
#######################################################
#                                                     #
#                        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 T0285TS599_2
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS599_2.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      R      11           -
LGA    D       6      L      12           -
LGA    S       7      L      13           -
LGA    P       8      F      14           -
LGA    A       9      Q      15           -
LGA    K      10      M      16           -
LGA    R      11      V      17           -
LGA    L      12      G      18           -
LGA    L      13      N      19           -
LGA    F      14      A      20           -
LGA    Q      15      I      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
LGA    M      16      N      24          2.321
LGA    V      17      T      25          1.488
LGA    G      18      Q      26          1.356
LGA    N      19      Q      27          0.339
LGA    A      20      L      28          0.471
LGA    I      21      T      29          1.180
LGA    N      22      Q      30          1.262
LGA    R      23      D      31          1.396
LGA    N      24      L      32          2.072
LGA    T      25      R      33          2.570
LGA    Q      26      A      34          2.445
LGA    Q      27      M      35          3.304
LGA    L      28      P      36          4.560
LGA    T      29      N      37          3.946
LGA    Q      30      W      38           #
LGA    D      31      S      39          3.513
LGA    L      32      L      40           #
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      R      41          2.549
LGA    L      40      F      42          1.960
LGA    R      41      V      43          4.326
LGA    F      42      Y      44          1.475
LGA    V      43      I      45          4.760
LGA    Y      44      V      46          0.995
LGA    I      45      D      47          4.335
LGA    V      46      R      48          1.764
LGA    D      47      -       -           -
LGA    R      48      -       -           -
LGA    N      49      -       -           -
LGA    N      50      -       -           -
LGA    Q      51      -       -           -
LGA    D      52      -       -           -
LGA    L      53      -       -           -
LGA    L      54      -       -           -
LGA    K      55      N      49          4.202
LGA    R      56      N      50           -
LGA    P      57      Q      51           #
LGA    L      58      D      52          5.664
LGA    -       -      L      53           -
LGA    P      59      L      54          3.688
LGA    P      60      K      55          3.174
LGA    G      61      R      56          0.815
LGA    I      62      P      57          4.276
LGA    M      63      L      58          3.400
LGA    V      64      P      59           -
LGA    -       -      P      60           -
LGA    -       -      G      61           -
LGA    -       -      I      62           -
LGA    L      65      M      63          5.302
LGA    A      66      -       -           -
LGA    P      67      -       -           -
LGA    R      68      -       -           -
LGA    L      69      -       -           -
LGA    T      70      -       -           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      -       -           -
LGA    K      77      -       -           -
LGA    V      78      -       -           -
LGA    Q      79      -       -           -
LGA    D      80      V      64          3.925
LGA    R      81      L      65          1.920
LGA    N      82      A      66          4.357
LGA    -       -      P      67           -
LGA    R      83      R      68           #
LGA    K      84      L      69           -
LGA    L      85      T      70           -
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    -       -      H      73           -
LGA    -       -      P      74           -
LGA    -       -      Y      75           -
LGA    Y      86      D      76          1.762
LGA    G      87      K      77          2.608
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    R      88      Y      86          1.378
LGA    H      89      G      87           #
LGA    I      90      R      88          2.554
LGA    T      91      H      89           #
LGA    L      92      I      90          2.382
LGA    N      93      T      91          3.956
LGA    D      94      L      92          1.752
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    G      95      G      95          1.583
LGA    N      96      N      96          3.247
LGA    S      97      S      97          1.366
LGA    V      98      V      98          1.425
LGA    K      99      K      99          2.586
LGA    V     100      V     100          2.131
LGA    V     101      V     101          2.254
LGA    T     102      T     102          1.840
LGA    I     103      I     103          2.638
LGA    S     104      S     104          2.981
LGA    A     105      A     105          1.987
LGA    G     106      -       -           -
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     52    2.90    21.15     32.184     1.733

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.240870 * X  +   0.028884 * Y  +  -0.970128 * Z  +  18.942450
  Y_new =  -0.965088 * X  +  -0.098834 * Y  +  -0.242561 * Z  +   0.510890
  Z_new =  -0.102888 * X  +   0.994685 * Y  +   0.004069 * Z  +  82.115234 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.566705   -1.574887  [ DEG:    89.7656    -90.2344 ]
  Theta =   0.103070    3.038522  [ DEG:     5.9055    174.0945 ]
  Phi   =  -1.326210    1.815383  [ DEG:   -75.9862    104.0138 ]
 
# 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: T0285TS599_2                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS599_2.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   52   2.90   21.15  32.184
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS599_2
PFRMAT TS                                                                       
TARGET T0285                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  ALA     1      24.551  -9.125  73.563  1.00  0.00              
ATOM      2  CA  TYR     2      22.183 -11.747  71.632  1.00  0.00              
ATOM      3  CA  LEU     3      21.836 -14.767  69.542  1.00  0.00              
ATOM      4  CA  PRO     4      21.650 -13.074  65.685  1.00  0.00              
ATOM      5  CA  ASP     5      22.513 -16.203  63.649  1.00  0.00              
ATOM      6  CA  ASP     6      21.695 -15.047  60.172  1.00  0.00              
ATOM      7  CA  SER     7      18.156 -13.723  60.844  1.00  0.00              
ATOM      8  CA  PRO     8      17.802 -10.019  60.064  1.00  0.00              
ATOM      9  CA  ALA     9      16.091  -9.108  63.342  1.00  0.00              
ATOM     10  CA  LYS    10      18.493 -10.347  66.009  1.00  0.00              
ATOM     11  CA  ARG    11      21.497  -8.958  64.001  1.00  0.00              
ATOM     12  CA  LEU    12      19.957  -5.496  63.471  1.00  0.00              
ATOM     13  CA  LEU    13      18.847  -5.267  67.130  1.00  0.00              
ATOM     14  CA  PHE    14      22.280  -6.238  68.541  1.00  0.00              
ATOM     15  CA  GLN    15      23.987  -3.671  66.311  1.00  0.00              
ATOM     16  CA  MET    16      21.595  -0.949  67.538  1.00  0.00              
ATOM     17  CA  VAL    17      22.263  -1.951  71.190  1.00  0.00              
ATOM     18  CA  GLY    18      26.011  -2.032  70.718  1.00  0.00              
ATOM     19  CA  ASN    19      26.048   1.409  69.076  1.00  0.00              
ATOM     20  CA  ALA    20      23.913   2.941  71.831  1.00  0.00              
ATOM     21  CA  ILE    21      26.088   1.511  74.635  1.00  0.00              
ATOM     22  CA  ASN    22      29.553   2.524  73.387  1.00  0.00              
ATOM     23  CA  ARG    23      28.475   6.170  72.774  1.00  0.00              
ATOM     24  CA  ASN    24      26.762   6.319  76.130  1.00  0.00              
ATOM     25  CA  THR    25      29.796   4.931  78.042  1.00  0.00              
ATOM     26  CA  GLN    26      32.073   7.675  76.760  1.00  0.00              
ATOM     27  CA  GLN    27      29.470  10.260  77.799  1.00  0.00              
ATOM     28  CA  LEU    28      29.165   8.727  81.232  1.00  0.00              
ATOM     29  CA  THR    29      32.871   8.803  81.808  1.00  0.00              
ATOM     30  CA  GLN    30      32.940  12.498  80.763  1.00  0.00              
ATOM     31  CA  ASP    31      30.040  13.355  83.014  1.00  0.00              
ATOM     32  CA  LEU    32      31.606  11.692  86.092  1.00  0.00              
ATOM     33  CA  ARG    33      34.825  13.474  85.471  1.00  0.00              
ATOM     34  CA  ALA    34      33.061  16.879  85.322  1.00  0.00              
ATOM     35  CA  MET    35      30.825  16.551  88.309  1.00  0.00              
ATOM     36  CA  PRO    36      33.177  15.243  90.937  1.00  0.00              
ATOM     37  CA  ASN    37      31.112  12.566  92.585  1.00  0.00              
ATOM     38  CA  TRP    38      28.777  11.796  89.625  1.00  0.00              
ATOM     39  CA  SER    39      26.689   8.705  89.923  1.00  0.00              
ATOM     40  CA  LEU    40      24.983   7.353  86.916  1.00  0.00              
ATOM     41  CA  ARG    41      22.229   4.963  87.260  1.00  0.00              
ATOM     42  CA  PHE    42      21.128   3.048  84.212  1.00  0.00              
ATOM     43  CA  VAL    43      17.661   1.615  83.968  1.00  0.00              
ATOM     44  CA  TYR    44      16.680  -0.538  81.073  1.00  0.00              
ATOM     45  CA  ILE    45      13.104  -0.757  80.088  1.00  0.00              
ATOM     46  CA  VAL    46      11.925  -3.872  78.285  1.00  0.00              
ATOM     47  CA  ASP    47       8.391  -4.436  77.138  1.00  0.00              
ATOM     48  CA  ARG    48       6.493  -7.617  77.888  1.00  0.00              
ATOM     49  CA  ASN    49       7.267  -9.501  74.627  1.00  0.00              
ATOM     50  CA  ASN    50      10.959  -8.852  74.834  1.00  0.00              
ATOM     51  CA  GLN    51      11.348  -9.991  78.466  1.00  0.00              
ATOM     52  CA  ASP    52      13.852 -12.646  77.465  1.00  0.00              
ATOM     53  CA  LEU    53      16.114 -10.381  75.487  1.00  0.00              
ATOM     54  CA  LEU    54      16.249  -7.855  78.347  1.00  0.00              
ATOM     55  CA  LYS    55      17.061 -10.628  80.841  1.00  0.00              
ATOM     56  CA  ARG    56      19.645 -12.451  78.757  1.00  0.00              
ATOM     57  CA  PRO    57      22.004  -9.615  77.686  1.00  0.00              
ATOM     58  CA  LEU    58      21.910  -7.439  80.729  1.00  0.00              
ATOM     59  CA  PRO    59      25.184  -5.701  81.587  1.00  0.00              
ATOM     60  CA  PRO    60      26.271  -6.423  85.119  1.00  0.00              
ATOM     61  CA  GLY    61      25.362  -2.959  86.528  1.00  0.00              
ATOM     62  CA  ILE    62      22.107  -2.510  84.674  1.00  0.00              
ATOM     63  CA  MET    63      18.630  -2.617  86.280  1.00  0.00              
ATOM     64  CA  VAL    64      15.800  -3.933  84.221  1.00  0.00              
ATOM     65  CA  LEU    65      12.274  -2.720  84.686  1.00  0.00              
ATOM     66  CA  ALA    66       9.496  -4.342  82.738  1.00  0.00              
ATOM     67  CA  PRO    67       6.814  -2.007  81.397  1.00  0.00              
ATOM     68  CA  ARG    68       3.957  -4.149  82.635  1.00  0.00              
ATOM     69  CA  LEU    69       5.264  -5.216  86.082  1.00  0.00              
ATOM     70  CA  THR    70       2.590  -4.951  88.778  1.00  0.00              
ATOM     71  CA  ALA    71       2.173  -8.165  90.757  1.00  0.00              
ATOM     72  CA  LYS    72       5.810  -9.130  90.267  1.00  0.00              
ATOM     73  CA  HIS    73       7.383  -5.876  91.400  1.00  0.00              
ATOM     74  CA  PRO    74       5.157  -4.484  94.084  1.00  0.00              
ATOM     75  CA  TYR    75       2.490  -2.436  92.348  1.00  0.00              
ATOM     76  CA  ASP    76       3.471   0.778  94.175  1.00  0.00              
ATOM     77  CA  LYS    77       7.110   0.108  93.217  1.00  0.00              
ATOM     78  CA  VAL    78       6.356  -0.102  89.471  1.00  0.00              
ATOM     79  CA  GLN    79       4.458   3.210  89.611  1.00  0.00              
ATOM     80  CA  ASP    80       7.289   4.946  91.509  1.00  0.00              
ATOM     81  CA  ARG    81       9.949   3.740  89.109  1.00  0.00              
ATOM     82  CA  ASN    82       8.008   5.141  86.121  1.00  0.00              
ATOM     83  CA  ARG    83       7.641   8.487  87.935  1.00  0.00              
ATOM     84  CA  LYS    84      11.397   8.775  88.562  1.00  0.00              
ATOM     85  CA  LEU    85      12.222   7.674  84.997  1.00  0.00              
ATOM     86  CA  TYR    86       9.793  10.150  83.455  1.00  0.00              
ATOM     87  CA  GLY    87      11.523  13.179  85.030  1.00  0.00              
ATOM     88  CA  ARG    88      15.135  11.999  84.434  1.00  0.00              
ATOM     89  CA  HIS    89      16.605  11.211  81.071  1.00  0.00              
ATOM     90  CA  ILE    90      14.892   8.798  78.755  1.00  0.00              
ATOM     91  CA  THR    91      16.668   7.467  75.762  1.00  0.00              
ATOM     92  CA  LEU    92      14.763   5.905  72.998  1.00  0.00              
ATOM     93  CA  ASN    93      16.563   3.639  70.614  1.00  0.00              
ATOM     94  CA  ASP    94      15.379   3.512  67.039  1.00  0.00              
ATOM     95  CA  GLY    95      13.869   0.008  66.999  1.00  0.00              
ATOM     96  CA  ASN    96      12.028   0.205  70.322  1.00  0.00              
ATOM     97  CA  SER    97      14.243  -0.344  73.329  1.00  0.00              
ATOM     98  CA  VAL    98      13.910   2.204  76.141  1.00  0.00              
ATOM     99  CA  LYS    99      16.911   3.251  78.124  1.00  0.00              
ATOM    100  CA  VAL   100      16.503   5.153  81.283  1.00  0.00              
ATOM    101  CA  VAL   101      19.298   7.152  82.604  1.00  0.00              
ATOM    102  CA  THR   102      19.321   8.360  86.144  1.00  0.00              
ATOM    103  CA  ILE   103      21.900  10.871  87.214  1.00  0.00              
ATOM    104  CA  SER   104      22.743  11.282  90.841  1.00  0.00              
ATOM    105  CA  ALA   105      25.174  13.906  91.966  1.00  0.00              
ATOM    106  CA  GLY   106      26.703  13.572  95.192  1.00  0.00              
ATOM    107  CA  ARG   107      28.234  11.440  97.754  1.00  0.00              
ATOM    108  CA  ASP   108      25.467   9.003  98.478  1.00  0.00              
ATOM    109  CA  GLU   109      27.237   5.832  99.475  1.00  0.00              
ATOM    110  CA  GLY   110      24.709   4.526 102.028  1.00  0.00              
ATOM    111  CA  PRO   111      22.825   1.372 101.340  1.00  0.00              
ATOM    112  CA  ASP   112      19.274   2.617 100.678  1.00  0.00              
ATOM    113  CA  ARG   113      20.109   5.492  98.397  1.00  0.00              
ATOM    114  CA  ASP   114      18.176   4.679  95.278  1.00  0.00              
ATOM    115  CA  ILE   115      21.085   4.592  92.698  1.00  0.00              
ATOM    116  CA  ILE   116      23.091   2.251  94.989  1.00  0.00              
ATOM    117  CA  TRP   117      20.179  -0.172  95.468  1.00  0.00              
ATOM    118  CA  GLU   118      19.539  -0.322  91.718  1.00  0.00              
ATOM    119  CA  MET   119      23.204  -1.028  90.896  1.00  0.00              
ATOM    120  CA  PHE   120      23.489  -3.883  93.406  1.00  0.00              
ATOM    121  CA  LEU   121      20.290  -5.585  92.177  1.00  0.00              
ATOM    122  CA  GLU   122      21.303  -5.458  88.528  1.00  0.00              
ATOM    123  CA  ASN   123      24.631  -6.869  89.113  1.00  0.00              
ATOM    124  CA  LEU   124      22.950  -9.923  91.476  1.00  0.00              
ATOM    125  CA  GLU   125      25.755  -8.026  89.903  1.00  0.00              
TER                                                                             
END
