
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0382TS599_3
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS599_3.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      K       3           #
LGA    S       2      -       -           -
LGA    K       3      -       -           -
LGA    L       4      L       4           #
LGA    D       5      D       5          4.560
LGA    L       6      L       6          2.847
LGA    H       7      H       7          3.148
LGA    Q       8      Q       8          1.733
LGA    M       9      M       9          1.070
LGA    T      10      T      10          0.562
LGA    T      11      T      11          0.237
LGA    Q      12      Q      12          0.574
LGA    D      13      D      13          0.775
LGA    L      14      L      14          1.063
LGA    V      15      V      15          1.431
LGA    A      16      A      16          1.275
LGA    L      17      L      17          1.190
LGA    F      18      F      18          2.042
LGA    A      19      A      19          1.947
LGA    K      20      K      20          0.933
LGA    V      21      V      21          1.162
LGA    T      22      T      22          1.713
LGA    V      23      V      23          1.375
LGA    E      24      E      24          0.575
LGA    Q      25      Q      25          2.382
LGA    D      26      D      26          2.224
LGA    D      27      D      27          1.094
LGA    A      28      A      28          1.893
LGA    L      29      L      29          2.234
LGA    L      30      L      30          1.712
LGA    G      31      G      31          2.656
LGA    N      32      N      32          2.650
LGA    Q      33      -       -           -
LGA    I      34      -       -           -
LGA    S      35      -       -           -
LGA    R      36      Q      33          4.774
LGA    F      37      I      34          4.302
LGA    N      38      S      35          4.306
LGA    R      39      -       -           -
LGA    L      40      -       -           -
LGA    F      41      R      36          4.362
LGA    G      42      F      37           -
LGA    V      43      -       -           -
LGA    M      44      -       -           -
LGA    A      45      -       -           -
LGA    E      46      -       -           -
LGA    I      47      -       -           -
LGA    A      48      -       -           -
LGA    D      49      -       -           -
LGA    E      50      -       -           -
LGA    L      51      -       -           -
LGA    K      52      -       -           -
LGA    A      53      -       -           -
LGA    R      54      -       -           -
LGA    D      55      -       -           -
LGA    G      56      -       -           -
LGA    D      57      -       -           -
LGA    Q      58      -       -           -
LGA    R      59      -       -           -
LGA    T      60      -       -           -
LGA    A      61      -       -           -
LGA    L      62      -       -           -
LGA    L      63      -       -           -
LGA    S      64      -       -           -
LGA    L      65      -       -           -
LGA    F      66      -       -           -
LGA    E      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    N      70      -       -           -
LGA    M      71      N      38          3.597
LGA    Q      72      R      39          1.979
LGA    -       -      L      40           -
LGA    V      73      F      41          2.219
LGA    -       -      G      42           -
LGA    R      74      V      43           #
LGA    L      75      M      44          3.651
LGA    Q      76      -       -           -
LGA    A      77      A      45          3.471
LGA    A      78      E      46          3.808
LGA    K      79      I      47          4.441
LGA    L      80      A      48          4.508
LGA    T      81      D      49          3.740
LGA    L      82      E      50          3.258
LGA    A      83      L      51          3.976
LGA    V      84      K      52          2.929
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    A      85      G      56          4.360
LGA    P      86      D      57          3.833
LGA    V      87      -       -           -
LGA    K      88      Q      58          4.105
LGA    A      89      R      59          3.124
LGA    R      90      T      60          3.089
LGA    E      91      A      61          3.748
LGA    Q      92      L      62          3.148
LGA    L      93      L      63          2.131
LGA    E      94      S      64          2.365
LGA    A      95      -       -           -
LGA    I      96      L      65          1.975
LGA    V      97      F      66          2.803
LGA    S      98      E      67          3.300
LGA    S      99      Y      68          4.075
LGA    K     100      P      69          2.354
LGA    W     101      N      70          3.322
LGA    F     102      M      71          3.910
LGA    -       -      Q      72           -
LGA    P     103      V      73          3.964
LGA    Q     104      R      74          3.165
LGA    A     105      L      75          3.011
LGA    G     106      -       -           -
LGA    D     107      Q      76          1.923
LGA    A     108      A      77          2.768
LGA    G     109      A      78          3.006
LGA    M     110      K      79          2.926
LGA    C     111      L      80          2.078
LGA    L     112      T      81          1.919
LGA    D     113      L      82          2.401
LGA    L     114      A      83          2.258
LGA    L     115      V      84          2.352
LGA    D     116      A      85          4.926
LGA    D     117      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    G     118      P     122           #
LGA    T     119      K     123          4.981
LGA    F     120      -       -           -
LGA    K     121      -       -           -
LGA    P     122      -       -           -
LGA    K     123      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  121    5.0     74    2.95    41.89     36.824     2.424

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.249976 * X  +   0.326754 * Y  +   0.911452 * Z  +  -9.124309
  Y_new =   0.698042 * X  +  -0.713171 * Y  +   0.064225 * Z  +  40.980793
  Z_new =   0.671007 * X  +   0.620177 * Y  +  -0.406363 * Z  +  -1.061910 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.150845   -0.990748  [ DEG:   123.2343    -56.7657 ]
  Theta =  -0.735565   -2.406027  [ DEG:   -42.1448   -137.8552 ]
  Phi   =   1.226915   -1.914678  [ DEG:    70.2971   -109.7029 ]
 
# 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: T0382TS599_3                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS599_3.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  121   5.0   74   2.95   41.89  36.824
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS599_3
PFRMAT TS                                                                       
TARGET T0382                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -5.320  32.859  -4.943  1.00  0.00              
ATOM      2  CA  SER     2      -2.900  29.818  -6.386  1.00  0.00              
ATOM      3  CA  LYS     3      -6.405  29.848  -8.718  1.00  0.00              
ATOM      4  CA  LEU     4      -7.373  33.158  -9.708  1.00  0.00              
ATOM      5  CA  ASP     5      -5.948  34.107 -13.124  1.00  0.00              
ATOM      6  CA  LEU     6      -6.212  37.914 -13.176  1.00  0.00              
ATOM      7  CA  HIS     7      -7.016  38.328 -16.882  1.00  0.00              
ATOM      8  CA  GLN     8      -9.924  35.862 -16.747  1.00  0.00              
ATOM      9  CA  MET     9     -11.525  36.908 -13.465  1.00  0.00              
ATOM     10  CA  THR    10     -15.142  38.024 -13.808  1.00  0.00              
ATOM     11  CA  THR    11     -16.351  40.705 -11.318  1.00  0.00              
ATOM     12  CA  GLN    12     -18.692  38.298  -9.638  1.00  0.00              
ATOM     13  CA  ASP    13     -15.988  35.730  -9.174  1.00  0.00              
ATOM     14  CA  LEU    14     -13.541  38.227  -7.805  1.00  0.00              
ATOM     15  CA  VAL    15     -15.979  39.780  -5.416  1.00  0.00              
ATOM     16  CA  ALA    16     -17.025  36.458  -3.972  1.00  0.00              
ATOM     17  CA  LEU    17     -13.494  35.243  -3.497  1.00  0.00              
ATOM     18  CA  PHE    18     -12.339  38.371  -1.687  1.00  0.00              
ATOM     19  CA  ALA    19     -15.312  38.354   0.615  1.00  0.00              
ATOM     20  CA  LYS    20     -14.936  34.714   1.551  1.00  0.00              
ATOM     21  CA  VAL    21     -11.278  35.109   2.372  1.00  0.00              
ATOM     22  CA  THR    22     -11.990  38.162   4.549  1.00  0.00              
ATOM     23  CA  VAL    23     -14.777  36.426   6.416  1.00  0.00              
ATOM     24  CA  GLU    24     -12.684  33.299   7.155  1.00  0.00              
ATOM     25  CA  GLN    25      -9.647  35.143   8.453  1.00  0.00              
ATOM     26  CA  ASP    26     -11.679  37.324  10.727  1.00  0.00              
ATOM     27  CA  ASP    27     -13.472  34.427  12.406  1.00  0.00              
ATOM     28  CA  ALA    28     -10.221  32.490  13.117  1.00  0.00              
ATOM     29  CA  LEU    29      -8.341  35.340  14.684  1.00  0.00              
ATOM     30  CA  LEU    30     -11.307  36.424  16.870  1.00  0.00              
ATOM     31  CA  GLY    31     -11.872  33.012  18.387  1.00  0.00              
ATOM     32  CA  ASN    32      -8.155  32.833  19.300  1.00  0.00              
ATOM     33  CA  GLN    33      -7.194  29.616  17.619  1.00  0.00              
ATOM     34  CA  ILE    34      -3.399  29.862  17.265  1.00  0.00              
ATOM     35  CA  SER    35      -2.919  26.961  14.850  1.00  0.00              
ATOM     36  CA  ARG    36      -5.454  28.164  12.284  1.00  0.00              
ATOM     37  CA  PHE    37      -4.018  31.671  12.212  1.00  0.00              
ATOM     38  CA  ASN    38      -0.463  30.462  11.712  1.00  0.00              
ATOM     39  CA  ARG    39      -1.565  28.149   8.851  1.00  0.00              
ATOM     40  CA  LEU    40      -3.339  31.038   7.124  1.00  0.00              
ATOM     41  CA  PHE    41      -0.201  33.230   7.505  1.00  0.00              
ATOM     42  CA  GLY    42       2.030  30.504   5.996  1.00  0.00              
ATOM     43  CA  VAL    43      -0.434  30.166   3.067  1.00  0.00              
ATOM     44  CA  MET    44      -0.367  33.874   2.456  1.00  0.00              
ATOM     45  CA  ALA    45       3.482  33.751   2.407  1.00  0.00              
ATOM     46  CA  GLU    46       3.439  30.876  -0.079  1.00  0.00              
ATOM     47  CA  ILE    47       1.000  32.752  -2.388  1.00  0.00              
ATOM     48  CA  ALA    48       2.924  35.991  -2.280  1.00  0.00              
ATOM     49  CA  ASP    49       6.119  34.253  -3.124  1.00  0.00              
ATOM     50  CA  GLU    50       4.402  32.472  -6.064  1.00  0.00              
ATOM     51  CA  LEU    51       2.949  35.741  -7.237  1.00  0.00              
ATOM     52  CA  LYS    52       6.344  37.449  -7.078  1.00  0.00              
ATOM     53  CA  ALA    53       7.644  34.894  -9.566  1.00  0.00              
ATOM     54  CA  ARG    54       4.778  35.464 -12.033  1.00  0.00              
ATOM     55  CA  ASP    55       4.607  37.717 -14.959  1.00  0.00              
ATOM     56  CA  GLY    56       5.206  41.445 -14.673  1.00  0.00              
ATOM     57  CA  ASP    57       1.626  42.795 -14.272  1.00  0.00              
ATOM     58  CA  GLN    58       1.112  40.232 -11.465  1.00  0.00              
ATOM     59  CA  ARG    59       4.315  41.178  -9.691  1.00  0.00              
ATOM     60  CA  THR    60       3.282  44.783  -9.242  1.00  0.00              
ATOM     61  CA  ALA    61      -0.056  43.763  -7.729  1.00  0.00              
ATOM     62  CA  LEU    62       1.605  41.291  -5.309  1.00  0.00              
ATOM     63  CA  LEU    63       4.166  43.866  -4.155  1.00  0.00              
ATOM     64  CA  SER    64       1.296  46.232  -3.301  1.00  0.00              
ATOM     65  CA  LEU    65      -0.445  43.488  -1.326  1.00  0.00              
ATOM     66  CA  PHE    66       2.780  42.722   0.559  1.00  0.00              
ATOM     67  CA  GLU    67       2.831  46.309   1.814  1.00  0.00              
ATOM     68  CA  TYR    68      -0.606  45.741   3.399  1.00  0.00              
ATOM     69  CA  PRO    69      -0.343  45.814   7.168  1.00  0.00              
ATOM     70  CA  ASN    70      -2.487  42.763   7.804  1.00  0.00              
ATOM     71  CA  MET    71       0.108  39.962   7.395  1.00  0.00              
ATOM     72  CA  GLN    72      -2.352  37.375   6.052  1.00  0.00              
ATOM     73  CA  VAL    73      -4.485  39.584   3.810  1.00  0.00              
ATOM     74  CA  ARG    74      -7.882  40.674   4.974  1.00  0.00              
ATOM     75  CA  LEU    75     -10.825  41.837   2.952  1.00  0.00              
ATOM     76  CA  GLN    76     -10.198  45.617   2.892  1.00  0.00              
ATOM     77  CA  ALA    77      -6.478  45.180   2.187  1.00  0.00              
ATOM     78  CA  ALA    78      -7.078  42.724  -0.658  1.00  0.00              
ATOM     79  CA  LYS    79      -9.839  44.881  -2.174  1.00  0.00              
ATOM     80  CA  LEU    80      -7.680  48.045  -2.078  1.00  0.00              
ATOM     81  CA  THR    81      -4.710  46.326  -3.749  1.00  0.00              
ATOM     82  CA  LEU    82      -7.077  45.106  -6.525  1.00  0.00              
ATOM     83  CA  ALA    83      -9.417  47.973  -7.542  1.00  0.00              
ATOM     84  CA  VAL    84     -12.887  47.149  -8.693  1.00  0.00              
ATOM     85  CA  ALA    85     -14.882  49.247 -11.112  1.00  0.00              
ATOM     86  CA  PRO    86     -17.399  51.649  -9.478  1.00  0.00              
ATOM     87  CA  VAL    87     -20.636  50.118 -10.540  1.00  0.00              
ATOM     88  CA  LYS    88     -19.615  46.590  -9.808  1.00  0.00              
ATOM     89  CA  ALA    89     -18.249  47.391  -6.324  1.00  0.00              
ATOM     90  CA  ARG    90     -21.384  49.274  -5.273  1.00  0.00              
ATOM     91  CA  GLU    91     -23.516  46.399  -6.458  1.00  0.00              
ATOM     92  CA  GLN    92     -21.394  43.870  -4.539  1.00  0.00              
ATOM     93  CA  LEU    93     -21.653  45.973  -1.309  1.00  0.00              
ATOM     94  CA  GLU    94     -25.409  46.173  -1.791  1.00  0.00              
ATOM     95  CA  ALA    95     -25.539  42.373  -2.243  1.00  0.00              
ATOM     96  CA  ILE    96     -23.513  41.852   0.937  1.00  0.00              
ATOM     97  CA  VAL    97     -25.725  44.160   2.904  1.00  0.00              
ATOM     98  CA  SER    98     -28.878  42.347   1.670  1.00  0.00              
ATOM     99  CA  SER    99     -27.589  38.828   2.350  1.00  0.00              
ATOM    100  CA  LYS   100     -26.764  39.163   6.001  1.00  0.00              
ATOM    101  CA  TRP   101     -22.915  38.973   5.719  1.00  0.00              
ATOM    102  CA  PHE   102     -22.595  42.370   7.307  1.00  0.00              
ATOM    103  CA  PRO   103     -20.342  44.738   5.420  1.00  0.00              
ATOM    104  CA  GLN   104     -18.212  46.016   8.201  1.00  0.00              
ATOM    105  CA  ALA   105     -17.406  49.700   8.079  1.00  0.00              
ATOM    106  CA  GLY   106     -13.704  49.679   7.131  1.00  0.00              
ATOM    107  CA  ASP   107     -14.270  47.667   3.959  1.00  0.00              
ATOM    108  CA  ALA   108     -17.493  49.168   2.560  1.00  0.00              
ATOM    109  CA  GLY   109     -16.963  52.865   3.136  1.00  0.00              
ATOM    110  CA  MET   110     -13.329  52.886   1.905  1.00  0.00              
ATOM    111  CA  CYS   111     -14.131  50.949  -1.241  1.00  0.00              
ATOM    112  CA  LEU   112     -17.064  53.150  -2.191  1.00  0.00              
ATOM    113  CA  ASP   113     -15.075  56.395  -1.716  1.00  0.00              
ATOM    114  CA  LEU   114     -12.311  54.907  -3.914  1.00  0.00              
ATOM    115  CA  LEU   115     -14.908  53.912  -6.574  1.00  0.00              
ATOM    116  CA  ASP   116     -16.494  57.418  -6.644  1.00  0.00              
ATOM    117  CA  ASP   117     -12.987  58.914  -6.917  1.00  0.00              
ATOM    118  CA  GLY   118     -11.992  56.790  -9.856  1.00  0.00              
ATOM    119  CA  THR   119      -9.161  54.944  -8.145  1.00  0.00              
ATOM    120  CA  PHE   120     -10.634  51.653  -9.201  1.00  0.00              
ATOM    121  CA  LYS   121      -8.889  49.407 -11.440  1.00  0.00              
ATOM    122  CA  PRO   122      -7.469  45.460 -11.022  1.00  0.00              
ATOM    123  CA  LYS   123      -8.806  44.654 -14.261  1.00  0.00              
TER                                                                             
END
