
#######################################################
#                                                     #
#                        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 T0382TS168_2
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS168_2.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    M       1      H       7          3.087
LGA    S       2      Q       8          4.051
LGA    K       3      M       9           -
LGA    L       4      T      10          4.836
LGA    D       5      T      11          3.495
LGA    L       6      Q      12           #
LGA    H       7      D      13           -
LGA    Q       8      L      14           #
LGA    M       9      V      15          2.426
LGA    T      10      -       -           -
LGA    T      11      -       -           -
LGA    Q      12      A      16          3.581
LGA    D      13      L      17          2.722
LGA    L      14      F      18          3.080
LGA    V      15      A      19          2.216
LGA    A      16      K      20          1.685
LGA    L      17      V      21          2.208
LGA    F      18      T      22          2.961
LGA    A      19      V      23          2.313
LGA    K      20      E      24          2.819
LGA    V      21      Q      25          4.134
LGA    -       -      D      26           -
LGA    T      22      D      27          2.256
LGA    V      23      A      28          4.379
LGA    E      24      L      29          3.552
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    Q      25      I      34          2.902
LGA    D      26      S      35           #
LGA    -       -      R      36           -
LGA    D      27      F      37           #
LGA    A      28      N      38           -
LGA    L      29      R      39           #
LGA    L      30      L      40           #
LGA    G      31      -       -           -
LGA    N      32      -       -           -
LGA    Q      33      F      41          5.078
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           -
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           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    I      34      R      74           #
LGA    S      35      L      75          4.354
LGA    R      36      Q      76          4.086
LGA    F      37      A      77          2.911
LGA    N      38      A      78          2.067
LGA    R      39      K      79          1.854
LGA    L      40      L      80          1.505
LGA    F      41      T      81          1.083
LGA    G      42      L      82          1.110
LGA    V      43      A      83          1.190
LGA    M      44      V      84          0.937
LGA    A      45      A      85          1.243
LGA    E      46      P      86          3.755
LGA    I      47      V      87           -
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      K      88          5.012
LGA    D      57      A      89           #
LGA    Q      58      R      90          4.803
LGA    R      59      E      91          1.596
LGA    T      60      Q      92          3.615
LGA    A      61      L      93           #
LGA    L      62      E      94          4.188
LGA    L      63      A      95          1.555
LGA    S      64      -       -           -
LGA    L      65      I      96          2.731
LGA    F      66      V      97          3.194
LGA    E      67      S      98           #
LGA    Y      68      S      99          2.001
LGA    P      69      K     100          1.292
LGA    N      70      W     101          2.058
LGA    M      71      F     102          2.051
LGA    Q      72      P     103          3.961
LGA    V      73      -       -           -
LGA    R      74      Q     104          3.092
LGA    L      75      A     105          2.131
LGA    Q      76      G     106          1.793
LGA    A      77      D     107          1.768
LGA    A      78      A     108          1.492
LGA    K      79      G     109          0.886
LGA    L      80      M     110          0.929
LGA    T      81      C     111          1.110
LGA    L      82      L     112          1.476
LGA    A      83      D     113          1.730
LGA    V      84      L     114          1.774
LGA    A      85      L     115          2.400
LGA    P      86      D     116          2.838
LGA    V      87      D     117          2.993
LGA    K      88      G     118          3.412
LGA    A      89      -       -           -
LGA    R      90      -       -           -
LGA    E      91      T     119           #
LGA    Q      92      F     120           -
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      K     121          4.232
LGA    D     117      P     122          2.216
LGA    G     118      K     123          4.540
LGA    T     119      -       -           -
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     63    2.92     6.35     32.373     2.086

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.283149 * X  +  -0.489371 * Y  +  -0.824829 * Z  + -15.225101
  Y_new =   0.611932 * X  +  -0.754402 * Y  +   0.237522 * Z  +  53.458740
  Z_new =  -0.738489 * X  +  -0.437485 * Y  +   0.513070 * Z  +   3.137593 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.706049    2.435544  [ DEG:   -40.4536    139.5464 ]
  Theta =   0.830827    2.310766  [ DEG:    47.6029    132.3971 ]
  Phi   =   2.004172   -1.137421  [ DEG:   114.8306    -65.1694 ]
 
# 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: T0382TS168_2                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS168_2.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   63   2.92    6.35  32.373
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS168_2
PFRMAT TS
TARGET T0382
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      -5.873  40.550 -16.329  1.00 25.00           C
ATOM      2  CA  SER     2      -9.633  39.924 -16.760  1.00 25.00           C
ATOM      3  CA  LYS     3     -12.922  41.715 -16.648  1.00 25.00           C
ATOM      4  CA  LEU     4     -16.376  41.963 -15.118  1.00 25.00           C
ATOM      5  CA  ASP     5     -17.186  43.932 -11.933  1.00 25.00           C
ATOM      6  CA  LEU     6     -13.685  43.322 -10.502  1.00 25.00           C
ATOM      7  CA  HIS     7     -14.479  45.598  -7.526  1.00 25.00           C
ATOM      8  CA  GLN     8     -17.750  43.702  -6.916  1.00 25.00           C
ATOM      9  CA  MET     9     -15.867  40.369  -7.029  1.00 25.00           C
ATOM     10  CA  THR    10     -13.297  41.708  -4.526  1.00 25.00           C
ATOM     11  CA  THR    11     -16.118  42.860  -2.208  1.00 25.00           C
ATOM     12  CA  GLN    12     -17.756  39.407  -2.442  1.00 25.00           C
ATOM     13  CA  ASP    13     -14.412  37.738  -1.605  1.00 25.00           C
ATOM     14  CA  LEU    14     -13.982  40.056   1.413  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.521  39.205   2.603  1.00 25.00           C
ATOM     16  CA  ALA    16     -16.768  35.467   2.247  1.00 25.00           C
ATOM     17  CA  LEU    17     -13.537  35.902   4.255  1.00 25.00           C
ATOM     18  CA  PHE    18     -15.459  37.773   6.988  1.00 25.00           C
ATOM     19  CA  ALA    19     -18.070  34.973   7.105  1.00 25.00           C
ATOM     20  CA  LYS    20     -15.288  32.359   7.406  1.00 25.00           C
ATOM     21  CA  VAL    21     -13.690  34.352  10.260  1.00 25.00           C
ATOM     22  CA  THR    22     -12.197  32.241  13.073  1.00 25.00           C
ATOM     23  CA  VAL    23      -9.380  31.396  15.577  1.00 25.00           C
ATOM     24  CA  GLU    24      -8.825  34.859  17.115  1.00 25.00           C
ATOM     25  CA  GLN    25      -6.231  35.669  14.415  1.00 25.00           C
ATOM     26  CA  ASP    26      -8.682  34.552  11.692  1.00 25.00           C
ATOM     27  CA  ASP    27     -11.417  36.758  13.215  1.00 25.00           C
ATOM     28  CA  ALA    28      -9.010  39.735  13.286  1.00 25.00           C
ATOM     29  CA  LEU    29      -8.105  39.123   9.616  1.00 25.00           C
ATOM     30  CA  LEU    30     -11.821  38.985   8.696  1.00 25.00           C
ATOM     31  CA  GLY    31     -12.429  42.273  10.564  1.00 25.00           C
ATOM     32  CA  ASN    32      -9.496  43.896   8.711  1.00 25.00           C
ATOM     33  CA  GLN    33     -10.900  42.673   5.365  1.00 25.00           C
ATOM     34  CA  ILE    34     -14.339  44.102   6.256  1.00 25.00           C
ATOM     35  CA  SER    35     -12.735  47.457   7.171  1.00 25.00           C
ATOM     36  CA  ARG    36     -10.847  47.490   3.840  1.00 25.00           C
ATOM     37  CA  PHE    37     -14.101  46.751   1.959  1.00 25.00           C
ATOM     38  CA  ASN    38     -15.852  49.602   3.821  1.00 25.00           C
ATOM     39  CA  ARG    39     -12.984  51.978   2.932  1.00 25.00           C
ATOM     40  CA  LEU    40     -13.222  50.929  -0.743  1.00 25.00           C
ATOM     41  CA  PHE    41     -17.002  51.545  -0.700  1.00 25.00           C
ATOM     42  CA  GLY    42     -16.445  55.008   0.838  1.00 25.00           C
ATOM     43  CA  VAL    43     -13.852  55.817  -1.863  1.00 25.00           C
ATOM     44  CA  MET    44     -16.303  54.701  -4.585  1.00 25.00           C
ATOM     45  CA  ALA    45     -19.038  56.907  -3.062  1.00 25.00           C
ATOM     46  CA  GLU    46     -16.632  59.884  -2.991  1.00 25.00           C
ATOM     47  CA  ILE    47     -15.726  59.271  -6.661  1.00 25.00           C
ATOM     48  CA  ALA    48     -19.442  59.134  -7.580  1.00 25.00           C
ATOM     49  CA  ASP    49     -20.050  62.422  -5.713  1.00 25.00           C
ATOM     50  CA  GLU    50     -17.117  64.045  -7.565  1.00 25.00           C
ATOM     51  CA  LEU    51     -18.521  62.822 -10.912  1.00 25.00           C
ATOM     52  CA  LYS    52     -21.961  64.251 -10.020  1.00 25.00           C
ATOM     53  CA  ALA    53     -24.248  61.624  -8.472  1.00 25.00           C
ATOM     54  CA  ARG    54     -26.402  59.876  -5.867  1.00 25.00           C
ATOM     55  CA  ASP    55     -28.252  59.044  -2.674  1.00 25.00           C
ATOM     56  CA  GLY    56     -28.123  55.838  -0.604  1.00 25.00           C
ATOM     57  CA  ASP    57     -24.973  53.732  -0.535  1.00 25.00           C
ATOM     58  CA  GLN    58     -22.093  53.567   1.969  1.00 25.00           C
ATOM     59  CA  ARG    59     -24.370  54.744   4.814  1.00 25.00           C
ATOM     60  CA  THR    60     -26.062  51.309   4.913  1.00 25.00           C
ATOM     61  CA  ALA    61     -22.638  49.599   5.052  1.00 25.00           C
ATOM     62  CA  LEU    62     -21.577  51.901   7.922  1.00 25.00           C
ATOM     63  CA  LEU    63     -24.811  51.085   9.804  1.00 25.00           C
ATOM     64  CA  SER    64     -24.191  47.340   9.297  1.00 25.00           C
ATOM     65  CA  LEU    65     -20.613  47.730  10.609  1.00 25.00           C
ATOM     66  CA  PHE    66     -21.917  49.613  13.677  1.00 25.00           C
ATOM     67  CA  GLU    67     -24.483  46.843  14.317  1.00 25.00           C
ATOM     68  CA  TYR    68     -25.820  48.217  17.657  1.00 25.00           C
ATOM     69  CA  PRO    69     -22.248  47.594  18.915  1.00 25.00           C
ATOM     70  CA  ASN    70     -19.471  44.988  19.131  1.00 25.00           C
ATOM     71  CA  MET    71     -15.892  43.590  19.078  1.00 25.00           C
ATOM     72  CA  GLN    72     -15.006  46.842  20.898  1.00 25.00           C
ATOM     73  CA  VAL    73     -11.603  46.926  19.143  1.00 25.00           C
ATOM     74  CA  ARG    74     -13.309  46.389  15.755  1.00 25.00           C
ATOM     75  CA  LEU    75     -15.757  49.235  16.511  1.00 25.00           C
ATOM     76  CA  GLN    76     -12.839  51.526  17.459  1.00 25.00           C
ATOM     77  CA  ALA    77     -11.043  50.629  14.198  1.00 25.00           C
ATOM     78  CA  ALA    78     -14.223  51.393  12.206  1.00 25.00           C
ATOM     79  CA  LYS    79     -14.553  54.770  13.982  1.00 25.00           C
ATOM     80  CA  LEU    80     -10.897  55.577  13.181  1.00 25.00           C
ATOM     81  CA  THR    81     -11.474  54.663   9.507  1.00 25.00           C
ATOM     82  CA  LEU    82     -14.569  56.917   9.408  1.00 25.00           C
ATOM     83  CA  ALA    83     -12.554  59.792  10.939  1.00 25.00           C
ATOM     84  CA  VAL    84      -9.798  59.284   8.330  1.00 25.00           C
ATOM     85  CA  ALA    85     -12.408  59.329   5.528  1.00 25.00           C
ATOM     86  CA  PRO    86     -13.896  62.566   6.934  1.00 25.00           C
ATOM     87  CA  VAL    87     -10.408  64.140   7.071  1.00 25.00           C
ATOM     88  CA  LYS    88      -9.768  63.101   3.441  1.00 25.00           C
ATOM     89  CA  ALA    89     -13.118  64.632   2.388  1.00 25.00           C
ATOM     90  CA  ARG    90     -12.232  67.883   4.208  1.00 25.00           C
ATOM     91  CA  GLU    91      -8.829  67.967   2.452  1.00 25.00           C
ATOM     92  CA  GLN    92     -10.534  67.430  -0.934  1.00 25.00           C
ATOM     93  CA  LEU    93     -12.983  70.276  -0.180  1.00 25.00           C
ATOM     94  CA  GLU    94     -10.065  72.568   0.769  1.00 25.00           C
ATOM     95  CA  ALA    95      -8.268  71.669  -2.492  1.00 25.00           C
ATOM     96  CA  ILE    96     -11.448  72.434  -4.484  1.00 25.00           C
ATOM     97  CA  VAL    97     -11.778  75.811  -2.708  1.00 25.00           C
ATOM     98  CA  SER    98      -8.121  76.618  -3.509  1.00 25.00           C
ATOM     99  CA  SER    99      -8.700  75.704  -7.183  1.00 25.00           C
ATOM    100  CA  LYS   100     -12.107  77.269  -7.826  1.00 25.00           C
ATOM    101  CA  TRP   101     -15.534  76.874  -6.205  1.00 25.00           C
ATOM    102  CA  PHE   102     -17.141  75.922  -2.924  1.00 25.00           C
ATOM    103  CA  PRO   103     -20.021  77.130  -0.823  1.00 25.00           C
ATOM    104  CA  GLN   104     -22.835  77.056   1.714  1.00 25.00           C
ATOM    105  CA  ALA   105     -25.299  75.246   3.921  1.00 25.00           C
ATOM    106  CA  GLY   106     -27.089  73.317   6.723  1.00 25.00           C
ATOM    107  CA  ASP   107     -27.280  70.044   8.720  1.00 25.00           C
ATOM    108  CA  ALA   108     -25.163  66.913   9.154  1.00 25.00           C
ATOM    109  CA  GLY   109     -23.471  63.511   8.663  1.00 25.00           C
ATOM    110  CA  MET   110     -23.224  59.756   7.951  1.00 25.00           C
ATOM    111  CA  CYS   111     -22.350  60.481   4.294  1.00 25.00           C
ATOM    112  CA  LEU   112     -19.647  62.958   5.405  1.00 25.00           C
ATOM    113  CA  ASP   113     -18.207  60.344   7.806  1.00 25.00           C
ATOM    114  CA  LEU   114     -18.157  57.749   4.991  1.00 25.00           C
ATOM    115  CA  LEU   115     -16.361  60.236   2.697  1.00 25.00           C
ATOM    116  CA  ASP   116     -13.164  60.114   0.628  1.00 25.00           C
ATOM    117  CA  ASP   117      -9.564  59.982  -0.504  1.00 25.00           C
ATOM    118  CA  GLY   118      -5.983  58.845  -1.362  1.00 25.00           C
ATOM    119  CA  THR   119      -2.496  59.653  -2.629  1.00 25.00           C
ATOM    120  CA  PHE   120       1.131  59.542  -3.785  1.00 25.00           C
ATOM    121  CA  LYS   121       4.643  57.961  -3.616  1.00 25.00           C
ATOM    122  CA  PRO   122       4.864  54.934  -5.921  1.00 25.00           C
ATOM    123  CA  LYS   123       1.774  52.732  -6.329  1.00 25.00           C
TER
END
