
#######################################################
#                                                     #
#                        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  129 (  129),  selected  129 , name T0302TS168_1-D1
# Molecule2: number of CA atoms  129 ( 2108),  selected  129 , name T0302_D1.pdb
# PARAMETERS: T0302TS168_1-D1.T0302_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V       3      V       3          4.309
LGA    S       4      S       4          3.666
LGA    P       5      P       5          2.735
LGA    E       6      E       6          2.359
LGA    E       7      E       7          3.973
LGA    A       8      A       8          4.185
LGA    V       9      V       9          3.177
LGA    K      10      K      10          2.782
LGA    W      11      -       -           -
LGA    G      12      -       -           -
LGA    E      13      W      11          0.887
LGA    S      14      G      12           #
LGA    -       -      E      13           -
LGA    -       -      S      14           -
LGA    -       -      F      15           -
LGA    F      15      D      16           #
LGA    D      16      K      17          4.108
LGA    K      17      L      18          4.619
LGA    L      18      L      19          4.422
LGA    L      19      S      20          4.409
LGA    S      20      -       -           -
LGA    H      21      H      21          2.331
LGA    R      22      R      22          1.045
LGA    D      23      D      23          2.191
LGA    G      24      G      24          2.743
LGA    L      25      L      25          1.520
LGA    E      26      E      26          1.595
LGA    A      27      A      27          2.913
LGA    F      28      F      28          2.042
LGA    T      29      T      29          1.195
LGA    R      30      R      30          2.459
LGA    F      31      F      31          2.575
LGA    L      32      L      32          1.442
LGA    K      33      K      33          1.512
LGA    T      34      T      34          1.669
LGA    E      35      E      35          1.471
LGA    F      36      F      36          2.992
LGA    S      37      S      37          2.557
LGA    E      38      E      38          1.949
LGA    E      39      E      39          2.759
LGA    N      40      N      40          1.418
LGA    I      41      I      41          1.441
LGA    E      42      E      42          2.179
LGA    F      43      F      43          1.034
LGA    W      44      W      44          1.317
LGA    I      45      I      45          1.189
LGA    A      46      A      46          0.822
LGA    C      47      C      47          0.791
LGA    E      48      E      48          1.104
LGA    D      49      D      49          0.614
LGA    F      50      F      50          0.984
LGA    K      51      K      51          0.925
LGA    K      52      K      52          4.738
LGA    S      53      S      53          2.818
LGA    K      54      K      54          0.776
LGA    G      55      G      55          2.477
LGA    P      56      P      56          1.577
LGA    Q      57      Q      57          1.141
LGA    Q      58      Q      58          1.108
LGA    I      59      I      59          0.905
LGA    H      60      H      60          1.132
LGA    L      61      L      61          0.961
LGA    K      62      K      62          1.221
LGA    A      63      A      63          0.839
LGA    K      64      K      64          0.390
LGA    A      65      A      65          0.832
LGA    I      66      I      66          1.179
LGA    Y      67      Y      67          0.163
LGA    E      68      E      68          1.462
LGA    K      69      K      69          1.886
LGA    F      70      F      70          0.761
LGA    -       -      I      71           -
LGA    I      71      Q      72          2.518
LGA    Q      72      T      73           #
LGA    T      73      D      74          5.261
LGA    D      74      A      75          5.012
LGA    A      75      -       -           -
LGA    P      76      P      76           #
LGA    K      77      K      77           -
LGA    E      78      -       -           -
LGA    V      79      E      78           #
LGA    N      80      V      79           -
LGA    L      81      N      80           #
LGA    D      82      L      81           -
LGA    F      83      D      82           #
LGA    H      84      F      83          3.916
LGA    T      85      H      84          3.753
LGA    -       -      T      85           -
LGA    K      86      K      86          2.915
LGA    E      87      E      87          2.946
LGA    V      88      V      88          1.807
LGA    I      89      I      89          1.444
LGA    T      90      T      90          1.845
LGA    N      91      N      91          1.481
LGA    S      92      S      92          1.511
LGA    I      93      I      93          1.542
LGA    T      94      T      94          1.802
LGA    Q      95      Q      95          2.222
LGA    P      96      P      96          2.089
LGA    T      97      T      97          1.095
LGA    L      98      L      98          3.524
LGA    H      99      H      99          5.228
LGA    S     100      S     100          3.236
LGA    F     101      F     101          1.023
LGA    D     102      D     102          0.670
LGA    A     103      A     103          0.896
LGA    A     104      A     104          1.086
LGA    Q     105      Q     105          1.040
LGA    S     106      S     106          1.129
LGA    R     107      R     107          0.683
LGA    V     108      V     108          0.479
LGA    Y     109      Y     109          0.510
LGA    Q     110      Q     110          1.214
LGA    L     111      L     111          1.046
LGA    M     112      M     112          1.182
LGA    E     113      E     113          1.402
LGA    Q     114      Q     114          1.380
LGA    D     115      D     115          2.176
LGA    S     116      S     116          1.234
LGA    Y     117      Y     117          0.610
LGA    T     118      T     118          1.281
LGA    R     119      R     119          1.965
LGA    F     120      F     120          1.900
LGA    L     121      L     121          2.692
LGA    K     122      K     122          4.874
LGA    S     123      S     123          5.048
LGA    D     124      D     124          4.195
LGA    I     125      I     125          3.543
LGA    Y     126      Y     126          1.626
LGA    L     127      L     127          2.038
LGA    D     128      D     128          2.619
LGA    L     129      L     129          2.691
LGA    M     130      M     130          2.095
LGA    E     131      E     131          1.412

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  129  129    5.0    114    2.41    92.11     61.016     4.535

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.315133 * X  +   0.529452 * Y  +  -0.787637 * Z  + 122.773567
  Y_new =   0.947466 * X  +   0.127623 * Y  +  -0.293292 * Z  +  -3.967847
  Z_new =  -0.054764 * X  +  -0.838685 * Y  +  -0.541856 * Z  +   0.574301 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.144410    0.997183  [ DEG:  -122.8656     57.1344 ]
  Theta =   0.054791    3.086802  [ DEG:     3.1393    176.8607 ]
  Phi   =   1.891892   -1.249700  [ DEG:   108.3974    -71.6026 ]
 
# 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: T0302TS168_1-D1                               
REMARK     2: T0302_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0302TS168_1-D1.T0302_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  129  129   5.0  114   2.41   92.11  61.016
REMARK  ---------------------------------------------------------- 
MOLECULE T0302TS168_1-D1
PFRMAT TS
TARGET T0302
MODEL 1
PARENT N/A
ATOM      3  CA  VAL     3     143.579   8.765   4.883  1.00 25.00           C
ATOM      4  CA  SER     4     145.220  10.804   2.201  1.00 25.00           C
ATOM      5  CA  PRO     5     144.028  12.365  -1.035  1.00 25.00           C
ATOM      6  CA  GLU     6     143.606  11.310  -4.692  1.00 25.00           C
ATOM      7  CA  GLU     7     144.603   7.722  -3.798  1.00 25.00           C
ATOM      8  CA  ALA     8     142.070   7.707  -0.926  1.00 25.00           C
ATOM      9  CA  VAL     9     139.343   8.984  -3.293  1.00 25.00           C
ATOM     10  CA  LYS    10     140.214   6.239  -5.817  1.00 25.00           C
ATOM     11  CA  TRP    11     140.028   3.600  -3.049  1.00 25.00           C
ATOM     12  CA  GLY    12     136.613   4.946  -1.961  1.00 25.00           C
ATOM     13  CA  GLU    13     135.375   4.803  -5.582  1.00 25.00           C
ATOM     14  CA  SER    14     136.611   1.191  -5.887  1.00 25.00           C
ATOM     15  CA  PHE    15     134.811   0.274  -2.635  1.00 25.00           C
ATOM     16  CA  ASP    16     131.590   1.888  -3.934  1.00 25.00           C
ATOM     17  CA  LYS    17     131.900  -0.071  -7.210  1.00 25.00           C
ATOM     18  CA  LEU    18     132.404  -3.321  -5.248  1.00 25.00           C
ATOM     19  CA  LEU    19     129.309  -2.550  -3.128  1.00 25.00           C
ATOM     20  CA  SER    20     131.804  -3.238  -0.303  1.00 25.00           C
ATOM     21  CA  HIS    21     135.463  -3.342   0.792  1.00 25.00           C
ATOM     22  CA  ARG    22     136.167  -1.114   3.867  1.00 25.00           C
ATOM     23  CA  ASP    23     136.389   1.990   6.099  1.00 25.00           C
ATOM     24  CA  GLY    24     134.525   4.050   3.462  1.00 25.00           C
ATOM     25  CA  LEU    25     131.804   1.363   3.250  1.00 25.00           C
ATOM     26  CA  GLU    26     131.467   1.368   7.065  1.00 25.00           C
ATOM     27  CA  ALA    27     131.159   5.186   7.057  1.00 25.00           C
ATOM     28  CA  PHE    28     128.458   4.987   4.350  1.00 25.00           C
ATOM     29  CA  THR    29     126.559   2.370   6.402  1.00 25.00           C
ATOM     30  CA  ARG    30     126.774   4.610   9.501  1.00 25.00           C
ATOM     31  CA  PHE    31     125.453   7.580   7.476  1.00 25.00           C
ATOM     32  CA  LEU    32     122.550   5.441   6.185  1.00 25.00           C
ATOM     33  CA  LYS    33     121.734   4.345   9.763  1.00 25.00           C
ATOM     34  CA  THR    34     121.774   7.998  10.916  1.00 25.00           C
ATOM     35  CA  GLU    35     118.392   8.180   9.165  1.00 25.00           C
ATOM     36  CA  PHE    36     117.319   6.070   6.185  1.00 25.00           C
ATOM     37  CA  SER    37     117.192   3.601   3.321  1.00 25.00           C
ATOM     38  CA  GLU    38     119.754   1.557   5.281  1.00 25.00           C
ATOM     39  CA  GLU    39     117.117  -1.208   5.021  1.00 25.00           C
ATOM     40  CA  ASN    40     118.461  -2.200   1.575  1.00 25.00           C
ATOM     41  CA  ILE    41     122.024  -2.323   2.975  1.00 25.00           C
ATOM     42  CA  GLU    42     120.835  -4.521   5.877  1.00 25.00           C
ATOM     43  CA  PHE    43     119.078  -6.867   3.411  1.00 25.00           C
ATOM     44  CA  TRP    44     122.270  -7.088   1.308  1.00 25.00           C
ATOM     45  CA  ILE    45     124.312  -7.899   4.445  1.00 25.00           C
ATOM     46  CA  ALA    46     121.804 -10.630   5.402  1.00 25.00           C
ATOM     47  CA  CYS    47     122.027 -12.104   1.874  1.00 25.00           C
ATOM     48  CA  GLU    48     125.850 -12.093   2.085  1.00 25.00           C
ATOM     49  CA  ASP    49     125.693 -13.856   5.481  1.00 25.00           C
ATOM     50  CA  PHE    50     123.316 -16.487   4.034  1.00 25.00           C
ATOM     51  CA  LYS    51     125.693 -17.044   1.082  1.00 25.00           C
ATOM     52  CA  LYS    52     127.569 -20.193   0.121  1.00 25.00           C
ATOM     53  CA  SER    53     128.491 -21.390   3.630  1.00 25.00           C
ATOM     54  CA  LYS    54     126.648 -24.491   4.982  1.00 25.00           C
ATOM     55  CA  GLY    55     123.649 -26.516   3.699  1.00 25.00           C
ATOM     56  CA  PRO    56     120.122 -27.910   3.302  1.00 25.00           C
ATOM     57  CA  GLN    57     117.826 -27.258   6.297  1.00 25.00           C
ATOM     58  CA  GLN    58     120.185 -24.510   7.540  1.00 25.00           C
ATOM     59  CA  ILE    59     120.200 -22.913   4.059  1.00 25.00           C
ATOM     60  CA  HIS    60     116.372 -23.014   3.971  1.00 25.00           C
ATOM     61  CA  LEU    61     116.224 -21.373   7.428  1.00 25.00           C
ATOM     62  CA  LYS    62     118.640 -18.640   6.260  1.00 25.00           C
ATOM     63  CA  ALA    63     116.485 -18.028   3.154  1.00 25.00           C
ATOM     64  CA  LYS    64     113.355 -17.772   5.345  1.00 25.00           C
ATOM     65  CA  ALA    65     115.134 -15.270   7.636  1.00 25.00           C
ATOM     66  CA  ILE    66     116.183 -13.193   4.595  1.00 25.00           C
ATOM     67  CA  TYR    67     112.578 -13.213   3.306  1.00 25.00           C
ATOM     68  CA  GLU    68     111.317 -12.082   6.741  1.00 25.00           C
ATOM     69  CA  LYS    69     113.898  -9.253   6.782  1.00 25.00           C
ATOM     70  CA  PHE    70     112.799  -8.165   3.279  1.00 25.00           C
ATOM     71  CA  ILE    71     109.137  -8.169   4.399  1.00 25.00           C
ATOM     72  CA  GLN    72     106.722  -9.972   6.783  1.00 25.00           C
ATOM     73  CA  THR    73     104.193  -9.927   9.625  1.00 25.00           C
ATOM     74  CA  ASP    74     104.575  -6.287  10.690  1.00 25.00           C
ATOM     75  CA  ALA    75     105.414  -4.857   7.299  1.00 25.00           C
ATOM     76  CA  PRO    76     104.398  -1.483   8.619  1.00 25.00           C
ATOM     77  CA  LYS    77     103.172  -0.236   5.257  1.00 25.00           C
ATOM     78  CA  GLU    78     101.443  -0.281   1.906  1.00 25.00           C
ATOM     79  CA  VAL    79     104.674  -1.361   0.123  1.00 25.00           C
ATOM     80  CA  ASN    80     103.286  -2.036  -3.391  1.00 25.00           C
ATOM     81  CA  LEU    81     105.411  -1.608  -6.516  1.00 25.00           C
ATOM     82  CA  ASP    82     104.481  -4.961  -8.121  1.00 25.00           C
ATOM     83  CA  PHE    83     105.262  -7.952  -5.893  1.00 25.00           C
ATOM     84  CA  HIS    84     106.625 -10.393  -8.510  1.00 25.00           C
ATOM     85  CA  THR    85     110.019 -10.437  -6.735  1.00 25.00           C
ATOM     86  CA  LYS    86     108.288 -11.132  -3.390  1.00 25.00           C
ATOM     87  CA  GLU    87     106.307 -13.998  -4.984  1.00 25.00           C
ATOM     88  CA  VAL    88     109.538 -15.459  -6.431  1.00 25.00           C
ATOM     89  CA  ILE    89     111.208 -15.238  -2.992  1.00 25.00           C
ATOM     90  CA  THR    90     108.209 -17.004  -1.394  1.00 25.00           C
ATOM     91  CA  ASN    91     108.392 -19.764  -4.044  1.00 25.00           C
ATOM     92  CA  SER    92     112.139 -20.190  -3.377  1.00 25.00           C
ATOM     93  CA  ILE    93     111.466 -20.435   0.386  1.00 25.00           C
ATOM     94  CA  THR    94     111.545 -24.209   0.351  1.00 25.00           C
ATOM     95  CA  GLN    95     114.176 -26.392  -1.429  1.00 25.00           C
ATOM     96  CA  PRO    96     116.921 -23.771  -1.547  1.00 25.00           C
ATOM     97  CA  THR    97     120.035 -22.203  -3.077  1.00 25.00           C
ATOM     98  CA  LEU    98     122.055 -18.964  -3.616  1.00 25.00           C
ATOM     99  CA  HIS    99     119.415 -18.112  -6.229  1.00 25.00           C
ATOM    100  CA  SER   100     116.362 -15.977  -5.341  1.00 25.00           C
ATOM    101  CA  PHE   101     118.276 -14.418  -2.413  1.00 25.00           C
ATOM    102  CA  ASP   102     121.230 -13.643  -4.722  1.00 25.00           C
ATOM    103  CA  ALA   103     118.858 -12.019  -7.253  1.00 25.00           C
ATOM    104  CA  ALA   104     117.293  -9.907  -4.468  1.00 25.00           C
ATOM    105  CA  GLN   105     120.776  -8.813  -3.309  1.00 25.00           C
ATOM    106  CA  SER   106     121.696  -7.854  -6.901  1.00 25.00           C
ATOM    107  CA  ARG   107     118.460  -5.830  -7.217  1.00 25.00           C
ATOM    108  CA  VAL   108     119.230  -4.039  -3.920  1.00 25.00           C
ATOM    109  CA  TYR   109     122.765  -3.234  -5.153  1.00 25.00           C
ATOM    110  CA  GLN   110     121.335  -1.852  -8.427  1.00 25.00           C
ATOM    111  CA  LEU   111     118.862   0.313  -6.461  1.00 25.00           C
ATOM    112  CA  MET   112     121.718   1.631  -4.274  1.00 25.00           C
ATOM    113  CA  GLU   113     123.764   2.459  -7.404  1.00 25.00           C
ATOM    114  CA  GLN   114     120.764   4.305  -8.907  1.00 25.00           C
ATOM    115  CA  ASP   115     120.582   6.971  -6.225  1.00 25.00           C
ATOM    116  CA  SER   116     121.634   8.042  -2.744  1.00 25.00           C
ATOM    117  CA  TYR   117     125.058   6.628  -3.558  1.00 25.00           C
ATOM    118  CA  THR   118     125.231   9.020  -6.543  1.00 25.00           C
ATOM    119  CA  ARG   119     125.279  12.023  -4.167  1.00 25.00           C
ATOM    120  CA  PHE   120     128.100  10.407  -2.142  1.00 25.00           C
ATOM    121  CA  LEU   121     130.085   9.785  -5.359  1.00 25.00           C
ATOM    122  CA  LYS   122     130.578  13.444  -6.176  1.00 25.00           C
ATOM    123  CA  SER   123     129.118  15.606  -3.395  1.00 25.00           C
ATOM    124  CA  ASP   124     129.609  17.493  -0.161  1.00 25.00           C
ATOM    125  CA  ILE   125     130.438  15.157   2.758  1.00 25.00           C
ATOM    126  CA  TYR   126     132.619  13.011   0.454  1.00 25.00           C
ATOM    127  CA  LEU   127     134.441  16.144  -0.780  1.00 25.00           C
ATOM    128  CA  ASP   128     135.035  17.254   2.836  1.00 25.00           C
ATOM    129  CA  LEU   129     136.414  13.786   3.699  1.00 25.00           C
ATOM    130  CA  MET   130     138.748  13.934   0.667  1.00 25.00           C
ATOM    131  CA  GLU   131     140.186  17.403   1.526  1.00 25.00           C
TER
END
