
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS168_4-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          1.648
LGA    S       2      S       2          2.873
LGA    I       3      I       3          2.353
LGA    T       4      T       4          1.239
LGA    S       5      S       5          1.570
LGA    T       6      T       6          1.354
LGA    D       7      D       7          2.098
LGA    I       8      I       8          2.090
LGA    C       9      -       -           -
LGA    Q      10      C       9          1.226
LGA    A      11      Q      10          2.487
LGA    A      12      A      11          4.253
LGA    D      13      A      12          4.103
LGA    A      14      D      13          3.902
LGA    L      15      -       -           -
LGA    K      16      A      14          2.291
LGA    G      17      L      15          3.160
LGA    F      18      K      16          4.520
LGA    V      19      G      17          4.652
LGA    G      20      F      18          3.539
LGA    F      21      V      19          3.807
LGA    -       -      G      20           -
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           -
LGA    -       -      V      30           -
LGA    -       -      R      31           -
LGA    -       -      F      32           -
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      D      43           -
LGA    -       -      D      44           -
LGA    -       -      S      45           -
LGA    N      22      I      46          4.243
LGA    R      23      -       -           -
LGA    K      24      -       -           -
LGA    T      25      T      47           #
LGA    G      26      P      48          4.318
LGA    R      27      T      49          4.984
LGA    Y      28      S      50          4.530
LGA    -       -      E      51           -
LGA    I      29      F      52          3.208
LGA    V      30      V      53          2.736
LGA    R      31      W      54          4.172
LGA    -       -      S      55           -
LGA    -       -      S      56           -
LGA    -       -      V      57           -
LGA    -       -      R      58           -
LGA    -       -      D      59           -
LGA    -       -      D      60           -
LGA    -       -      V      61           -
LGA    -       -      M      62           -
LGA    -       -      R      63           -
LGA    F      32      L      64          4.500
LGA    S      33      G      65          4.643
LGA    E      34      -       -           -
LGA    D      35      -       -           -
LGA    S      36      R      66          3.100
LGA    F      37      E      67          1.436
LGA    G      38      Q      68           #
LGA    M      39      L      69          3.101
LGA    D      40      Q      70          3.683
LGA    -       -      I      71           -
LGA    V      41      L      72          0.360
LGA    A      42      L      73          4.028
LGA    D      43      E      74          1.799
LGA    D      44      Q      75           #
LGA    S      45      N      76           -
LGA    I      46      I      77           -
LGA    T      47      N      78           -
LGA    P      48      E      79           -
LGA    T      49      R      80           -
LGA    S      50      -       -           -
LGA    E      51      -       -           -
LGA    F      52      -       -           -
LGA    V      53      -       -           -
LGA    W      54      -       -           -
LGA    S      55      L      81           #
LGA    S      56      N      82           -
LGA    V      57      I      83           -
LGA    R      58      G      84           -
LGA    D      59      E      85           -
LGA    D      60      P      86           -
LGA    V      61      L      87           -
LGA    M      62      L      88           -
LGA    R      63      V      89           -
LGA    L      64      Y      90           -
LGA    G      65      L      91           -
LGA    R      66      R      92           -
LGA    E      67      R      93           -
LGA    -       -      Q      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      P      97           -
LGA    -       -      E      98           -
LGA    -       -      I      99           -
LGA    Q      68      T     100           #
LGA    L      69      A     101          5.230
LGA    Q      70      Q     102          6.020
LGA    I      71      R     103          3.469
LGA    L      72      -       -           -
LGA    L      73      -       -           -
LGA    E      74      -       -           -
LGA    Q      75      -       -           -
LGA    N      76      -       -           -
LGA    I      77      -       -           -
LGA    N      78      -       -           -
LGA    E      79      -       -           -
LGA    R      80      -       -           -
LGA    L      81      -       -           -
LGA    N      82      -       -           -
LGA    I      83      -       -           -
LGA    G      84      -       -           -
LGA    E      85      -       -           -
LGA    P      86      -       -           -
LGA    L      87      -       -           -
LGA    L      88      -       -           -
LGA    V      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    R      92      -       -           -
LGA    R      93      -       -           -
LGA    Q      94      -       -           -
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     38    3.49    28.95     20.418     1.059

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.101136 * X  +  -0.423574 * Y  +  -0.900198 * Z  +   6.332860
  Y_new =   0.967353 * X  +  -0.169481 * Y  +   0.188427 * Z  +  12.027192
  Z_new =  -0.232379 * X  +  -0.889866 * Y  +   0.392605 * Z  + -12.249328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.155289    1.986304  [ DEG:   -66.1932    113.8068 ]
  Theta =   0.234523    2.907070  [ DEG:    13.4372    166.5628 ]
  Phi   =   1.466626   -1.674967  [ DEG:    84.0315    -95.9685 ]
 
# 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_4-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS168_4-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   38   3.49   28.95  20.418
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS168_4-D1
PFRMAT TS
TARGET T0314
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       2.904   1.681  -2.075  1.00 25.00           C
ATOM      2  CA  SER     2       2.037   4.715   0.077  1.00 25.00           C
ATOM      3  CA  ILE     3       2.522   6.671  -3.083  1.00 25.00           C
ATOM      4  CA  THR     4       2.543  10.417  -2.212  1.00 25.00           C
ATOM      5  CA  SER     5       3.340  14.134  -2.122  1.00 25.00           C
ATOM      6  CA  THR     6       4.635  16.603  -4.748  1.00 25.00           C
ATOM      7  CA  ASP     7       8.240  15.908  -3.660  1.00 25.00           C
ATOM      8  CA  ILE     8       7.619  12.137  -3.924  1.00 25.00           C
ATOM      9  CA  CYS     9       6.155  12.599  -7.432  1.00 25.00           C
ATOM     10  CA  GLN    10       9.211  14.667  -8.461  1.00 25.00           C
ATOM     11  CA  ALA    11      11.539  11.944  -7.107  1.00 25.00           C
ATOM     12  CA  ALA    12       9.601   9.280  -9.060  1.00 25.00           C
ATOM     13  CA  ASP    13       9.871  11.385 -12.248  1.00 25.00           C
ATOM     14  CA  ALA    14      13.642  11.775 -11.700  1.00 25.00           C
ATOM     15  CA  LEU    15      13.987   7.992 -11.214  1.00 25.00           C
ATOM     16  CA  LYS    16      15.071   8.344  -7.583  1.00 25.00           C
ATOM     17  CA  GLY    17      16.577   5.074  -6.547  1.00 25.00           C
ATOM     18  CA  PHE    18      17.369   3.798 -10.022  1.00 25.00           C
ATOM     19  CA  VAL    19      18.639   4.800 -13.494  1.00 25.00           C
ATOM     20  CA  GLY    20      21.146   3.344 -15.983  1.00 25.00           C
ATOM     21  CA  PHE    21      24.695   4.832 -16.294  1.00 25.00           C
ATOM     22  CA  ASN    22      26.876   6.919 -18.623  1.00 25.00           C
ATOM     23  CA  ARG    23      27.371   8.851 -21.864  1.00 25.00           C
ATOM     24  CA  LYS    24      25.252  11.676 -23.219  1.00 25.00           C
ATOM     25  CA  THR    25      26.217  13.807 -20.200  1.00 25.00           C
ATOM     26  CA  GLY    26      24.115  11.906 -17.684  1.00 25.00           C
ATOM     27  CA  ARG    27      22.692   9.641 -14.956  1.00 25.00           C
ATOM     28  CA  TYR    28      19.768   8.200 -17.009  1.00 25.00           C
ATOM     29  CA  ILE    29      17.313   5.929 -18.892  1.00 25.00           C
ATOM     30  CA  VAL    30      13.956   6.351 -17.131  1.00 25.00           C
ATOM     31  CA  ARG    31      11.104   8.511 -18.534  1.00 25.00           C
ATOM     32  CA  PHE    32       7.572   8.539 -19.947  1.00 25.00           C
ATOM     33  CA  SER    33       6.660  10.711 -22.943  1.00 25.00           C
ATOM     34  CA  GLU    34       4.910   7.599 -24.169  1.00 25.00           C
ATOM     35  CA  ASP    35       3.890   5.248 -21.413  1.00 25.00           C
ATOM     36  CA  SER    36       3.993   5.656 -17.647  1.00 25.00           C
ATOM     37  CA  PHE    37       7.024   3.423 -17.875  1.00 25.00           C
ATOM     38  CA  GLY    38       6.107   1.474 -14.691  1.00 25.00           C
ATOM     39  CA  MET    39       9.140   3.350 -13.273  1.00 25.00           C
ATOM     40  CA  ASP    40      11.563   1.538 -15.580  1.00 25.00           C
ATOM     41  CA  VAL    41      14.509  -0.885 -15.211  1.00 25.00           C
ATOM     42  CA  ALA    42      16.268  -4.209 -15.820  1.00 25.00           C
ATOM     43  CA  ASP    43      14.914  -7.323 -17.473  1.00 25.00           C
ATOM     44  CA  ASP    44      15.169  -8.020 -21.254  1.00 25.00           C
ATOM     45  CA  SER    45      13.338  -5.218 -23.049  1.00 25.00           C
ATOM     46  CA  ILE    46      14.648  -2.103 -21.294  1.00 25.00           C
ATOM     47  CA  THR    47      14.096   0.475 -24.106  1.00 25.00           C
ATOM     48  CA  PRO    48      11.200   2.194 -25.890  1.00 25.00           C
ATOM     49  CA  THR    49      11.297   4.772 -23.117  1.00 25.00           C
ATOM     50  CA  SER    50      12.048   8.118 -24.730  1.00 25.00           C
ATOM     51  CA  GLU    51      15.088   8.906 -22.607  1.00 25.00           C
ATOM     52  CA  PHE    52      15.102  11.772 -20.141  1.00 25.00           C
ATOM     53  CA  VAL    53      15.887  11.751 -16.409  1.00 25.00           C
ATOM     54  CA  TRP    54      18.170  11.407 -13.420  1.00 25.00           C
ATOM     55  CA  SER    55      19.310   9.252 -10.437  1.00 25.00           C
ATOM     56  CA  SER    56      23.013   9.647  -9.729  1.00 25.00           C
ATOM     57  CA  VAL    57      25.344  12.075  -7.876  1.00 25.00           C
ATOM     58  CA  ARG    58      22.598  12.167  -5.209  1.00 25.00           C
ATOM     59  CA  ASP    59      22.940  15.972  -4.951  1.00 25.00           C
ATOM     60  CA  ASP    60      22.681  16.278  -8.760  1.00 25.00           C
ATOM     61  CA  VAL    61      19.541  14.085  -8.747  1.00 25.00           C
ATOM     62  CA  MET    62      18.004  16.260  -5.995  1.00 25.00           C
ATOM     63  CA  ARG    63      18.791  19.417  -8.016  1.00 25.00           C
ATOM     64  CA  LEU    64      17.168  17.865 -11.119  1.00 25.00           C
ATOM     65  CA  GLY    65      14.058  16.966  -9.073  1.00 25.00           C
ATOM     66  CA  ARG    66      13.874  20.550  -7.734  1.00 25.00           C
ATOM     67  CA  GLU    67      14.162  21.923 -11.297  1.00 25.00           C
ATOM     68  CA  GLN    68      11.359  19.582 -12.451  1.00 25.00           C
ATOM     69  CA  LEU    69       9.158  20.742  -9.539  1.00 25.00           C
ATOM     70  CA  GLN    70       9.838  24.399 -10.448  1.00 25.00           C
ATOM     71  CA  ILE    71       8.916  23.688 -14.097  1.00 25.00           C
ATOM     72  CA  LEU    72       5.669  21.997 -12.973  1.00 25.00           C
ATOM     73  CA  LEU    73       4.832  25.014 -10.767  1.00 25.00           C
ATOM     74  CA  GLU    74       5.483  27.377 -13.710  1.00 25.00           C
ATOM     75  CA  GLN    75       3.207  25.258 -15.946  1.00 25.00           C
ATOM     76  CA  ASN    76       0.460  25.351 -13.279  1.00 25.00           C
ATOM     77  CA  ILE    77       0.803  29.156 -13.022  1.00 25.00           C
ATOM     78  CA  ASN    78       0.545  29.462 -16.831  1.00 25.00           C
ATOM     79  CA  GLU    79      -2.596  27.269 -16.818  1.00 25.00           C
ATOM     80  CA  ARG    80      -4.133  29.444 -14.066  1.00 25.00           C
ATOM     81  CA  LEU    81      -3.346  32.601 -16.087  1.00 25.00           C
ATOM     82  CA  ASN    82      -4.469  31.371 -19.553  1.00 25.00           C
ATOM     83  CA  ILE    83      -6.999  28.634 -18.980  1.00 25.00           C
ATOM     84  CA  GLY    84      -9.192  26.116 -17.102  1.00 25.00           C
ATOM     85  CA  GLU    85      -9.126  22.361 -16.764  1.00 25.00           C
ATOM     86  CA  PRO    86      -8.244  18.853 -18.022  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.257  18.177 -14.820  1.00 25.00           C
ATOM     88  CA  LEU    88      -9.222  19.356 -12.701  1.00 25.00           C
ATOM     89  CA  VAL    89     -11.572  17.059 -14.669  1.00 25.00           C
ATOM     90  CA  TYR    90      -9.184  14.114 -14.132  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.055  14.870 -10.379  1.00 25.00           C
ATOM     92  CA  ARG    92     -12.881  14.989 -10.248  1.00 25.00           C
ATOM     93  CA  ARG    93     -13.073  11.628 -12.075  1.00 25.00           C
ATOM     94  CA  GLN    94     -16.349   9.873 -11.352  1.00 25.00           C
ATOM     95  CA  ASP    95     -18.925  12.324  -9.955  1.00 25.00           C
ATOM     96  CA  LEU    96     -18.195  13.635  -6.425  1.00 25.00           C
ATOM     97  CA  PRO    97     -19.824  12.238  -3.254  1.00 25.00           C
ATOM     98  CA  GLU    98     -20.533   8.474  -3.251  1.00 25.00           C
ATOM     99  CA  ILE    99     -16.859   7.756  -4.057  1.00 25.00           C
ATOM    100  CA  THR   100     -15.758  10.053  -1.196  1.00 25.00           C
ATOM    101  CA  ALA   101     -18.148   8.258   1.198  1.00 25.00           C
ATOM    102  CA  GLN   102     -16.751   4.868   0.089  1.00 25.00           C
ATOM    103  CA  ARG   103     -13.179   6.124   0.663  1.00 25.00           C
TER
END
