
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338TS393_2-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      A       1           -
LGA    S       2      S       2           -
LGA    S       3      S       3           -
LGA    R       4      R       4           -
LGA    W       5      W       5           -
LGA    F       6      F       6           -
LGA    F       7      F       7           -
LGA    T       8      T       8           -
LGA    R       9      R       9           -
LGA    E      10      E      10           -
LGA    Q      11      Q      11           -
LGA    L      12      L      12           -
LGA    E      13      E      13           -
LGA    N      14      N      14           -
LGA    T      15      T      15           -
LGA    P      16      P      16           -
LGA    -       -      S      17           -
LGA    -       -      R      18           -
LGA    -       -      R      19           -
LGA    -       -      C      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      E      23           -
LGA    S      17      A      24           #
LGA    R      18      D      25          1.396
LGA    -       -      K      26           -
LGA    -       -      E      27           -
LGA    R      19      L      28           #
LGA    C      20      S      29           -
LGA    G      21      C      30           -
LGA    V      22      R      31           -
LGA    E      23      -       -           -
LGA    A      24      -       -           -
LGA    D      25      -       -           -
LGA    K      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    S      29      -       -           -
LGA    C      30      Q      32           #
LGA    R      31      Q      33           -
LGA    Q      32      -       -           -
LGA    Q      33      A      34           #
LGA    A      34      A      35          4.229
LGA    A      35      N      36           -
LGA    -       -      L      37           -
LGA    -       -      I      38           -
LGA    N      36      Q      39          3.863
LGA    L      37      E      40          3.567
LGA    I      38      M      41           #
LGA    Q      39      G      42          3.805
LGA    E      40      Q      43          1.547
LGA    M      41      R      44          3.501
LGA    G      42      L      45          1.981
LGA    Q      43      N      46          3.327
LGA    R      44      V      47           -
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    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      -       -           -
LGA    N      72      S      48           #
LGA    -       -      Q      49           -
LGA    K      73      L      50          1.811
LGA    N      74      T      51          2.408
LGA    I      75      I      52          2.986
LGA    I      76      N      53          2.465
LGA    S      77      T      54          2.449
LGA    S      78      A      55          3.383
LGA    T      79      I      56          3.705
LGA    A      80      V      57          3.498
LGA    L      81      Y      58          3.752
LGA    F      82      -       -           -
LGA    L      83      -       -           -
LGA    A      84      M      59          3.049
LGA    A      85      H      60           -
LGA    K      86      R      61           -
LGA    V      87      F      62          3.828
LGA    E      88      Y      63          5.516
LGA    -       -      M      64           -
LGA    -       -      H      65           -
LGA    E      89      H      66          2.450
LGA    Q      90      S      67          2.550
LGA    -       -      F      68           -
LGA    A      91      T      69          5.942
LGA    R      92      K      70          1.867
LGA    K      93      -       -           -
LGA    L      94      F      71          1.541
LGA    E      95      N      72          1.146
LGA    H      96      K      73           #
LGA    V      97      -       -           -
LGA    I      98      N      74          2.315
LGA    K      99      -       -           -
LGA    V     100      -       -           -
LGA    A     101      I      75          4.213
LGA    H     102      I      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      F      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      K      86           -
LGA    -       -      V      87           -
LGA    -       -      E      88           -
LGA    -       -      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     103      A     101          5.368
LGA    C     104      H     102          1.629
LGA    L     105      A     103           #
LGA    -       -      C     104           -
LGA    -       -      L     105           -
LGA    -       -      H     106           -
LGA    -       -      P     107           -
LGA    -       -      L     108           -
LGA    H     106      E     109          3.796
LGA    P     107      P     110          1.535
LGA    L     108      L     111          4.185
LGA    E     109      L     112           #
LGA    P     110      D     113          2.879
LGA    L     111      T     114          5.939
LGA    L     112      K     115          2.520
LGA    D     113      C     116          1.406
LGA    T     114      -       -           -
LGA    K     115      -       -           -
LGA    C     116      D     117          3.336
LGA    D     117      A     118          2.280
LGA    A     118      Y     119          2.385
LGA    Y     119      L     120          2.911
LGA    L     120      Q     121          1.856
LGA    Q     121      Q     122          1.372
LGA    Q     122      T     123          2.491
LGA    T     123      R     124          2.403
LGA    R     124      E     125          1.672
LGA    E     125      L     126          2.264
LGA    L     126      V     127          2.749
LGA    V     127      I     128          2.249
LGA    I     128      L     129          2.329
LGA    L     129      E     130          2.749
LGA    E     130      T     131          2.256
LGA    T     131      I     132          1.974
LGA    I     132      M     133          2.482
LGA    M     133      L     134          2.312
LGA    L     134      Q     135          1.893
LGA    Q     135      T     136          2.185
LGA    T     136      L     137          2.419
LGA    L     137      G     138          2.039
LGA    G     138      -       -           -
LGA    F     139      -       -           -
LGA    E     140      -       -           -
LGA    I     141      -       -           -
LGA    T     142      -       -           -
LGA    I     143      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     60    3.01    10.00     26.611     1.930

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.485049 * X  +  -0.618069 * Y  +  -0.618643 * Z  + -20.395157
  Y_new =  -0.704597 * X  +  -0.695226 * Y  +   0.142140 * Z  +  31.301929
  Z_new =  -0.517949 * X  +   0.366949 * Y  +  -0.772708 * Z  +  48.000603 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.698237   -0.443356  [ DEG:   154.5976    -25.4024 ]
  Theta =   0.544452    2.597141  [ DEG:    31.1948    148.8052 ]
  Phi   =  -0.967894    2.173699  [ DEG:   -55.4562    124.5438 ]
 
# 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_2-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_2-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   60   3.01   10.00  26.611
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_2-D1
PFRMAT TS
TARGET T0338
MODEL 2
PARENT N/A
ATOM      1  CA  ALA     1       8.198  44.379  58.872  1.00 25.00           C
ATOM      2  CA  SER     2       5.336  43.014  60.954  1.00 25.00           C
ATOM      3  CA  SER     3       1.668  42.539  61.675  1.00 25.00           C
ATOM      4  CA  ARG     4       2.680  39.190  60.226  1.00 25.00           C
ATOM      5  CA  TRP     5      -0.525  38.040  58.597  1.00 25.00           C
ATOM      6  CA  PHE     6      -1.985  35.798  61.349  1.00 25.00           C
ATOM      7  CA  PHE     7      -3.117  32.141  60.854  1.00 25.00           C
ATOM      8  CA  THR     8      -6.502  32.668  62.593  1.00 25.00           C
ATOM      9  CA  ARG     9      -4.335  31.842  65.645  1.00 25.00           C
ATOM     10  CA  GLU    10      -4.032  32.534  69.400  1.00 25.00           C
ATOM     11  CA  GLN    11      -7.421  34.318  69.370  1.00 25.00           C
ATOM     12  CA  LEU    12      -8.995  31.346  67.537  1.00 25.00           C
ATOM     13  CA  GLU    13      -7.507  28.936  70.114  1.00 25.00           C
ATOM     14  CA  ASN    14      -4.352  28.083  72.018  1.00 25.00           C
ATOM     15  CA  THR    15      -3.617  25.511  69.305  1.00 25.00           C
ATOM     16  CA  PRO    16      -2.680  21.801  69.429  1.00 25.00           C
ATOM     17  CA  SER    17       0.680  20.275  68.524  1.00 25.00           C
ATOM     18  CA  ARG    18      -0.557  17.774  65.885  1.00 25.00           C
ATOM     19  CA  ARG    19      -3.308  15.372  64.771  1.00 25.00           C
ATOM     20  CA  CYS    20      -6.580  14.074  66.206  1.00 25.00           C
ATOM     21  CA  GLY    21      -8.671  11.640  64.253  1.00 25.00           C
ATOM     22  CA  VAL    22     -11.873  10.930  66.106  1.00 25.00           C
ATOM     23  CA  GLU    23     -15.156  11.211  64.202  1.00 25.00           C
ATOM     24  CA  ALA    24     -16.834  11.961  67.533  1.00 25.00           C
ATOM     25  CA  ASP    25     -16.700  14.144  70.677  1.00 25.00           C
ATOM     26  CA  LYS    26     -13.866  16.215  69.147  1.00 25.00           C
ATOM     27  CA  GLU    27     -15.893  16.660  65.929  1.00 25.00           C
ATOM     28  CA  LEU    28     -18.934  17.781  67.971  1.00 25.00           C
ATOM     29  CA  SER    29     -16.759  20.294  69.874  1.00 25.00           C
ATOM     30  CA  CYS    30     -15.384  21.647  66.567  1.00 25.00           C
ATOM     31  CA  ARG    31     -18.946  22.011  65.207  1.00 25.00           C
ATOM     32  CA  GLN    32     -19.994  23.880  68.382  1.00 25.00           C
ATOM     33  CA  GLN    33     -16.978  26.213  68.034  1.00 25.00           C
ATOM     34  CA  ALA    34     -17.887  26.882  64.374  1.00 25.00           C
ATOM     35  CA  ALA    35     -21.497  27.663  65.388  1.00 25.00           C
ATOM     36  CA  ASN    36     -20.244  30.070  68.090  1.00 25.00           C
ATOM     37  CA  LEU    37     -17.979  31.801  65.532  1.00 25.00           C
ATOM     38  CA  ILE    38     -20.929  32.140  63.114  1.00 25.00           C
ATOM     39  CA  GLN    39     -23.078  33.639  65.906  1.00 25.00           C
ATOM     40  CA  GLU    40     -20.292  36.126  66.750  1.00 25.00           C
ATOM     41  CA  MET    41     -20.019  37.111  63.059  1.00 25.00           C
ATOM     42  CA  GLY    42     -23.810  37.627  62.892  1.00 25.00           C
ATOM     43  CA  GLN    43     -23.676  39.811  66.036  1.00 25.00           C
ATOM     44  CA  ARG    44     -20.841  41.883  64.506  1.00 25.00           C
ATOM     45  CA  LEU    45     -19.957  41.768  60.858  1.00 25.00           C
ATOM     46  CA  ASN    46     -23.116  43.911  60.393  1.00 25.00           C
ATOM     47  CA  VAL    47     -24.797  41.519  57.918  1.00 25.00           C
ATOM     48  CA  SER    48     -23.547  42.557  54.431  1.00 25.00           C
ATOM     49  CA  GLN    49     -21.598  40.876  51.668  1.00 25.00           C
ATOM     50  CA  LEU    50     -22.105  38.944  48.400  1.00 25.00           C
ATOM     51  CA  THR    51     -19.175  36.639  49.281  1.00 25.00           C
ATOM     52  CA  ILE    52     -20.668  36.030  52.755  1.00 25.00           C
ATOM     53  CA  ASN    53     -24.059  35.203  51.180  1.00 25.00           C
ATOM     54  CA  THR    54     -22.370  32.758  48.765  1.00 25.00           C
ATOM     55  CA  ALA    55     -20.546  31.091  51.692  1.00 25.00           C
ATOM     56  CA  ILE    56     -23.849  30.773  53.602  1.00 25.00           C
ATOM     57  CA  VAL    57     -25.507  29.208  50.525  1.00 25.00           C
ATOM     58  CA  TYR    58     -22.610  26.727  50.195  1.00 25.00           C
ATOM     59  CA  MET    59     -22.939  25.811  53.899  1.00 25.00           C
ATOM     60  CA  HIS    60     -26.704  25.268  53.456  1.00 25.00           C
ATOM     61  CA  ARG    61     -26.048  23.029  50.418  1.00 25.00           C
ATOM     62  CA  PHE    62     -23.491  21.007  52.429  1.00 25.00           C
ATOM     63  CA  TYR    63     -26.016  20.605  55.280  1.00 25.00           C
ATOM     64  CA  MET    64     -28.676  19.424  52.791  1.00 25.00           C
ATOM     65  CA  HIS    65     -26.209  16.894  51.317  1.00 25.00           C
ATOM     66  CA  HIS    66     -24.639  15.734  54.647  1.00 25.00           C
ATOM     67  CA  SER    67     -27.869  15.663  56.713  1.00 25.00           C
ATOM     68  CA  PHE    68     -26.611  17.761  59.553  1.00 25.00           C
ATOM     69  CA  THR    69     -30.091  17.140  61.068  1.00 25.00           C
ATOM     70  CA  LYS    70     -31.501  20.580  61.871  1.00 25.00           C
ATOM     71  CA  PHE    71     -28.266  22.194  63.055  1.00 25.00           C
ATOM     72  CA  ASN    72     -30.176  25.283  63.974  1.00 25.00           C
ATOM     73  CA  LYS    73     -28.253  27.310  61.419  1.00 25.00           C
ATOM     74  CA  ASN    74     -27.317  30.133  59.008  1.00 25.00           C
ATOM     75  CA  ILE    75     -24.259  30.984  61.151  1.00 25.00           C
ATOM     76  CA  ILE    76     -23.207  27.301  61.153  1.00 25.00           C
ATOM     77  CA  SER    77     -23.579  27.166  57.344  1.00 25.00           C
ATOM     78  CA  SER    78     -21.452  30.332  56.999  1.00 25.00           C
ATOM     79  CA  THR    79     -18.767  28.804  59.262  1.00 25.00           C
ATOM     80  CA  ALA    80     -18.776  25.605  57.156  1.00 25.00           C
ATOM     81  CA  LEU    81     -18.407  27.681  53.958  1.00 25.00           C
ATOM     82  CA  PHE    82     -15.476  29.595  55.511  1.00 25.00           C
ATOM     83  CA  LEU    83     -13.812  26.292  56.504  1.00 25.00           C
ATOM     84  CA  ALA    84     -14.271  24.961  52.942  1.00 25.00           C
ATOM     85  CA  ALA    85     -12.724  28.162  51.520  1.00 25.00           C
ATOM     86  CA  LYS    86      -9.752  27.818  53.911  1.00 25.00           C
ATOM     87  CA  VAL    87      -9.280  24.172  52.837  1.00 25.00           C
ATOM     88  CA  GLU    88      -9.366  25.220  49.154  1.00 25.00           C
ATOM     89  CA  GLU    89      -5.979  24.064  47.787  1.00 25.00           C
ATOM     90  CA  GLN    90      -2.750  24.493  49.785  1.00 25.00           C
ATOM     91  CA  ALA    91      -0.326  25.918  47.141  1.00 25.00           C
ATOM     92  CA  ARG    92      -0.691  29.037  49.304  1.00 25.00           C
ATOM     93  CA  LYS    93      -3.143  31.860  48.597  1.00 25.00           C
ATOM     94  CA  LEU    94      -6.143  30.439  50.412  1.00 25.00           C
ATOM     95  CA  GLU    95      -4.514  30.635  53.873  1.00 25.00           C
ATOM     96  CA  HIS    96      -3.504  34.270  53.219  1.00 25.00           C
ATOM     97  CA  VAL    97      -7.083  35.096  52.135  1.00 25.00           C
ATOM     98  CA  ILE    98      -8.450  33.457  55.316  1.00 25.00           C
ATOM     99  CA  LYS    99      -5.996  35.484  57.445  1.00 25.00           C
ATOM    100  CA  VAL   100      -7.081  38.703  55.675  1.00 25.00           C
ATOM    101  CA  ALA   101     -10.758  37.841  56.311  1.00 25.00           C
ATOM    102  CA  HIS   102      -9.996  37.206  60.010  1.00 25.00           C
ATOM    103  CA  ALA   103      -8.184  40.571  60.239  1.00 25.00           C
ATOM    104  CA  CYS   104     -11.176  42.321  58.611  1.00 25.00           C
ATOM    105  CA  LEU   105     -10.090  45.857  57.660  1.00 25.00           C
ATOM    106  CA  HIS   106      -7.463  47.832  59.547  1.00 25.00           C
ATOM    107  CA  PRO   107      -8.506  50.347  62.227  1.00 25.00           C
ATOM    108  CA  LEU   108      -8.148  53.623  60.232  1.00 25.00           C
ATOM    109  CA  GLU   109     -10.074  56.420  58.444  1.00 25.00           C
ATOM    110  CA  PRO   110     -10.519  54.569  55.139  1.00 25.00           C
ATOM    111  CA  LEU   111     -11.124  55.986  51.618  1.00 25.00           C
ATOM    112  CA  LEU   112     -11.413  54.962  47.939  1.00 25.00           C
ATOM    113  CA  ASP   113      -8.247  52.830  48.259  1.00 25.00           C
ATOM    114  CA  THR   114      -9.664  51.153  51.397  1.00 25.00           C
ATOM    115  CA  LYS   115     -12.944  50.426  49.557  1.00 25.00           C
ATOM    116  CA  CYS   116     -10.994  48.915  46.628  1.00 25.00           C
ATOM    117  CA  ASP   117      -8.998  46.725  49.055  1.00 25.00           C
ATOM    118  CA  ALA   118     -12.247  45.556  50.711  1.00 25.00           C
ATOM    119  CA  TYR   119     -13.722  44.710  47.279  1.00 25.00           C
ATOM    120  CA  LEU   120     -10.567  42.730  46.384  1.00 25.00           C
ATOM    121  CA  GLN   121     -10.795  40.822  49.697  1.00 25.00           C
ATOM    122  CA  GLN   122     -14.476  40.022  49.011  1.00 25.00           C
ATOM    123  CA  THR   123     -13.576  38.767  45.506  1.00 25.00           C
ATOM    124  CA  ARG   124     -10.813  36.562  46.979  1.00 25.00           C
ATOM    125  CA  GLU   125     -13.280  35.141  49.542  1.00 25.00           C
ATOM    126  CA  LEU   126     -15.792  34.399  46.749  1.00 25.00           C
ATOM    127  CA  VAL   127     -13.060  32.635  44.726  1.00 25.00           C
ATOM    128  CA  ILE   128     -12.103  30.549  47.792  1.00 25.00           C
ATOM    129  CA  LEU   129     -15.774  29.595  48.319  1.00 25.00           C
ATOM    130  CA  GLU   130     -16.063  28.571  44.641  1.00 25.00           C
ATOM    131  CA  THR   131     -12.898  26.439  44.960  1.00 25.00           C
ATOM    132  CA  ILE   132     -14.314  24.762  48.098  1.00 25.00           C
ATOM    133  CA  MET   133     -17.594  24.036  46.259  1.00 25.00           C
ATOM    134  CA  LEU   134     -15.644  22.522  43.330  1.00 25.00           C
ATOM    135  CA  GLN   135     -13.648  20.333  45.756  1.00 25.00           C
ATOM    136  CA  THR   136     -16.898  19.164  47.412  1.00 25.00           C
ATOM    137  CA  LEU   137     -18.371  18.319  43.980  1.00 25.00           C
ATOM    138  CA  GLY   138     -16.271  15.174  43.568  1.00 25.00           C
ATOM    139  CA  PHE   139     -13.810  14.990  46.473  1.00 25.00           C
ATOM    140  CA  GLU   140     -16.510  12.814  47.964  1.00 25.00           C
ATOM    141  CA  ILE   141     -18.843  14.871  50.082  1.00 25.00           C
ATOM    142  CA  THR   142     -21.207  14.716  47.124  1.00 25.00           C
ATOM    143  CA  ILE   143     -23.278  17.778  46.378  1.00 25.00           C
TER
END
