
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0356AL044_1-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_1-D2.T0356_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    D     290      D     141           #
LGA    H     291      L     142          1.429
LGA    T     292      N     143          5.502
LGA    G     293      R     144          5.524
LGA    Y     294      I     145          0.758
LGA    Y     295      P     146          2.954
LGA    N     296      I     147          1.402
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    E     297      L     158          3.621
LGA    V     298      I     159          4.067
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    -       -      G     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      V     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      G     168           -
LGA    -       -      P     169           -
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    D     299      I     190          3.610
LGA    F     301      M     191          4.680
LGA    -       -      R     192           -
LGA    P     302      W     193          0.984
LGA    -       -      L     194           -
LGA    V     303      S     195          4.443
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    F     304      A     200          2.203
LGA    T     305      L     201          2.499
LGA    V     306      D     202          2.364
LGA    T     307      Y     203          2.133
LGA    H     308      Q     204          2.419
LGA    I     309      E     205          1.315
LGA    T     310      W     206          1.272
LGA    Q     311      C     207          1.662
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    R     312      E     213          2.706
LGA    E     313      R     214          3.090
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    -       -      L     239           -
LGA    -       -      S     240           -
LGA    -       -      E     241           -
LGA    -       -      Y     242           -
LGA    -       -      A     243           -
LGA    -       -      F     244           -
LGA    -       -      A     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      L     248           -
LGA    -       -      R     249           -
LGA    -       -      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    -       -      E     274           -
LGA    -       -      G     275           -
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  192    5.0     22    3.09     0.00      7.691     0.691

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.648683 * X  +  -0.759349 * Y  +  -0.050997 * Z  +  90.259819
  Y_new =   0.188431 * X  +   0.225169 * Y  +  -0.955925 * Z  + 102.696869
  Z_new =   0.737363 * X  +   0.610483 * Y  +   0.289148 * Z  +  40.043503 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.128459   -2.013133  [ DEG:    64.6560   -115.3440 ]
  Theta =  -0.829159   -2.312434  [ DEG:   -47.5073   -132.4927 ]
  Phi   =   0.282703   -2.858890  [ DEG:    16.1977   -163.8023 ]
 
# 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: T0356AL044_1-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_1-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  192   5.0   22   3.09    0.00   7.691
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_1-D2
REMARK Aligment from pdb entry: 1jwq_A
ATOM      1  N   ASP   290      77.676  57.393  92.941  1.00  0.00              
ATOM      2  CA  ASP   290      76.297  57.750  93.256  1.00  0.00              
ATOM      3  C   ASP   290      76.087  58.450  94.602  1.00  0.00              
ATOM      4  O   ASP   290      75.485  59.521  94.660  1.00  0.00              
ATOM      5  N   HIS   291      76.572  57.855  95.703  1.00  0.00              
ATOM      6  CA  HIS   291      76.391  58.491  97.014  1.00  0.00              
ATOM      7  C   HIS   291      77.039  59.869  97.092  1.00  0.00              
ATOM      8  O   HIS   291      76.574  60.740  97.825  1.00  0.00              
ATOM      9  N   THR   292      78.112  60.064  96.330  1.00  0.00              
ATOM     10  CA  THR   292      78.818  61.339  96.328  1.00  0.00              
ATOM     11  C   THR   292      77.989  62.488  95.756  1.00  0.00              
ATOM     12  O   THR   292      78.129  63.625  96.196  1.00  0.00              
ATOM     13  N   GLY   293      77.135  62.211  94.774  1.00  0.00              
ATOM     14  CA  GLY   293      76.318  63.279  94.206  1.00  0.00              
ATOM     15  C   GLY   293      75.211  63.662  95.182  1.00  0.00              
ATOM     16  O   GLY   293      74.778  64.815  95.227  1.00  0.00              
ATOM     17  N   TYR   294      74.760  62.685  95.964  1.00  0.00              
ATOM     18  CA  TYR   294      73.700  62.938  96.922  1.00  0.00              
ATOM     19  C   TYR   294      72.377  63.188  96.223  1.00  0.00              
ATOM     20  O   TYR   294      71.395  63.573  96.856  1.00  0.00              
ATOM     21  N   TYR   295      72.351  62.974  94.912  1.00  0.00              
ATOM     22  CA  TYR   295      71.138  63.174  94.130  1.00  0.00              
ATOM     23  C   TYR   295      70.381  61.854  94.051  1.00  0.00              
ATOM     24  O   TYR   295      70.868  60.823  94.519  1.00  0.00              
ATOM     25  N   ASN   296      69.191  61.879  93.464  1.00  0.00              
ATOM     26  CA  ASN   296      68.408  60.659  93.363  1.00  0.00              
ATOM     27  C   ASN   296      69.181  59.599  92.592  1.00  0.00              
ATOM     28  O   ASN   296      69.648  59.838  91.478  1.00  0.00              
ATOM     29  N   GLU   297      69.315  58.429  93.206  1.00  0.00              
ATOM     30  CA  GLU   297      70.034  57.318  92.603  1.00  0.00              
ATOM     31  C   GLU   297      69.197  56.645  91.528  1.00  0.00              
ATOM     32  O   GLU   297      68.289  55.868  91.830  1.00  0.00              
ATOM     33  N   VAL   298      69.507  56.937  90.269  1.00  0.00              
ATOM     34  CA  VAL   298      68.771  56.347  89.162  1.00  0.00              
ATOM     35  C   VAL   298      69.393  55.024  88.712  1.00  0.00              
ATOM     36  O   VAL   298      68.976  54.435  87.715  1.00  0.00              
ATOM     37  N   ASP   299      72.500  51.574  84.304  1.00  0.00              
ATOM     38  CA  ASP   299      71.671  51.216  83.161  1.00  0.00              
ATOM     39  C   ASP   299      72.469  50.916  81.904  1.00  0.00              
ATOM     40  O   ASP   299      73.618  51.327  81.766  1.00  0.00              
ATOM     41  N   PHE   301      71.840  50.193  80.984  1.00  0.00              
ATOM     42  CA  PHE   301      72.474  49.883  79.720  1.00  0.00              
ATOM     43  C   PHE   301      72.296  51.115  78.849  1.00  0.00              
ATOM     44  O   PHE   301      71.227  51.726  78.835  1.00  0.00              
ATOM     45  N   PRO   302      73.354  51.489  78.142  1.00  0.00              
ATOM     46  CA  PRO   302      73.286  52.638  77.264  1.00  0.00              
ATOM     47  C   PRO   302      74.106  52.366  76.020  1.00  0.00              
ATOM     48  O   PRO   302      75.301  52.077  76.111  1.00  0.00              
ATOM     49  N   VAL   303      73.471  52.434  74.857  1.00  0.00              
ATOM     50  CA  VAL   303      74.180  52.196  73.612  1.00  0.00              
ATOM     51  C   VAL   303      74.857  53.477  73.148  1.00  0.00              
ATOM     52  O   VAL   303      74.431  54.108  72.185  1.00  0.00              
ATOM     53  N   PHE   304      75.924  53.848  73.847  1.00  0.00              
ATOM     54  CA  PHE   304      76.674  55.060  73.537  1.00  0.00              
ATOM     55  C   PHE   304      78.023  54.684  72.939  1.00  0.00              
ATOM     56  O   PHE   304      78.741  53.843  73.477  1.00  0.00              
ATOM     57  N   THR   305      78.359  55.327  71.827  1.00  0.00              
ATOM     58  CA  THR   305      79.595  55.065  71.103  1.00  0.00              
ATOM     59  C   THR   305      80.841  54.875  71.965  1.00  0.00              
ATOM     60  O   THR   305      81.515  53.854  71.870  1.00  0.00              
ATOM     61  N   VAL   306      81.150  55.852  72.809  1.00  0.00              
ATOM     62  CA  VAL   306      82.359  55.755  73.621  1.00  0.00              
ATOM     63  C   VAL   306      82.452  54.560  74.569  1.00  0.00              
ATOM     64  O   VAL   306      83.558  54.129  74.895  1.00  0.00              
ATOM     65  N   THR   307      81.322  54.014  75.012  1.00  0.00              
ATOM     66  CA  THR   307      81.387  52.856  75.902  1.00  0.00              
ATOM     67  C   THR   307      81.119  51.550  75.144  1.00  0.00              
ATOM     68  O   THR   307      81.313  50.455  75.672  1.00  0.00              
ATOM     69  N   HIS   308      80.698  51.683  73.890  1.00  0.00              
ATOM     70  CA  HIS   308      80.416  50.530  73.040  1.00  0.00              
ATOM     71  C   HIS   308      81.640  50.102  72.237  1.00  0.00              
ATOM     72  O   HIS   308      81.966  48.917  72.171  1.00  0.00              
ATOM     73  N   ILE   309      82.299  51.079  71.619  1.00  0.00              
ATOM     74  CA  ILE   309      83.460  50.824  70.773  1.00  0.00              
ATOM     75  C   ILE   309      84.766  50.613  71.528  1.00  0.00              
ATOM     76  O   ILE   309      85.747  50.145  70.952  1.00  0.00              
ATOM     77  N   THR   310      84.777  50.959  72.810  1.00  0.00              
ATOM     78  CA  THR   310      85.963  50.757  73.631  1.00  0.00              
ATOM     79  C   THR   310      86.046  49.264  73.930  1.00  0.00              
ATOM     80  O   THR   310      85.030  48.564  73.890  1.00  0.00              
ATOM     81  N   GLN   311      87.249  48.775  74.220  1.00  0.00              
ATOM     82  CA  GLN   311      87.439  47.356  74.504  1.00  0.00              
ATOM     83  C   GLN   311      87.801  47.069  75.955  1.00  0.00              
ATOM     84  O   GLN   311      87.899  45.908  76.350  1.00  0.00              
ATOM     85  N   ARG   312      88.029  48.120  76.739  1.00  0.00              
ATOM     86  CA  ARG   312      88.347  47.946  78.150  1.00  0.00              
ATOM     87  C   ARG   312      87.102  48.352  78.937  1.00  0.00              
ATOM     88  O   ARG   312      86.164  48.913  78.366  1.00  0.00              
ATOM     89  N   GLU   313      87.065  48.065  80.250  1.00  0.00              
ATOM     90  CA  GLU   313      85.878  48.451  81.021  1.00  0.00              
ATOM     91  C   GLU   313      85.609  49.932  80.803  1.00  0.00              
ATOM     92  O   GLU   313      86.489  50.764  81.011  1.00  0.00              
END
