ASP    40      31.178   8.384   6.995  1.00 25.00           C
ATOM     41  CA  LYS    41      32.116   4.758   7.286  1.00 25.00           C
ATOM     42  CA  LYS    42      30.002   3.304   4.528  1.00 25.00           C
ATOM     43  CA  GLY    43      27.782   2.135   7.389  1.00 25.00           C
ATOM     44  CA  ASP    44      25.339   4.885   6.417  1.00 25.00           C
ATOM     45  CA  GLU    45      24.124   8.101   7.930  1.00 25.00           C
ATOM     46  CA  TRP    46      22.517  11.130   9.671  1.00 25.00           C
ATOM     47  CA  TYR    47      18.913  12.422   9.804  1.00 25.00           C
ATOM     48  CA  LYS    48      15.331  13.312   8.718  1.00 25.00           C
ATOM     49  CA  VAL    49      14.229  16.440  10.523  1.00 25.00           C
ATOM     50  CA  GLU    50      10.789  18.188  10.432  1.00 25.00           C
ATOM     51  CA  GLU    51       7.714  18.895  12.614  1.00 25.00           C
ATOM     52  CA  ALA    52       7.267  19.942  16.184  1.00 25.00           C
ATOM     53  CA  PRO    53       8.420  22.517  18.798  1.00 25.00           C
ATOM     54  CA  ASN    54       6.806  25.806  17.780  1.00 25.00           C
ATOM     55  CA  VAL    55       6.465  24.542  14.207  1.00 25.00           C
ATOM     56  CA  GLN    56       7.829  27.416  12.074  1.00 25.00           C
ATOM     57  CA  ASN    57      11.401  26.557  13.156  1.00 25.00           C
ATOM     58  CA  TYR    58      10.818  22.882  12.248  1.00 25.00           C
ATOM     59  CA  ARG    59       9.470  23.919   8.816  1.00 25.00           C
ATOM     60  CA  GLU    60      12.542  26.134   8.251  1.00 25.00           C
ATOM     61  CA  ALA    61      14.845  23.229   9.214  1.00 25.00           C
ATOM     62  CA  VAL    62      12.994  20.923   6.780  1.00 25.00           C
ATOM     63  CA  GLU    63      13.355  23.529   3.997  1.00 25.00           C
ATOM     64  CA  TRP    64      17.102  23.830   4.733  1.00 25.00           C
ATOM     65  CA  ALA    65      17.460  20.020   4.594  1.00 25.00           C
ATOM     66  CA  ILE    66      15.610  19.943   1.242  1.00 25.00           C
ATOM     67  CA  GLU    67      17.916  22.680  -0.121  1.00 25.00           C
ATOM     68  CA  VAL    68      20.986  20.707   1.040  1.00 25.00           C
ATOM     69  CA  LEU    69      19.636  17.555  -0.665  1.00 25.00           C
ATOM     70  CA  GLU    70      19.056  19.523  -3.899  1.00 25.00           C
ATOM     71  CA  ARG    71      22.628  20.892  -3.735  1.00 25.00           C
ATOM     72  CA  ILE    72      23.989  17.349  -3.224  1.00 25.00           C
ATOM     73  CA  ARG    73      21.965  16.112  -6.229  1.00 25.00           C
ATOM     74  CA  ASP    74      23.857  18.613  -8.279  1.00 25.00           C
ATOM     75  CA  GLY    75      27.448  17.782  -7.418  1.00 25.00           C
ATOM     76  CA  GLU    76      27.794  21.415  -6.252  1.00 25.00           C
ATOM     77  CA  ASN    77      30.565  20.144  -3.948  1.00 25.00           C
ATOM     78  CA  VAL    78      29.357  19.169  -0.413  1.00 25.00           C
ATOM     79  CA  LYS    79      26.397  18.393   1.860  1.00 25.00           C
ATOM     80  CA  LEU    80      24.909  16.049   4.464  1.00 25.00           C
ATOM     81  CA  VAL    81      21.948  15.030   6.587  1.00 25.00           C
ATOM     82  CA  SER    82      21.311  11.775   4.696  1.00 25.00           C
ATOM     83  CA  LEU    83      17.870  10.316   5.328  1.00 25.00           C
ATOM     84  CA  ASP    84      16.301   7.121   3.940  1.00 25.00           C
ATOM     85  CA  GLY    85      13.245   6.145   1.809  1.00 25.00           C
ATOM     86  CA  PRO    86      10.330   5.845   4.290  1.00 25.00           C
ATOM     87  CA  ALA    87      11.563   9.253   5.479  1.00 25.00           C
ATOM     88  CA  PRO    88       9.104   8.533   8.342  1.00 25.00           C
ATOM     89  CA  PRO    89       9.563   4.876   9.282  1.00 25.00           C
ATOM     90  CA  LYS    90      12.641   2.699   9.955  1.00 25.00           C
ATOM     91  CA  VAL    91      14.935   5.692   9.289  1.00 25.00           C
ATOM     92  CA  MET    92      12.869   7.841  11.693  1.00 25.00           C
ATOM     93  CA  LYS    93      13.101   5.113  14.371  1.00 25.00           C
ATOM     94  CA  ARG    94      16.895   4.922  13.883  1.00 25.00           C
ATOM     95  CA  LEU    95      17.154   8.729  14.221  1.00 25.00           C
ATOM     96  CA  SER    96      15.079   8.609  17.438  1.00 25.00           C
ATOM     97  CA  LEU    97      17.349   5.856  18.829  1.00 25.00           C
ATOM     98  CA  ALA    98      20.445   7.944  17.976  1.00 25.00           C
ATOM     99  CA  LEU    99      18.908  10.983  19.728  1.00 25.00           C
ATOM    100  CA  GLN   100      18.155   8.851  22.819  1.00 25.00           C
ATOM    101  CA  LYS   101      21.762   7.564  22.840  1.00 25.00           C
ATOM    102  CA  LEU   102      23.071  11.154  22.587  1.00 25.00           C
ATOM    103  CA  THR   103      20.815  14.146  23.282  1.00 25.00           C
ATOM    104  CA  GLU   104      17.163  13.934  24.374  1.00 25.00           C
TER
END
