
#######################################################
#                                                     #
#                        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  143 (  143),  selected  143 , name T0338TS393_4-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338TS393_4-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      -       -           -
LGA    S       2      -       -           -
LGA    S       3      -       -           -
LGA    R       4      A       1          5.296
LGA    W       5      S       2          1.784
LGA    -       -      S       3           -
LGA    F       6      R       4           #
LGA    F       7      W       5          3.192
LGA    T       8      F       6          3.392
LGA    R       9      F       7          3.764
LGA    E      10      -       -           -
LGA    Q      11      T       8          2.945
LGA    L      12      R       9          3.553
LGA    E      13      E      10           -
LGA    N      14      Q      11           -
LGA    T      15      -       -           -
LGA    P      16      -       -           -
LGA    S      17      -       -           -
LGA    R      18      -       -           -
LGA    R      19      -       -           -
LGA    C      20      -       -           -
LGA    G      21      -       -           -
LGA    V      22      -       -           -
LGA    E      23      -       -           -
LGA    A      24      -       -           -
LGA    D      25      -       -           -
LGA    K      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    S      29      -       -           -
LGA    C      30      -       -           -
LGA    R      31      -       -           -
LGA    Q      32      -       -           -
LGA    Q      33      -       -           -
LGA    A      34      -       -           -
LGA    A      35      -       -           -
LGA    N      36      L      12           #
LGA    L      37      E      13          2.319
LGA    I      38      -       -           -
LGA    Q      39      N      14          4.506
LGA    E      40      T      15          4.684
LGA    M      41      P      16          4.075
LGA    -       -      S      17           -
LGA    G      42      R      18          2.163
LGA    Q      43      R      19          4.115
LGA    R      44      C      20           -
LGA    L      45      G      21           -
LGA    N      46      V      22           -
LGA    V      47      E      23           -
LGA    S      48      A      24           -
LGA    Q      49      -       -           -
LGA    L      50      -       -           -
LGA    T      51      -       -           -
LGA    I      52      -       -           -
LGA    N      53      -       -           -
LGA    T      54      -       -           -
LGA    A      55      -       -           -
LGA    I      56      -       -           -
LGA    V      57      -       -           -
LGA    Y      58      -       -           -
LGA    M      59      -       -           -
LGA    H      60      -       -           -
LGA    R      61      -       -           -
LGA    F      62      -       -           -
LGA    Y      63      -       -           -
LGA    M      64      -       -           -
LGA    H      65      -       -           -
LGA    H      66      -       -           -
LGA    S      67      -       -           -
LGA    F      68      -       -           -
LGA    T      69      -       -           -
LGA    K      70      -       -           -
LGA    F      71      D      25          3.684
LGA    N      72      K      26          2.839
LGA    K      73      -       -           -
LGA    N      74      -       -           -
LGA    I      75      E      27          4.783
LGA    I      76      L      28          5.124
LGA    S      77      S      29          2.854
LGA    S      78      C      30          1.954
LGA    T      79      R      31          4.165
LGA    A      80      Q      32          4.797
LGA    L      81      Q      33          3.612
LGA    F      82      A      34          4.058
LGA    L      83      -       -           -
LGA    A      84      A      35          3.823
LGA    A      85      N      36           #
LGA    -       -      L      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      E      40           -
LGA    -       -      M      41           -
LGA    -       -      G      42           -
LGA    -       -      Q      43           -
LGA    -       -      R      44           -
LGA    -       -      L      45           -
LGA    -       -      N      46           -
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      Q      49           -
LGA    -       -      L      50           -
LGA    -       -      T      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      T      54           -
LGA    -       -      A      55           -
LGA    K      86      I      56          1.480
LGA    V      87      V      57          4.058
LGA    E      88      -       -           -
LGA    E      89      -       -           -
LGA    Q      90      -       -           -
LGA    A      91      -       -           -
LGA    R      92      -       -           -
LGA    K      93      -       -           -
LGA    L      94      -       -           -
LGA    E      95      Y      58          1.916
LGA    H      96      M      59          1.839
LGA    V      97      H      60          1.935
LGA    I      98      R      61          3.288
LGA    K      99      F      62          3.563
LGA    V     100      Y      63          4.054
LGA    A     101      M      64          4.640
LGA    -       -      H      65           -
LGA    H     102      H      66          2.002
LGA    A     103      S      67          4.065
LGA    C     104      F      68          1.828
LGA    L     105      T      69          3.333
LGA    H     106      K      70           -
LGA    P     107      F      71           -
LGA    L     108      -       -           -
LGA    E     109      -       -           -
LGA    P     110      -       -           -
LGA    L     111      -       -           -
LGA    L     112      -       -           -
LGA    D     113      -       -           -
LGA    T     114      -       -           -
LGA    K     115      -       -           -
LGA    C     116      -       -           -
LGA    D     117      -       -           -
LGA    A     118      -       -           -
LGA    Y     119      -       -           -
LGA    L     120      -       -           -
LGA    Q     121      -       -           -
LGA    Q     122      -       -           -
LGA    T     123      -       -           -
LGA    R     124      -       -           -
LGA    E     125      N      72          2.526
LGA    L     126      K      73          1.470
LGA    V     127      N      74          2.783
LGA    I     128      I      75          2.189
LGA    L     129      I      76          1.239
LGA    E     130      S      77          1.764
LGA    T     131      S      78          1.780
LGA    I     132      T      79          1.450
LGA    M     133      A      80          1.573
LGA    L     134      L      81          1.516
LGA    Q     135      F      82          1.231
LGA    T     136      L      83          1.481
LGA    L     137      A      84          2.375
LGA    -       -      A      85           -
LGA    -       -      K      86           -
LGA    G     138      V      87          2.076
LGA    F     139      E      88           -
LGA    E     140      E      89           -
LGA    -       -      Q      90           -
LGA    -       -      A      91           -
LGA    -       -      R      92           -
LGA    -       -      K      93           -
LGA    -       -      L      94           -
LGA    -       -      E      95           -
LGA    -       -      H      96           -
LGA    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      K      99           -
LGA    -       -      V     100           -
LGA    -       -      A     101           -
LGA    -       -      H     102           -
LGA    -       -      A     103           -
LGA    -       -      C     104           -
LGA    -       -      L     105           -
LGA    -       -      H     106           -
LGA    -       -      P     107           -
LGA    -       -      L     108           -
LGA    -       -      E     109           -
LGA    -       -      P     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      T     114           -
LGA    -       -      K     115           -
LGA    -       -      C     116           -
LGA    -       -      D     117           -
LGA    -       -      A     118           -
LGA    -       -      Y     119           -
LGA    -       -      L     120           -
LGA    -       -      Q     121           -
LGA    -       -      Q     122           -
LGA    -       -      T     123           -
LGA    -       -      R     124           -
LGA    -       -      E     125           -
LGA    -       -      L     126           -
LGA    -       -      V     127           -
LGA    -       -      I     128           -
LGA    -       -      L     129           -
LGA    -       -      E     130           -
LGA    -       -      T     131           -
LGA    -       -      I     132           -
LGA    -       -      M     133           -
LGA    I     141      L     134          0.729
LGA    T     142      Q     135          0.900
LGA    I     143      T     136          3.823
LGA    -       -      L     137           -
LGA    -       -      G     138           -
LGA    -       -      F     139           -
LGA    -       -      E     140           -
LGA    -       -      I     141           -
LGA    -       -      T     142           -
LGA    -       -      I     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  143  143    5.0     54    3.14    11.11     22.733     1.666

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.669009 * X  +   0.732720 * Y  +   0.124690 * Z  +  -8.588583
  Y_new =   0.170940 * X  +  -0.314950 * Y  +   0.933588 * Z  +  29.463015
  Z_new =   0.723330 * X  +  -0.603264 * Y  +  -0.335956 * Z  +  52.361919 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.078919    1.062674  [ DEG:  -119.1133     60.8867 ]
  Theta =  -0.808612   -2.332980  [ DEG:   -46.3301   -133.6699 ]
  Phi   =   0.250160   -2.891432  [ DEG:    14.3331   -165.6669 ]
 
# 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: T0338TS393_4-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_4-D1.T0338_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  143  143   5.0   54   3.14   11.11  22.733
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_4-D1
PFRMAT TS
TARGET T0338
MODEL 4
PARENT N/A
ATOM      1  CA  ALA     1     -21.617   7.985  39.121  1.00 25.00           C
ATOM      2  CA  SER     2     -22.539   9.272  42.596  1.00 25.00           C
ATOM      3  CA  SER     3     -24.300   8.793  45.983  1.00 25.00           C
ATOM      4  CA  ARG     4     -24.522  12.055  47.924  1.00 25.00           C
ATOM      5  CA  TRP     5     -22.133  13.549  50.481  1.00 25.00           C
ATOM      6  CA  PHE     6     -22.105  13.513  54.228  1.00 25.00           C
ATOM      7  CA  PHE     7     -18.466  13.153  55.212  1.00 25.00           C
ATOM      8  CA  THR     8     -15.640  12.084  57.568  1.00 25.00           C
ATOM      9  CA  ARG     9     -15.219   8.299  57.260  1.00 25.00           C
ATOM     10  CA  GLU    10     -15.320   4.565  56.409  1.00 25.00           C
ATOM     11  CA  GLN    11     -11.492   4.450  56.351  1.00 25.00           C
ATOM     12  CA  LEU    12     -11.364   6.194  59.759  1.00 25.00           C
ATOM     13  CA  GLU    13     -13.878   3.674  61.170  1.00 25.00           C
ATOM     14  CA  ASN    14     -17.146   1.856  62.133  1.00 25.00           C
ATOM     15  CA  THR    15     -17.847   4.838  64.403  1.00 25.00           C
ATOM     16  CA  PRO    16     -20.910   2.833  65.442  1.00 25.00           C
ATOM     17  CA  SER    17     -24.294   2.566  67.111  1.00 25.00           C
ATOM     18  CA  ARG    18     -24.442   4.977  70.068  1.00 25.00           C
ATOM     19  CA  ARG    19     -23.113   7.087  72.922  1.00 25.00           C
ATOM     20  CA  CYS    20     -22.051   9.964  75.201  1.00 25.00           C
ATOM     21  CA  GLY    21     -18.759   9.604  77.168  1.00 25.00           C
ATOM     22  CA  VAL    22     -16.421  12.239  75.643  1.00 25.00           C
ATOM     23  CA  GLU    23     -14.382  14.679  77.749  1.00 25.00           C
ATOM     24  CA  ALA    24     -10.680  13.669  77.568  1.00 25.00           C
ATOM     25  CA  ASP    25      -9.348  10.362  76.168  1.00 25.00           C
ATOM     26  CA  LYS    26     -11.954  10.472  73.365  1.00 25.00           C
ATOM     27  CA  GLU    27     -10.950  14.074  72.539  1.00 25.00           C
ATOM     28  CA  LEU    28      -7.263  13.047  72.429  1.00 25.00           C
ATOM     29  CA  SER    29      -8.117  10.136  70.093  1.00 25.00           C
ATOM     30  CA  CYS    30     -10.078  12.508  67.814  1.00 25.00           C
ATOM     31  CA  ARG    31      -7.112  14.930  67.742  1.00 25.00           C
ATOM     32  CA  GLN    32      -4.752  12.050  66.846  1.00 25.00           C
ATOM     33  CA  GLN    33      -7.107  10.962  64.029  1.00 25.00           C
ATOM     34  CA  ALA    34      -7.219  14.553  62.703  1.00 25.00           C
ATOM     35  CA  ALA    35      -3.394  14.728  62.780  1.00 25.00           C
ATOM     36  CA  ASN    36      -3.181  11.410  60.879  1.00 25.00           C
ATOM     37  CA  LEU    37      -5.650  12.722  58.262  1.00 25.00           C
ATOM     38  CA  ILE    38      -3.576  15.917  57.872  1.00 25.00           C
ATOM     39  CA  GLN    39      -0.397  13.830  57.424  1.00 25.00           C
ATOM     40  CA  GLU    40      -2.144  11.692  54.770  1.00 25.00           C
ATOM     41  CA  MET    41      -3.286  14.857  52.939  1.00 25.00           C
ATOM     42  CA  GLY    42       0.288  16.229  53.030  1.00 25.00           C
ATOM     43  CA  GLN    43       1.619  12.922  51.629  1.00 25.00           C
ATOM     44  CA  ARG    44      -0.988  13.032  48.825  1.00 25.00           C
ATOM     45  CA  LEU    45       0.517  16.292  47.566  1.00 25.00           C
ATOM     46  CA  ASN    46       2.088  15.011  44.338  1.00 25.00           C
ATOM     47  CA  VAL    47       2.052  18.661  43.373  1.00 25.00           C
ATOM     48  CA  SER    48      -0.184  19.089  40.377  1.00 25.00           C
ATOM     49  CA  GLN    49      -1.112  22.126  38.308  1.00 25.00           C
ATOM     50  CA  LEU    50      -1.785  24.735  41.029  1.00 25.00           C
ATOM     51  CA  THR    51      -5.559  24.312  40.538  1.00 25.00           C
ATOM     52  CA  ILE    52      -5.193  20.510  40.814  1.00 25.00           C
ATOM     53  CA  ASN    53      -3.163  20.914  44.036  1.00 25.00           C
ATOM     54  CA  THR    54      -5.850  23.237  45.467  1.00 25.00           C
ATOM     55  CA  ALA    55      -8.564  20.687  44.574  1.00 25.00           C
ATOM     56  CA  ILE    56      -6.551  17.910  46.280  1.00 25.00           C
ATOM     57  CA  VAL    57      -6.153  20.086  49.407  1.00 25.00           C
ATOM     58  CA  TYR    58      -9.921  20.767  49.442  1.00 25.00           C
ATOM     59  CA  MET    59     -10.627  17.015  49.129  1.00 25.00           C
ATOM     60  CA  HIS    60      -8.230  16.298  52.029  1.00 25.00           C
ATOM     61  CA  ARG    61      -9.974  18.959  54.161  1.00 25.00           C
ATOM     62  CA  PHE    62     -13.382  17.414  53.348  1.00 25.00           C
ATOM     63  CA  TYR    63     -12.071  13.950  54.325  1.00 25.00           C
ATOM     64  CA  MET    64     -10.735  15.359  57.625  1.00 25.00           C
ATOM     65  CA  HIS    65     -14.126  16.994  58.329  1.00 25.00           C
ATOM     66  CA  HIS    66     -13.235  17.539  61.952  1.00 25.00           C
ATOM     67  CA  SER    67     -11.915  19.037  65.237  1.00 25.00           C
ATOM     68  CA  PHE    68      -9.893  21.366  67.520  1.00 25.00           C
ATOM     69  CA  THR    69      -8.469  21.846  71.015  1.00 25.00           C
ATOM     70  CA  LYS    70      -4.711  21.249  70.563  1.00 25.00           C
ATOM     71  CA  PHE    71      -2.211  20.751  67.730  1.00 25.00           C
ATOM     72  CA  ASN    72       0.713  20.491  65.356  1.00 25.00           C
ATOM     73  CA  LYS    73       2.901  21.494  62.346  1.00 25.00           C
ATOM     74  CA  ASN    74       1.672  25.057  61.663  1.00 25.00           C
ATOM     75  CA  ILE    75      -0.072  23.870  58.467  1.00 25.00           C
ATOM     76  CA  ILE    76      -1.742  21.022  60.408  1.00 25.00           C
ATOM     77  CA  SER    77      -2.924  23.501  63.078  1.00 25.00           C
ATOM     78  CA  SER    78      -4.347  25.789  60.358  1.00 25.00           C
ATOM     79  CA  THR    79      -6.178  22.818  58.781  1.00 25.00           C
ATOM     80  CA  ALA    80      -7.622  21.863  62.196  1.00 25.00           C
ATOM     81  CA  LEU    81      -8.796  25.469  62.736  1.00 25.00           C
ATOM     82  CA  PHE    82     -10.447  25.473  59.281  1.00 25.00           C
ATOM     83  CA  LEU    83     -12.206  22.169  60.090  1.00 25.00           C
ATOM     84  CA  ALA    84     -13.448  23.614  63.412  1.00 25.00           C
ATOM     85  CA  ALA    85     -14.763  26.719  61.597  1.00 25.00           C
ATOM     86  CA  LYS    86     -16.569  24.498  59.053  1.00 25.00           C
ATOM     87  CA  VAL    87     -18.132  22.466  61.899  1.00 25.00           C
ATOM     88  CA  GLU    88     -19.288  25.696  63.602  1.00 25.00           C
ATOM     89  CA  GLU    89     -22.951  25.474  64.581  1.00 25.00           C
ATOM     90  CA  GLN    90     -23.336  22.998  61.713  1.00 25.00           C
ATOM     91  CA  ALA    91     -25.976  24.156  59.155  1.00 25.00           C
ATOM     92  CA  ARG    92     -25.256  20.740  57.623  1.00 25.00           C
ATOM     93  CA  LYS    93     -21.844  21.997  56.564  1.00 25.00           C
ATOM     94  CA  LEU    94     -18.320  21.759  55.190  1.00 25.00           C
ATOM     95  CA  GLU    95     -17.545  24.571  52.707  1.00 25.00           C
ATOM     96  CA  HIS    96     -15.361  26.314  55.328  1.00 25.00           C
ATOM     97  CA  VAL    97     -13.496  23.035  55.991  1.00 25.00           C
ATOM     98  CA  ILE    98     -12.928  22.569  52.232  1.00 25.00           C
ATOM     99  CA  LYS    99     -11.591  26.148  51.966  1.00 25.00           C
ATOM    100  CA  VAL   100      -9.225  25.509  54.908  1.00 25.00           C
ATOM    101  CA  ALA   101      -7.985  22.290  53.244  1.00 25.00           C
ATOM    102  CA  HIS   102      -7.383  24.185  49.971  1.00 25.00           C
ATOM    103  CA  ALA   103      -5.433  26.884  51.864  1.00 25.00           C
ATOM    104  CA  CYS   104      -3.313  24.191  53.572  1.00 25.00           C
ATOM    105  CA  LEU   105       0.426  23.568  53.636  1.00 25.00           C
ATOM    106  CA  HIS   106       4.131  23.552  54.394  1.00 25.00           C
ATOM    107  CA  PRO   107       7.872  22.985  54.871  1.00 25.00           C
ATOM    108  CA  LEU   108      11.457  23.658  55.847  1.00 25.00           C
ATOM    109  CA  GLU   109      14.431  25.427  57.542  1.00 25.00           C
ATOM    110  CA  PRO   110      13.226  28.497  59.409  1.00 25.00           C
ATOM    111  CA  LEU   111      13.040  30.562  62.643  1.00 25.00           C
ATOM    112  CA  LEU   112      10.515  30.199  65.500  1.00 25.00           C
ATOM    113  CA  ASP   113       9.256  33.762  64.873  1.00 25.00           C
ATOM    114  CA  THR   114       8.874  32.996  61.140  1.00 25.00           C
ATOM    115  CA  LYS   115       6.920  29.807  61.968  1.00 25.00           C
ATOM    116  CA  CYS   116       4.636  31.789  64.319  1.00 25.00           C
ATOM    117  CA  ASP   117       4.039  34.398  61.580  1.00 25.00           C
ATOM    118  CA  ALA   118       3.186  31.619  59.086  1.00 25.00           C
ATOM    119  CA  TYR   119       0.735  30.084  61.597  1.00 25.00           C
ATOM    120  CA  LEU   120      -0.906  33.504  62.124  1.00 25.00           C
ATOM    121  CA  GLN   121      -1.230  33.960  58.336  1.00 25.00           C
ATOM    122  CA  GLN   122      -2.822  30.490  58.029  1.00 25.00           C
ATOM    123  CA  THR   123      -5.289  31.349  60.830  1.00 25.00           C
ATOM    124  CA  ARG   124      -6.185  34.629  59.069  1.00 25.00           C
ATOM    125  CA  GLU   125      -6.751  32.741  55.785  1.00 25.00           C
ATOM    126  CA  LEU   126      -9.003  30.224  57.592  1.00 25.00           C
ATOM    127  CA  VAL   127     -11.000  33.096  59.153  1.00 25.00           C
ATOM    128  CA  ILE   128     -11.399  34.723  55.711  1.00 25.00           C
ATOM    129  CA  LEU   129     -12.608  31.395  54.250  1.00 25.00           C
ATOM    130  CA  GLU   130     -15.134  31.032  57.106  1.00 25.00           C
ATOM    131  CA  THR   131     -16.392  34.594  56.480  1.00 25.00           C
ATOM    132  CA  ILE   132     -16.775  33.829  52.747  1.00 25.00           C
ATOM    133  CA  MET   133     -18.729  30.641  53.575  1.00 25.00           C
ATOM    134  CA  LEU   134     -21.012  32.622  55.926  1.00 25.00           C
ATOM    135  CA  GLN   135     -21.610  35.231  53.187  1.00 25.00           C
ATOM    136  CA  THR   136     -22.464  32.453  50.692  1.00 25.00           C
ATOM    137  CA  LEU   137     -24.914  30.917  53.204  1.00 25.00           C
ATOM    138  CA  GLY   138     -26.221  28.279  50.731  1.00 25.00           C
ATOM    139  CA  PHE   139     -23.203  26.521  49.308  1.00 25.00           C
ATOM    140  CA  GLU   140     -22.913  25.174  45.733  1.00 25.00           C
ATOM    141  CA  ILE   141     -19.165  25.505  45.988  1.00 25.00           C
ATOM    142  CA  THR   142     -17.736  23.866  42.888  1.00 25.00           C
ATOM    143  CA  ILE   143     -14.496  25.621  43.898  1.00 25.00           C
TER
END
