
#######################################################
#                                                     #
#                        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  119 (  119),  selected  119 , name T0382TS393_4-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS393_4-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    L       4      N      32          3.567
LGA    D       5      Q      33          3.511
LGA    L       6      I      34          2.028
LGA    H       7      S      35          2.758
LGA    Q       8      R      36          2.879
LGA    M       9      F      37          1.658
LGA    T      10      N      38          0.407
LGA    T      11      R      39          1.136
LGA    Q      12      L      40          2.304
LGA    D      13      F      41          2.189
LGA    L      14      G      42          1.653
LGA    V      15      V      43          2.189
LGA    A      16      M      44          4.136
LGA    L      17      A      45          4.469
LGA    F      18      E      46          3.859
LGA    A      19      I      47           #
LGA    -       -      A      48           -
LGA    K      20      D      49          4.176
LGA    V      21      E      50           -
LGA    T      22      L      51           -
LGA    V      23      K      52           -
LGA    E      24      A      53           -
LGA    Q      25      R      54           -
LGA    D      26      D      55           -
LGA    D      27      G      56           -
LGA    A      28      D      57           -
LGA    L      29      Q      58           -
LGA    L      30      R      59           -
LGA    G      31      T      60           -
LGA    N      32      A      61           -
LGA    Q      33      L      62           -
LGA    I      34      L      63           -
LGA    S      35      S      64           -
LGA    R      36      -       -           -
LGA    F      37      -       -           -
LGA    N      38      -       -           -
LGA    R      39      -       -           -
LGA    L      40      L      65           #
LGA    F      41      F      66           #
LGA    G      42      -       -           -
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      E      67          5.116
LGA    D      57      Y      68          3.360
LGA    Q      58      P      69          4.115
LGA    -       -      N      70           -
LGA    R      59      M      71           #
LGA    T      60      Q      72           -
LGA    A      61      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    L      62      A      77          5.200
LGA    L      63      A      78           -
LGA    S      64      K      79           -
LGA    L      65      L      80           #
LGA    F      66      -       -           -
LGA    E      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    N      70      -       -           -
LGA    M      71      -       -           -
LGA    Q      72      -       -           -
LGA    V      73      -       -           -
LGA    R      74      -       -           -
LGA    L      75      -       -           -
LGA    Q      76      -       -           -
LGA    A      77      -       -           -
LGA    A      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      -       -           -
LGA    T      81      T      81          4.747
LGA    L      82      L      82          5.452
LGA    A      83      A      83          5.293
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    V      84      V      87          5.391
LGA    A      85      K      88          5.172
LGA    P      86      A      89          2.735
LGA    V      87      R      90          1.451
LGA    K      88      E      91          1.983
LGA    A      89      Q      92          2.523
LGA    R      90      L      93          3.702
LGA    E      91      E      94          3.579
LGA    Q      92      -       -           -
LGA    L      93      A      95          4.867
LGA    E      94      I      96           -
LGA    A      95      V      97           -
LGA    I      96      S      98          3.819
LGA    V      97      S      99           -
LGA    S      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    W     101      -       -           -
LGA    F     102      K     100           #
LGA    P     103      W     101           -
LGA    Q     104      F     102           -
LGA    A     105      P     103           -
LGA    G     106      Q     104           -
LGA    D     107      A     105           -
LGA    A     108      G     106          4.870
LGA    G     109      D     107          3.448
LGA    M     110      A     108          2.593
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    C     111      C     111          3.004
LGA    L     112      L     112          3.712
LGA    D     113      D     113           #
LGA    L     114      L     114           #
LGA    L     115      L     115          2.563
LGA    D     116      D     116          3.694
LGA    D     117      D     117          2.749
LGA    G     118      G     118          3.979
LGA    T     119      T     119           #
LGA    F     120      F     120           -
LGA    K     121      K     121           -
LGA    P     122      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  119  119    5.0     42    3.61    28.57     21.323     1.132

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.553020 * X  +   0.489715 * Y  +  -0.674054 * Z  + -15.365137
  Y_new =   0.582552 * X  +  -0.351116 * Y  +  -0.733042 * Z  +  48.614330
  Z_new =  -0.595653 * X  +  -0.798058 * Y  +  -0.091110 * Z  +   6.178267 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.684469    1.457123  [ DEG:   -96.5130     83.4870 ]
  Theta =   0.638078    2.503515  [ DEG:    36.5592    143.4408 ]
  Phi   =   2.330194   -0.811399  [ DEG:   133.5103    -46.4897 ]
 
# 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: T0382TS393_4-D1                               
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS393_4-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  119  119   5.0   42   3.61   28.57  21.323
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS393_4-D1
PFRMAT TS
TARGET T0382
MODEL 4
PARENT N/A
ATOM      4  CA  LEU     4      -8.578  31.406  15.587  1.00 25.00           C
ATOM      5  CA  ASP     5      -8.541  33.191  12.300  1.00 25.00           C
ATOM      6  CA  LEU     6      -5.476  35.462  12.637  1.00 25.00           C
ATOM      7  CA  HIS     7      -3.809  33.693   9.676  1.00 25.00           C
ATOM      8  CA  GLN     8      -6.987  34.145   7.586  1.00 25.00           C
ATOM      9  CA  MET     9      -7.084  37.865   8.491  1.00 25.00           C
ATOM     10  CA  THR    10      -3.406  38.230   7.485  1.00 25.00           C
ATOM     11  CA  THR    11      -4.121  36.491   4.149  1.00 25.00           C
ATOM     12  CA  GLN    12      -7.083  38.838   3.532  1.00 25.00           C
ATOM     13  CA  ASP    13      -4.874  41.870   4.302  1.00 25.00           C
ATOM     14  CA  LEU    14      -2.213  40.578   1.870  1.00 25.00           C
ATOM     15  CA  VAL    15      -4.881  40.103  -0.836  1.00 25.00           C
ATOM     16  CA  ALA    16      -6.149  43.668  -0.246  1.00 25.00           C
ATOM     17  CA  LEU    17      -2.574  45.013  -0.526  1.00 25.00           C
ATOM     18  CA  PHE    18      -2.081  43.089  -3.801  1.00 25.00           C
ATOM     19  CA  ALA    19      -5.361  44.520  -5.165  1.00 25.00           C
ATOM     20  CA  LYS    20      -4.249  48.056  -4.197  1.00 25.00           C
ATOM     21  CA  VAL    21      -0.888  47.505  -5.950  1.00 25.00           C
ATOM     22  CA  THR    22       1.865  47.880  -3.427  1.00 25.00           C
ATOM     23  CA  VAL    23       4.030  48.693  -0.428  1.00 25.00           C
ATOM     24  CA  GLU    24       3.285  50.478   2.878  1.00 25.00           C
ATOM     25  CA  GLN    25       0.679  52.676   1.132  1.00 25.00           C
ATOM     26  CA  ASP    26      -0.947  49.568  -0.406  1.00 25.00           C
ATOM     27  CA  ASP    27      -1.052  47.891   3.036  1.00 25.00           C
ATOM     28  CA  ALA    28      -2.665  51.022   4.540  1.00 25.00           C
ATOM     29  CA  LEU    29      -5.276  51.052   1.739  1.00 25.00           C
ATOM     30  CA  LEU    30      -6.033  47.351   2.370  1.00 25.00           C
ATOM     31  CA  GLY    31      -6.435  48.046   6.114  1.00 25.00           C
ATOM     32  CA  ASN    32      -8.816  50.946   5.345  1.00 25.00           C
ATOM     33  CA  GLN    33     -10.863  48.684   3.030  1.00 25.00           C
ATOM     34  CA  ILE    34     -11.048  46.011   5.765  1.00 25.00           C
ATOM     35  CA  SER    35     -12.212  48.642   8.293  1.00 25.00           C
ATOM     36  CA  ARG    36     -14.900  49.842   5.841  1.00 25.00           C
ATOM     37  CA  PHE    37     -16.078  46.235   5.327  1.00 25.00           C
ATOM     38  CA  ASN    38     -16.257  45.727   9.119  1.00 25.00           C
ATOM     39  CA  ARG    39     -18.294  48.952   9.478  1.00 25.00           C
ATOM     40  CA  LEU    40     -20.682  47.780   6.724  1.00 25.00           C
ATOM     41  CA  PHE    41     -21.093  44.403   8.483  1.00 25.00           C
ATOM     42  CA  GLY    42     -21.838  46.189  11.788  1.00 25.00           C
ATOM     43  CA  VAL    43     -24.445  48.385  10.043  1.00 25.00           C
ATOM     44  CA  MET    44     -26.071  45.278   8.506  1.00 25.00           C
ATOM     45  CA  ALA    45     -26.176  43.600  11.948  1.00 25.00           C
ATOM     46  CA  GLU    46     -27.789  46.732  13.451  1.00 25.00           C
ATOM     47  CA  ILE    47     -30.400  46.761  10.649  1.00 25.00           C
ATOM     48  CA  ALA    48     -31.156  43.061  11.281  1.00 25.00           C
ATOM     49  CA  ASP    49     -31.559  43.756  15.025  1.00 25.00           C
ATOM     50  CA  GLU    50     -33.939  46.656  14.255  1.00 25.00           C
ATOM     51  CA  LEU    51     -35.987  44.393  11.940  1.00 25.00           C
ATOM     52  CA  LYS    52     -36.171  41.720  14.676  1.00 25.00           C
ATOM     53  CA  ALA    53     -34.604  39.981  11.680  1.00 25.00           C
ATOM     54  CA  ARG    54     -33.297  39.755   8.103  1.00 25.00           C
ATOM     55  CA  ASP    55     -31.063  40.094   5.065  1.00 25.00           C
ATOM     56  CA  GLY    56     -28.001  38.698   3.291  1.00 25.00           C
ATOM     57  CA  ASP    57     -26.931  42.308   3.184  1.00 25.00           C
ATOM     58  CA  GLN    58     -23.520  41.713   4.716  1.00 25.00           C
ATOM     59  CA  ARG    59     -20.722  39.266   3.791  1.00 25.00           C
ATOM     60  CA  THR    60     -22.734  38.070   0.761  1.00 25.00           C
ATOM     61  CA  ALA    61     -23.290  41.698  -0.332  1.00 25.00           C
ATOM     62  CA  LEU    62     -19.541  42.400   0.007  1.00 25.00           C
ATOM     63  CA  LEU    63     -18.744  39.295  -2.087  1.00 25.00           C
ATOM     64  CA  SER    64     -21.227  40.438  -4.770  1.00 25.00           C
ATOM     65  CA  LEU    65     -19.617  43.913  -4.814  1.00 25.00           C
ATOM     66  CA  PHE    66     -16.150  42.330  -5.187  1.00 25.00           C
ATOM     67  CA  GLU    67     -17.421  40.172  -8.084  1.00 25.00           C
ATOM     68  CA  TYR    68     -20.455  41.920  -9.492  1.00 25.00           C
ATOM     69  CA  PRO    69     -18.479  42.067 -12.781  1.00 25.00           C
ATOM     70  CA  ASN    70     -15.144  42.661 -14.629  1.00 25.00           C
ATOM     71  CA  MET    71     -12.308  45.083 -15.555  1.00 25.00           C
ATOM     72  CA  GLN    72     -11.513  48.732 -14.702  1.00 25.00           C
ATOM     73  CA  VAL    73     -15.247  49.584 -14.759  1.00 25.00           C
ATOM     74  CA  ARG    74     -15.982  46.622 -12.445  1.00 25.00           C
ATOM     75  CA  LEU    75     -13.231  47.780 -10.046  1.00 25.00           C
ATOM     76  CA  GLN    76     -14.689  51.323 -10.047  1.00 25.00           C
ATOM     77  CA  ALA    77     -18.171  49.916  -9.298  1.00 25.00           C
ATOM     78  CA  ALA    78     -16.742  47.846  -6.412  1.00 25.00           C
ATOM     79  CA  LYS    79     -14.994  50.953  -5.016  1.00 25.00           C
ATOM     80  CA  LEU    80     -18.267  52.928  -5.242  1.00 25.00           C
ATOM     81  CA  THR    81     -20.117  50.116  -3.412  1.00 25.00           C
ATOM     82  CA  LEU    82     -17.438  50.101  -0.676  1.00 25.00           C
ATOM     83  CA  ALA    83     -17.757  53.899  -0.308  1.00 25.00           C
ATOM     84  CA  VAL    84     -21.563  53.578  -0.027  1.00 25.00           C
ATOM     85  CA  ALA    85     -21.160  50.873   2.655  1.00 25.00           C
ATOM     86  CA  PRO    86     -18.732  53.117   4.588  1.00 25.00           C
ATOM     87  CA  VAL    87     -21.215  56.024   4.382  1.00 25.00           C
ATOM     88  CA  LYS    88     -24.019  53.753   5.667  1.00 25.00           C
ATOM     89  CA  ALA    89     -21.799  52.616   8.573  1.00 25.00           C
ATOM     90  CA  ARG    90     -21.004  56.265   9.425  1.00 25.00           C
ATOM     91  CA  GLU    91     -24.738  57.117   9.369  1.00 25.00           C
ATOM     92  CA  GLN    92     -25.474  54.155  11.683  1.00 25.00           C
ATOM     93  CA  LEU    93     -22.723  55.314  14.082  1.00 25.00           C
ATOM     94  CA  GLU    94     -24.180  58.856  14.082  1.00 25.00           C
ATOM     95  CA  ALA    95     -27.662  57.449  14.829  1.00 25.00           C
ATOM     96  CA  ILE    96     -26.234  55.378  17.716  1.00 25.00           C
ATOM     97  CA  VAL    97     -24.485  58.487  19.113  1.00 25.00           C
ATOM     98  CA  SER    98     -27.759  60.460  18.887  1.00 25.00           C
ATOM     99  CA  SER    99     -29.608  57.648  20.716  1.00 25.00           C
ATOM    100  CA  LYS   100     -27.122  58.438  23.523  1.00 25.00           C
ATOM    101  CA  TRP   101     -23.894  56.757  24.555  1.00 25.00           C
ATOM    102  CA  PHE   102     -21.555  54.777  22.290  1.00 25.00           C
ATOM    103  CA  PRO   103     -19.059  55.245  25.153  1.00 25.00           C
ATOM    104  CA  GLN   104     -15.774  54.750  26.997  1.00 25.00           C
ATOM    105  CA  ALA   105     -13.314  52.817  24.768  1.00 25.00           C
ATOM    106  CA  GLY   106     -10.272  55.080  25.214  1.00 25.00           C
ATOM    107  CA  ASP   107      -8.816  54.112  21.840  1.00 25.00           C
ATOM    108  CA  ALA   108     -10.441  53.066  18.617  1.00 25.00           C
ATOM    109  CA  GLY   109     -11.378  52.988  14.971  1.00 25.00           C
ATOM    110  CA  MET   110     -12.972  51.387  11.878  1.00 25.00           C
ATOM    111  CA  CYS   111     -14.894  54.622  11.163  1.00 25.00           C
ATOM    112  CA  LEU   112     -11.659  56.646  11.494  1.00 25.00           C
ATOM    113  CA  ASP   113      -9.888  54.254   9.083  1.00 25.00           C
ATOM    114  CA  LEU   114     -12.764  54.608   6.580  1.00 25.00           C
ATOM    115  CA  LEU   115     -12.563  58.422   6.849  1.00 25.00           C
ATOM    116  CA  ASP   116     -11.220  61.952   7.319  1.00 25.00           C
ATOM    117  CA  ASP   117      -9.833  65.492   7.168  1.00 25.00           C
ATOM    118  CA  GLY   118      -8.818  69.090   6.811  1.00 25.00           C
ATOM    119  CA  THR   119      -6.700  69.416  10.003  1.00 25.00           C
ATOM    120  CA  PHE   120     -10.037  70.541  11.510  1.00 25.00           C
ATOM    121  CA  LYS   121      -7.761  71.572  14.436  1.00 25.00           C
ATOM    122  CA  PRO   122      -4.017  71.625  13.951  1.00 25.00           C
TER
END
