
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0285TS168_1
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS168_1.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      S       7           -
LGA    Y       2      P       8           -
LGA    L       3      A       9           -
LGA    P       4      K      10           -
LGA    D       5      -       -           -
LGA    D       6      -       -           -
LGA    S       7      -       -           -
LGA    P       8      -       -           -
LGA    A       9      -       -           -
LGA    K      10      -       -           -
LGA    R      11      -       -           -
LGA    L      12      -       -           -
LGA    L      13      R      11           #
LGA    F      14      L      12           -
LGA    Q      15      L      13           -
LGA    -       -      F      14           -
LGA    M      16      Q      15          2.171
LGA    V      17      M      16          3.023
LGA    G      18      V      17          2.660
LGA    -       -      G      18           -
LGA    N      19      N      19          2.701
LGA    A      20      A      20           #
LGA    -       -      I      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      T      25           -
LGA    -       -      Q      26           -
LGA    -       -      Q      27           -
LGA    I      21      L      28          5.148
LGA    N      22      T      29           #
LGA    R      23      Q      30           #
LGA    N      24      D      31          4.396
LGA    T      25      L      32          3.439
LGA    Q      26      R      33          4.639
LGA    Q      27      -       -           -
LGA    L      28      A      34           #
LGA    T      29      M      35           -
LGA    Q      30      P      36           -
LGA    D      31      N      37           -
LGA    L      32      W      38           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      -       -           -
LGA    L      40      -       -           -
LGA    R      41      -       -           -
LGA    F      42      -       -           -
LGA    V      43      -       -           -
LGA    Y      44      -       -           -
LGA    I      45      -       -           -
LGA    V      46      -       -           -
LGA    D      47      -       -           -
LGA    R      48      S      39          1.202
LGA    N      49      -       -           -
LGA    N      50      -       -           -
LGA    Q      51      -       -           -
LGA    D      52      -       -           -
LGA    L      53      L      40          2.959
LGA    L      54      R      41           #
LGA    K      55      F      42           -
LGA    R      56      V      43           -
LGA    P      57      Y      44           -
LGA    L      58      I      45           -
LGA    P      59      V      46           -
LGA    P      60      D      47           -
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    G      61      D      52          3.870
LGA    I      62      L      53          4.670
LGA    -       -      L      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    M      63      P      57           #
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      P      60           -
LGA    -       -      G      61           -
LGA    V      64      I      62           #
LGA    L      65      M      63           -
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    A      66      A      66          4.245
LGA    -       -      P      67           -
LGA    P      67      R      68          4.337
LGA    R      68      L      69          3.902
LGA    L      69      T      70          2.672
LGA    T      70      A      71          4.633
LGA    A      71      K      72          2.928
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      H      73           #
LGA    Y      75      P      74           -
LGA    D      76      Y      75           -
LGA    K      77      -       -           -
LGA    V      78      D      76           #
LGA    Q      79      -       -           -
LGA    D      80      -       -           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    L      85      -       -           -
LGA    Y      86      -       -           -
LGA    G      87      -       -           -
LGA    R      88      -       -           -
LGA    H      89      K      77          4.440
LGA    -       -      V      78           -
LGA    -       -      Q      79           -
LGA    -       -      D      80           -
LGA    -       -      R      81           -
LGA    -       -      N      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      L      85           -
LGA    I      90      Y      86          2.281
LGA    T      91      G      87          3.004
LGA    L      92      R      88          2.192
LGA    N      93      H      89          1.527
LGA    D      94      I      90          3.421
LGA    G      95      T      91          3.760
LGA    N      96      L      92          4.563
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    S      97      N      96          2.464
LGA    V      98      S      97          3.831
LGA    K      99      V      98          3.749
LGA    V     100      K      99          3.926
LGA    V     101      V     100          1.799
LGA    T     102      V     101          1.696
LGA    I     103      T     102          3.558
LGA    S     104      I     103          2.251
LGA    A     105      S     104          1.692
LGA    G     106      A     105          3.881
LGA    R     107      -       -           -
LGA    D     108      -       -           -
LGA    E     109      -       -           -
LGA    G     110      -       -           -
LGA    P     111      -       -           -
LGA    D     112      -       -           -
LGA    R     113      -       -           -
LGA    D     114      -       -           -
LGA    I     115      -       -           -
LGA    I     116      -       -           -
LGA    W     117      -       -           -
LGA    E     118      -       -           -
LGA    M     119      -       -           -
LGA    F     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    N     123      -       -           -
LGA    L     124      -       -           -
LGA    E     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     36    3.43    11.11     20.706     1.020

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.816002 * X  +  -0.532799 * Y  +   0.224202 * Z  +  17.184507
  Y_new =   0.503578 * X  +   0.464793 * Y  +  -0.728270 * Z  +   5.779901
  Z_new =   0.283814 * X  +   0.707173 * Y  +   0.647578 * Z  +  80.789871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.829360   -2.312233  [ DEG:    47.5188   -132.4812 ]
  Theta =  -0.287769   -2.853824  [ DEG:   -16.4879   -163.5121 ]
  Phi   =   0.552919   -2.588673  [ DEG:    31.6799   -148.3201 ]
 
# 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: T0285TS168_1                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS168_1.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125   99   5.0   36   3.43   11.11  20.706
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS168_1
PFRMAT TS
TARGET T0285
MODEL 1
PARENT N/A
ATOM      1  CA  ALA     1      -4.281  21.347  63.182  1.00 25.00           C
ATOM      2  CA  TYR     2      -1.134  19.140  63.452  1.00 25.00           C
ATOM      3  CA  LEU     3       1.883  21.177  64.430  1.00 25.00           C
ATOM      4  CA  PRO     4       0.660  20.688  67.981  1.00 25.00           C
ATOM      5  CA  ASP     5       3.295  23.099  69.204  1.00 25.00           C
ATOM      6  CA  ASP     6       6.673  22.740  67.417  1.00 25.00           C
ATOM      7  CA  SER     7       9.310  23.559  70.112  1.00 25.00           C
ATOM      8  CA  PRO     8       9.564  20.601  72.553  1.00 25.00           C
ATOM      9  CA  ALA     9      11.231  20.399  75.996  1.00 25.00           C
ATOM     10  CA  LYS    10      10.163  16.737  76.326  1.00 25.00           C
ATOM     11  CA  ARG    11      11.592  15.982  72.853  1.00 25.00           C
ATOM     12  CA  LEU    12      14.888  17.678  73.815  1.00 25.00           C
ATOM     13  CA  LEU    13      15.039  15.615  77.037  1.00 25.00           C
ATOM     14  CA  PHE    14      14.415  12.407  75.042  1.00 25.00           C
ATOM     15  CA  GLN    15      17.205  13.355  72.597  1.00 25.00           C
ATOM     16  CA  MET    16      19.585  14.006  75.526  1.00 25.00           C
ATOM     17  CA  VAL    17      18.692  10.602  77.039  1.00 25.00           C
ATOM     18  CA  GLY    18      19.347   8.905  73.670  1.00 25.00           C
ATOM     19  CA  ASN    19      22.737  10.670  73.412  1.00 25.00           C
ATOM     20  CA  ALA    20      23.629   9.525  76.956  1.00 25.00           C
ATOM     21  CA  ILE    21      22.654   5.930  76.067  1.00 25.00           C
ATOM     22  CA  ASN    22      24.825   6.093  72.916  1.00 25.00           C
ATOM     23  CA  ARG    23      27.770   7.404  74.984  1.00 25.00           C
ATOM     24  CA  ASN    24      27.301   4.556  77.502  1.00 25.00           C
ATOM     25  CA  THR    25      27.244   2.006  74.645  1.00 25.00           C
ATOM     26  CA  GLN    26      30.457   3.511  73.204  1.00 25.00           C
ATOM     27  CA  GLN    27      32.123   3.310  76.646  1.00 25.00           C
ATOM     28  CA  LEU    28      31.055  -0.354  76.976  1.00 25.00           C
ATOM     29  CA  THR    29      32.485  -1.109  73.504  1.00 25.00           C
ATOM     30  CA  GLN    30      35.781   0.588  74.465  1.00 25.00           C
ATOM     31  CA  ASP    31      35.932  -1.475  77.688  1.00 25.00           C
ATOM     32  CA  LEU    32      35.307  -4.684  75.693  1.00 25.00           C
ATOM     33  CA  ARG    33      38.098  -3.735  73.247  1.00 25.00           C
ATOM     34  CA  ALA    34      35.645  -3.999  70.314  1.00 25.00           C
ATOM     35  CA  MET    35      32.343  -5.494  69.228  1.00 25.00           C
ATOM     36  CA  PRO    36      30.489  -8.000  71.418  1.00 25.00           C
ATOM     37  CA  ASN    37      27.503  -5.605  71.409  1.00 25.00           C
ATOM     38  CA  TRP    38      23.861  -6.610  71.815  1.00 25.00           C
ATOM     39  CA  SER    39      20.538  -5.407  70.312  1.00 25.00           C
ATOM     40  CA  LEU    40      21.045  -2.305  72.479  1.00 25.00           C
ATOM     41  CA  ARG    41      22.581  -1.022  75.710  1.00 25.00           C
ATOM     42  CA  PHE    42      22.116   1.738  78.215  1.00 25.00           C
ATOM     43  CA  VAL    43      22.414   4.559  80.693  1.00 25.00           C
ATOM     44  CA  TYR    44      22.985   8.163  81.774  1.00 25.00           C
ATOM     45  CA  ILE    45      23.066  11.853  82.700  1.00 25.00           C
ATOM     46  CA  VAL    46      25.908  13.016  80.536  1.00 25.00           C
ATOM     47  CA  ASP    47      28.313  14.463  83.165  1.00 25.00           C
ATOM     48  CA  ARG    48      29.013  10.735  83.689  1.00 25.00           C
ATOM     49  CA  ASN    49      31.939   9.899  81.336  1.00 25.00           C
ATOM     50  CA  ASN    50      35.199   8.801  82.894  1.00 25.00           C
ATOM     51  CA  GLN    51      35.949   6.336  85.766  1.00 25.00           C
ATOM     52  CA  ASP    52      33.330   6.505  88.556  1.00 25.00           C
ATOM     53  CA  LEU    53      30.519   6.266  85.965  1.00 25.00           C
ATOM     54  CA  LEU    54      30.552   2.586  84.882  1.00 25.00           C
ATOM     55  CA  LYS    55      32.668   1.940  87.907  1.00 25.00           C
ATOM     56  CA  ARG    56      32.154  -1.517  89.515  1.00 25.00           C
ATOM     57  CA  PRO    57      31.012  -4.121  86.990  1.00 25.00           C
ATOM     58  CA  LEU    58      29.519  -3.443  83.557  1.00 25.00           C
ATOM     59  CA  PRO    59      27.672  -6.694  83.793  1.00 25.00           C
ATOM     60  CA  PRO    60      25.581  -6.402  80.651  1.00 25.00           C
ATOM     61  CA  GLY    61      24.674  -2.693  80.338  1.00 25.00           C
ATOM     62  CA  ILE    62      24.190   0.576  82.256  1.00 25.00           C
ATOM     63  CA  MET    63      20.375   0.057  82.549  1.00 25.00           C
ATOM     64  CA  VAL    64      17.553   2.479  81.709  1.00 25.00           C
ATOM     65  CA  LEU    65      14.720   1.850  79.247  1.00 25.00           C
ATOM     66  CA  ALA    66      11.235   2.639  80.488  1.00 25.00           C
ATOM     67  CA  PRO    67       7.616   3.854  80.356  1.00 25.00           C
ATOM     68  CA  ARG    68       5.335   6.323  78.608  1.00 25.00           C
ATOM     69  CA  LEU    69       4.720   3.832  75.776  1.00 25.00           C
ATOM     70  CA  THR    70       1.136   2.577  76.418  1.00 25.00           C
ATOM     71  CA  ALA    71      -0.655   5.898  77.125  1.00 25.00           C
ATOM     72  CA  LYS    72      -3.090   4.922  79.894  1.00 25.00           C
ATOM     73  CA  HIS    73      -1.095   2.432  82.034  1.00 25.00           C
ATOM     74  CA  PRO    74       0.911   5.263  83.594  1.00 25.00           C
ATOM     75  CA  TYR    75       0.908   2.945  86.619  1.00 25.00           C
ATOM     76  CA  ASP    76       1.566   3.345  90.315  1.00 25.00           C
ATOM     77  CA  LYS    77       4.642   5.512  91.022  1.00 25.00           C
ATOM     78  CA  VAL    78       4.443   6.989  87.495  1.00 25.00           C
ATOM     79  CA  GLN    79       0.726   7.757  87.998  1.00 25.00           C
ATOM     80  CA  ASP    80       1.505   9.462  91.338  1.00 25.00           C
ATOM     81  CA  ARG    81       4.242  11.551  89.661  1.00 25.00           C
ATOM     82  CA  ASN    82       1.802  12.568  86.890  1.00 25.00           C
ATOM     83  CA  ARG    83      -0.798  13.575  89.516  1.00 25.00           C
ATOM     84  CA  LYS    84       1.836  15.656  91.361  1.00 25.00           C
ATOM     85  CA  LEU    85       4.680  15.717  93.823  1.00 25.00           C
ATOM     86  CA  TYR    86       7.879  17.683  94.336  1.00 25.00           C
ATOM     87  CA  GLY    87       7.721  18.101  90.592  1.00 25.00           C
ATOM     88  CA  ARG    88       9.607  15.601  88.363  1.00 25.00           C
ATOM     89  CA  HIS    89      12.798  15.716  86.234  1.00 25.00           C
ATOM     90  CA  ILE    90      14.159  13.150  83.779  1.00 25.00           C
ATOM     91  CA  THR    91      12.733  11.161  80.830  1.00 25.00           C
ATOM     92  CA  LEU    92      12.705   7.351  80.826  1.00 25.00           C
ATOM     93  CA  ASN    93      12.256   6.678  77.138  1.00 25.00           C
ATOM     94  CA  ASP    94      10.002   4.204  75.228  1.00 25.00           C
ATOM     95  CA  GLY    95      10.321   1.368  72.722  1.00 25.00           C
ATOM     96  CA  ASN    96      12.855   0.105  70.177  1.00 25.00           C
ATOM     97  CA  SER    97      16.577  -0.871  69.945  1.00 25.00           C
ATOM     98  CA  VAL    98      16.721   0.581  73.465  1.00 25.00           C
ATOM     99  CA  LYS    99      16.305   4.306  74.001  1.00 25.00           C
ATOM    100  CA  VAL   100      17.227   5.820  77.352  1.00 25.00           C
ATOM    101  CA  VAL   101      17.673   7.336  80.798  1.00 25.00           C
ATOM    102  CA  THR   102      17.633   8.067  84.508  1.00 25.00           C
ATOM    103  CA  ILE   103      20.838   6.816  86.153  1.00 25.00           C
ATOM    104  CA  SER   104      21.829  10.067  87.798  1.00 25.00           C
ATOM    105  CA  ALA   105      19.967  12.025  90.544  1.00 25.00           C
ATOM    106  CA  GLY   106      21.184  11.137  94.022  1.00 25.00           C
ATOM    107  CA  ARG   107      21.877   9.378  97.367  1.00 25.00           C
ATOM    108  CA  ASP   108      18.968   6.923  97.907  1.00 25.00           C
ATOM    109  CA  GLU   109      18.268   5.712 101.410  1.00 25.00           C
ATOM    110  CA  GLY   110      16.247   2.906  99.758  1.00 25.00           C
ATOM    111  CA  PRO   111      16.765   0.263  97.118  1.00 25.00           C
ATOM    112  CA  ASP   112      18.140   2.602  94.477  1.00 25.00           C
ATOM    113  CA  ARG   113      18.331   3.720  90.829  1.00 25.00           C
ATOM    114  CA  ASP   114      14.635   3.757  89.823  1.00 25.00           C
ATOM    115  CA  ILE   115      15.618   3.841  86.122  1.00 25.00           C
ATOM    116  CA  ILE   116      17.992   0.884  86.660  1.00 25.00           C
ATOM    117  CA  TRP   117      15.203  -1.065  88.420  1.00 25.00           C
ATOM    118  CA  GLU   118      12.818  -0.322  85.517  1.00 25.00           C
ATOM    119  CA  MET   119      15.454  -1.523  83.012  1.00 25.00           C
ATOM    120  CA  PHE   120      15.943  -4.740  85.031  1.00 25.00           C
ATOM    121  CA  LEU   121      12.157  -5.313  85.082  1.00 25.00           C
ATOM    122  CA  GLU   122      12.001  -4.788  81.291  1.00 25.00           C
ATOM    123  CA  ASN   123      14.861  -7.289  80.803  1.00 25.00           C
ATOM    124  CA  LEU   124      13.369  -8.713  77.569  1.00 25.00           C
ATOM    125  CA  GLU   125      13.776 -12.398  76.689  1.00 25.00           C
TER
END
