
#######################################################
#                                                     #
#                        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  106 (  106),  selected  106 , name T0314TS168_3
# Molecule2: number of CA atoms  106 ( 1704),  selected  106 , name T0314.pdb
# PARAMETERS: T0314TS168_3.T0314.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    -       -      S       2           -
LGA    -       -      I       3           -
LGA    -       -      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    M       1      D       7           #
LGA    S       2      I       8           -
LGA    I       3      C       9           #
LGA    T       4      Q      10          3.059
LGA    -       -      A      11           -
LGA    S       5      A      12          1.200
LGA    T       6      D      13           #
LGA    D       7      -       -           -
LGA    I       8      A      14           #
LGA    C       9      L      15          0.707
LGA    Q      10      -       -           -
LGA    A      11      -       -           -
LGA    A      12      K      16          2.463
LGA    D      13      -       -           -
LGA    A      14      -       -           -
LGA    L      15      -       -           -
LGA    K      16      G      17          3.582
LGA    G      17      F      18          1.871
LGA    F      18      V      19          1.870
LGA    V      19      G      20          1.893
LGA    G      20      F      21          3.418
LGA    F      21      N      22          0.529
LGA    N      22      R      23          3.720
LGA    R      23      K      24          3.264
LGA    K      24      T      25          4.734
LGA    T      25      G      26          2.141
LGA    G      26      R      27          2.172
LGA    R      27      Y      28          3.626
LGA    Y      28      I      29          0.984
LGA    I      29      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    V      30      S      45          4.485
LGA    R      31      I      46          2.691
LGA    F      32      T      47          4.776
LGA    S      33      -       -           -
LGA    E      34      -       -           -
LGA    D      35      -       -           -
LGA    S      36      P      48          3.418
LGA    F      37      T      49           #
LGA    -       -      S      50           -
LGA    G      38      E      51          1.689
LGA    M      39      F      52          2.679
LGA    D      40      V      53           #
LGA    -       -      W      54           -
LGA    V      41      S      55           #
LGA    A      42      S      56           -
LGA    D      43      V      57           -
LGA    D      44      R      58           -
LGA    S      45      D      59           -
LGA    I      46      D      60           -
LGA    T      47      V      61           -
LGA    P      48      M      62           -
LGA    T      49      R      63           -
LGA    S      50      L      64           -
LGA    E      51      G      65           -
LGA    F      52      R      66           -
LGA    V      53      E      67           -
LGA    W      54      Q      68           -
LGA    S      55      L      69           -
LGA    S      56      Q      70           -
LGA    V      57      I      71           -
LGA    R      58      L      72           -
LGA    D      59      L      73           -
LGA    D      60      -       -           -
LGA    V      61      -       -           -
LGA    M      62      E      74           #
LGA    R      63      Q      75          3.789
LGA    L      64      N      76          3.512
LGA    G      65      I      77          4.015
LGA    R      66      -       -           -
LGA    E      67      -       -           -
LGA    Q      68      N      78          3.534
LGA    L      69      E      79           -
LGA    Q      70      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    -       -      I      83           -
LGA    -       -      G      84           -
LGA    -       -      E      85           -
LGA    -       -      P      86           -
LGA    I      71      L      87           #
LGA    L      72      L      88          3.111
LGA    L      73      -       -           -
LGA    E      74      V      89          4.656
LGA    Q      75      Y      90          3.749
LGA    N      76      L      91          3.148
LGA    I      77      R      92          1.984
LGA    N      78      R      93          4.444
LGA    E      79      Q      94          3.468
LGA    R      80      -       -           -
LGA    L      81      -       -           -
LGA    N      82      -       -           -
LGA    I      83      -       -           -
LGA    G      84      -       -           -
LGA    E      85      -       -           -
LGA    P      86      D      95          3.244
LGA    L      87      L      96          2.762
LGA    L      88      P      97          4.267
LGA    V      89      E      98           -
LGA    Y      90      I      99           #
LGA    L      91      T     100          3.842
LGA    R      92      A     101           -
LGA    R      93      -       -           -
LGA    Q      94      -       -           -
LGA    D      95      -       -           -
LGA    L      96      -       -           -
LGA    P      97      Q     102          4.084
LGA    E      98      -       -           -
LGA    I      99      -       -           -
LGA    T     100      R     103          3.293
LGA    A     101      Q     104          2.187
LGA    Q     102      L     105          2.483
LGA    R     103      R     106          4.448
LGA    Q     104      -       -           -
LGA    L     105      -       -           -
LGA    R     106      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  106  106    5.0     43    3.24     6.98     22.591     1.288

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.819651 * X  +  -0.130869 * Y  +  -0.557714 * Z  +  14.905647
  Y_new =   0.372691 * X  +   0.861177 * Y  +   0.345652 * Z  +   7.453794
  Z_new =   0.435056 * X  +  -0.491169 * Y  +   0.754639 * Z  + -15.569499 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.576984    2.564609  [ DEG:   -33.0587    146.9413 ]
  Theta =  -0.450100   -2.691493  [ DEG:   -25.7888   -154.2112 ]
  Phi   =   0.426751   -2.714842  [ DEG:    24.4510   -155.5490 ]
 
# 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_3                                  
REMARK     2: T0314.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS168_3.T0314.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  106  106   5.0   43   3.24    6.98  22.591
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS168_3
PFRMAT TS
TARGET T0314
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      15.728  13.922  -0.854  1.00 25.00           C
ATOM      2  CA  SER     2      16.657  15.791  -4.055  1.00 25.00           C
ATOM      3  CA  ILE     3      16.742  14.139  -7.462  1.00 25.00           C
ATOM      4  CA  THR     4      13.398  12.332  -7.519  1.00 25.00           C
ATOM      5  CA  SER     5      11.559   9.636  -9.496  1.00 25.00           C
ATOM      6  CA  THR     6      12.340   7.220  -6.628  1.00 25.00           C
ATOM      7  CA  ASP     7      12.192   4.258  -9.051  1.00 25.00           C
ATOM      8  CA  ILE     8      14.561   6.071 -11.451  1.00 25.00           C
ATOM      9  CA  CYS     9      16.984   6.774  -8.570  1.00 25.00           C
ATOM     10  CA  GLN    10      16.872   3.086  -7.545  1.00 25.00           C
ATOM     11  CA  ALA    11      17.586   2.035 -11.157  1.00 25.00           C
ATOM     12  CA  ALA    12      20.548   4.458 -11.303  1.00 25.00           C
ATOM     13  CA  ASP    13      21.904   3.037  -8.015  1.00 25.00           C
ATOM     14  CA  ALA    14      21.569  -0.523  -9.386  1.00 25.00           C
ATOM     15  CA  LEU    15      23.427   0.503 -12.573  1.00 25.00           C
ATOM     16  CA  LYS    16      26.145   2.932 -11.546  1.00 25.00           C
ATOM     17  CA  GLY    17      25.217   5.126 -14.510  1.00 25.00           C
ATOM     18  CA  PHE    18      23.745   3.030 -17.276  1.00 25.00           C
ATOM     19  CA  VAL    19      25.345   2.517 -20.669  1.00 25.00           C
ATOM     20  CA  GLY    20      26.545   0.400 -23.556  1.00 25.00           C
ATOM     21  CA  PHE    21      25.738  -3.207 -24.593  1.00 25.00           C
ATOM     22  CA  ASN    22      27.740  -6.502 -24.765  1.00 25.00           C
ATOM     23  CA  ARG    23      27.107  -6.064 -28.530  1.00 25.00           C
ATOM     24  CA  LYS    24      23.474  -7.223 -28.917  1.00 25.00           C
ATOM     25  CA  THR    25      21.923  -8.222 -25.614  1.00 25.00           C
ATOM     26  CA  GLY    26      19.264  -6.591 -23.427  1.00 25.00           C
ATOM     27  CA  ARG    27      22.191  -5.137 -21.436  1.00 25.00           C
ATOM     28  CA  TYR    28      22.907  -1.888 -19.601  1.00 25.00           C
ATOM     29  CA  ILE    29      20.525   0.691 -21.159  1.00 25.00           C
ATOM     30  CA  VAL    30      20.989   4.364 -22.088  1.00 25.00           C
ATOM     31  CA  ARG    31      22.758   7.728 -22.004  1.00 25.00           C
ATOM     32  CA  PHE    32      21.793  10.892 -23.786  1.00 25.00           C
ATOM     33  CA  SER    33      21.045  12.185 -20.328  1.00 25.00           C
ATOM     34  CA  GLU    34      23.241  15.234 -19.722  1.00 25.00           C
ATOM     35  CA  ASP    35      26.260  13.558 -18.125  1.00 25.00           C
ATOM     36  CA  SER    36      24.001  11.183 -16.291  1.00 25.00           C
ATOM     37  CA  PHE    37      20.489  12.373 -15.272  1.00 25.00           C
ATOM     38  CA  GLY    38      17.580  10.317 -16.680  1.00 25.00           C
ATOM     39  CA  MET    39      18.358   7.163 -18.743  1.00 25.00           C
ATOM     40  CA  ASP    40      16.418   8.365 -21.752  1.00 25.00           C
ATOM     41  CA  VAL    41      15.909   6.725 -25.208  1.00 25.00           C
ATOM     42  CA  ALA    42      15.498   3.844 -27.708  1.00 25.00           C
ATOM     43  CA  ASP    43      13.503   6.116 -29.922  1.00 25.00           C
ATOM     44  CA  ASP    44      14.335   8.990 -32.340  1.00 25.00           C
ATOM     45  CA  SER    45      17.881   8.536 -33.634  1.00 25.00           C
ATOM     46  CA  ILE    46      19.840   7.304 -30.614  1.00 25.00           C
ATOM     47  CA  THR    47      23.186   7.025 -28.953  1.00 25.00           C
ATOM     48  CA  PRO    48      26.862   6.120 -28.942  1.00 25.00           C
ATOM     49  CA  THR    49      27.566   6.429 -25.189  1.00 25.00           C
ATOM     50  CA  SER    50      27.576   9.321 -22.692  1.00 25.00           C
ATOM     51  CA  GLU    51      29.223   9.225 -19.200  1.00 25.00           C
ATOM     52  CA  PHE    52      28.719   5.524 -18.440  1.00 25.00           C
ATOM     53  CA  VAL    53      29.988   2.120 -17.304  1.00 25.00           C
ATOM     54  CA  TRP    54      30.278  -1.600 -17.928  1.00 25.00           C
ATOM     55  CA  SER    55      28.674  -2.010 -14.487  1.00 25.00           C
ATOM     56  CA  SER    56      28.024  -4.709 -11.907  1.00 25.00           C
ATOM     57  CA  VAL    57      27.675  -8.447 -12.620  1.00 25.00           C
ATOM     58  CA  ARG    58      25.882  -7.244 -15.783  1.00 25.00           C
ATOM     59  CA  ASP    59      23.155  -9.884 -15.269  1.00 25.00           C
ATOM     60  CA  ASP    60      22.730  -8.773 -11.629  1.00 25.00           C
ATOM     61  CA  VAL    61      22.439  -5.123 -12.751  1.00 25.00           C
ATOM     62  CA  MET    62      19.800  -6.106 -15.346  1.00 25.00           C
ATOM     63  CA  ARG    63      17.842  -8.019 -12.668  1.00 25.00           C
ATOM     64  CA  LEU    64      17.996  -4.975 -10.347  1.00 25.00           C
ATOM     65  CA  GLY    65      16.736  -2.723 -13.176  1.00 25.00           C
ATOM     66  CA  ARG    66      13.854  -5.151 -13.858  1.00 25.00           C
ATOM     67  CA  GLU    67      12.951  -5.164 -10.137  1.00 25.00           C
ATOM     68  CA  GLN    68      12.981  -1.335 -10.091  1.00 25.00           C
ATOM     69  CA  LEU    69      10.709  -1.255 -13.173  1.00 25.00           C
ATOM     70  CA  GLN    70       8.302  -3.717 -11.493  1.00 25.00           C
ATOM     71  CA  ILE    71       8.245  -1.544  -8.339  1.00 25.00           C
ATOM     72  CA  LEU    72       7.506   1.558 -10.459  1.00 25.00           C
ATOM     73  CA  LEU    73       4.655  -0.296 -12.221  1.00 25.00           C
ATOM     74  CA  GLU    74       3.220  -1.358  -8.833  1.00 25.00           C
ATOM     75  CA  GLN    75       3.404   2.261  -7.592  1.00 25.00           C
ATOM     76  CA  ASN    76       1.611   3.462 -10.755  1.00 25.00           C
ATOM     77  CA  ILE    77      -1.116   0.823 -10.242  1.00 25.00           C
ATOM     78  CA  ASN    78      -1.541   1.934  -6.602  1.00 25.00           C
ATOM     79  CA  GLU    79      -1.831   5.584  -7.723  1.00 25.00           C
ATOM     80  CA  ARG    80      -4.471   4.602 -10.319  1.00 25.00           C
ATOM     81  CA  LEU    81      -6.429   2.689  -7.640  1.00 25.00           C
ATOM     82  CA  ASN    82      -6.621   5.906  -5.530  1.00 25.00           C
ATOM     83  CA  ILE    83      -6.321   8.757  -8.083  1.00 25.00           C
ATOM     84  CA  GLY    84      -6.716  12.203  -9.671  1.00 25.00           C
ATOM     85  CA  GLU    85      -3.079  12.810 -10.754  1.00 25.00           C
ATOM     86  CA  PRO    86       0.201  13.921  -9.119  1.00 25.00           C
ATOM     87  CA  LEU    87       1.924  13.949 -12.539  1.00 25.00           C
ATOM     88  CA  LEU    88      -0.933  16.047 -13.988  1.00 25.00           C
ATOM     89  CA  VAL    89      -0.643  18.506 -11.066  1.00 25.00           C
ATOM     90  CA  TYR    90       3.135  18.771 -11.635  1.00 25.00           C
ATOM     91  CA  LEU    91       2.553  19.437 -15.361  1.00 25.00           C
ATOM     92  CA  ARG    92      -0.001  22.158 -14.502  1.00 25.00           C
ATOM     93  CA  ARG    93       2.489  23.764 -12.076  1.00 25.00           C
ATOM     94  CA  GLN    94       1.389  27.254 -11.034  1.00 25.00           C
ATOM     95  CA  ASP    95       1.245  28.556 -14.612  1.00 25.00           C
ATOM     96  CA  LEU    96       4.352  26.857 -15.922  1.00 25.00           C
ATOM     97  CA  PRO    97       7.243  25.873 -18.121  1.00 25.00           C
ATOM     98  CA  GLU    98       7.585  29.095 -20.162  1.00 25.00           C
ATOM     99  CA  ILE    99       7.415  31.176 -16.951  1.00 25.00           C
ATOM    100  CA  THR   100      10.114  28.979 -15.354  1.00 25.00           C
ATOM    101  CA  ALA   101      12.329  29.408 -18.448  1.00 25.00           C
ATOM    102  CA  GLN   102      11.842  33.205 -18.300  1.00 25.00           C
ATOM    103  CA  ARG   103      12.778  33.204 -14.586  1.00 25.00           C
ATOM    104  CA  GLN   104      15.922  31.156 -15.353  1.00 25.00           C
ATOM    105  CA  LEU   105      18.701  32.454 -13.127  1.00 25.00           C
ATOM    106  CA  ARG   106      17.808  35.880 -11.887  1.00 25.00           C
TER
END
