
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0356AL044_2-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_2-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          3.354
LGA    T     292      N     143          4.313
LGA    G     293      R     144          3.143
LGA    Y     294      I     145          2.606
LGA    Y     295      P     146          1.851
LGA    N     296      I     147          1.358
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    E     297      P     157          3.123
LGA    V     298      L     158          0.746
LGA    -       -      I     159           -
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          4.163
LGA    S     300      M     191          5.274
LGA    -       -      R     192           -
LGA    F     301      W     193          2.642
LGA    P     302      L     194          5.388
LGA    V     303      S     195          2.779
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    F     304      A     200          2.056
LGA    T     305      L     201          2.151
LGA    V     306      D     202          2.165
LGA    T     307      Y     203          1.949
LGA    H     308      Q     204          2.186
LGA    I     309      E     205          1.156
LGA    T     310      W     206          1.456
LGA    Q     311      C     207          0.762
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    R     312      P     211          3.824
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
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    E     313      Q     279          0.984
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)   24  192    5.0     23    2.89     0.00      7.905     0.768

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.371763 * X  +   0.850406 * Y  +   0.372293 * Z  +  96.014572
  Y_new =   0.594522 * X  +   0.526105 * Y  +  -0.608077 * Z  +  10.106556
  Z_new =  -0.712977 * X  +  -0.004724 * Y  +  -0.701171 * Z  + 149.013382 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.134855    0.006737  [ DEG:  -179.6140      0.3860 ]
  Theta =   0.793735    2.347858  [ DEG:    45.4777    134.5223 ]
  Phi   =   2.129621   -1.011971  [ DEG:   122.0183    -57.9817 ]
 
# 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_2-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  192   5.0   23   2.89    0.00   7.905
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D2
REMARK Aligment from pdb entry: 1xov_A
ATOM      1  N   ASP   290      75.818  58.500  94.555  1.00  0.00              
ATOM      2  CA  ASP   290      74.574  59.101  95.033  1.00  0.00              
ATOM      3  C   ASP   290      74.637  59.318  96.530  1.00  0.00              
ATOM      4  O   ASP   290      74.229  60.333  97.030  1.00  0.00              
ATOM      5  N   HIS   291      75.173  58.331  97.231  1.00  0.00              
ATOM      6  CA  HIS   291      75.371  58.445  98.673  1.00  0.00              
ATOM      7  C   HIS   291      76.370  59.538  99.046  1.00  0.00              
ATOM      8  O   HIS   291      76.125  60.303  99.962  1.00  0.00              
ATOM      9  N   THR   292      77.476  59.647  98.321  1.00  0.00              
ATOM     10  CA  THR   292      78.440  60.732  98.589  1.00  0.00              
ATOM     11  C   THR   292      77.824  62.111  98.380  1.00  0.00              
ATOM     12  O   THR   292      78.027  63.021  99.196  1.00  0.00              
ATOM     13  N   GLY   293      77.076  62.267  97.288  1.00  0.00              
ATOM     14  CA  GLY   293      76.519  63.571  96.877  1.00  0.00              
ATOM     15  C   GLY   293      75.279  63.964  97.660  1.00  0.00              
ATOM     16  O   GLY   293      74.952  65.151  97.785  1.00  0.00              
ATOM     17  N   TYR   294      74.611  62.953  98.211  1.00  0.00              
ATOM     18  CA  TYR   294      73.358  63.115  98.920  1.00  0.00              
ATOM     19  C   TYR   294      72.225  63.405  97.953  1.00  0.00              
ATOM     20  O   TYR   294      71.305  64.181  98.289  1.00  0.00              
ATOM     21  N   TYR   295      72.292  62.812  96.771  1.00  0.00              
ATOM     22  CA  TYR   295      71.286  62.951  95.723  1.00  0.00              
ATOM     23  C   TYR   295      70.627  61.635  95.450  1.00  0.00              
ATOM     24  O   TYR   295      71.180  60.571  95.784  1.00  0.00              
ATOM     25  N   ASN   296      69.480  61.636  94.781  1.00  0.00              
ATOM     26  CA  ASN   296      68.897  60.366  94.359  1.00  0.00              
ATOM     27  C   ASN   296      69.734  59.522  93.413  1.00  0.00              
ATOM     28  O   ASN   296      70.448  60.032  92.567  1.00  0.00              
ATOM     29  N   GLU   297      69.625  58.218  93.554  1.00  0.00              
ATOM     30  CA  GLU   297      70.196  57.289  92.644  1.00  0.00              
ATOM     31  C   GLU   297      69.208  56.938  91.547  1.00  0.00              
ATOM     32  O   GLU   297      68.206  56.220  91.759  1.00  0.00              
ATOM     33  N   VAL   298      69.483  57.427  90.341  1.00  0.00              
ATOM     34  CA  VAL   298      68.679  57.057  89.199  1.00  0.00              
ATOM     35  C   VAL   298      69.003  55.649  88.697  1.00  0.00              
ATOM     36  O   VAL   298      68.260  55.038  87.917  1.00  0.00              
ATOM     37  N   ASP   299      71.930  51.835  84.100  1.00  0.00              
ATOM     38  CA  ASP   299      71.084  51.807  82.921  1.00  0.00              
ATOM     39  C   ASP   299      71.816  51.154  81.769  1.00  0.00              
ATOM     40  O   ASP   299      72.937  51.536  81.482  1.00  0.00              
ATOM     41  N   SER   300      71.159  50.179  81.128  1.00  0.00              
ATOM     42  CA  SER   300      71.695  49.394  80.027  1.00  0.00              
ATOM     43  C   SER   300      71.390  50.081  78.698  1.00  0.00              
ATOM     44  O   SER   300      70.307  50.663  78.508  1.00  0.00              
ATOM     45  N   PHE   301      72.325  50.026  77.774  1.00  0.00              
ATOM     46  CA  PHE   301      72.075  50.535  76.440  1.00  0.00              
ATOM     47  C   PHE   301      73.003  49.916  75.407  1.00  0.00              
ATOM     48  O   PHE   301      74.112  49.470  75.737  1.00  0.00              
ATOM     49  N   PRO   302      72.536  49.886  74.156  1.00  0.00              
ATOM     50  CA  PRO   302      73.406  49.550  73.035  1.00  0.00              
ATOM     51  C   PRO   302      73.519  50.733  72.065  1.00  0.00              
ATOM     52  O   PRO   302      73.830  50.563  70.860  1.00  0.00              
ATOM     53  N   VAL   303      73.173  51.907  72.546  1.00  0.00              
ATOM     54  CA  VAL   303      73.060  53.078  71.705  1.00  0.00              
ATOM     55  C   VAL   303      74.189  54.089  71.882  1.00  0.00              
ATOM     56  O   VAL   303      74.191  55.104  71.197  1.00  0.00              
ATOM     57  N   PHE   304      75.140  53.827  72.773  1.00  0.00              
ATOM     58  CA  PHE   304      76.207  54.806  73.035  1.00  0.00              
ATOM     59  C   PHE   304      77.499  54.373  72.408  1.00  0.00              
ATOM     60  O   PHE   304      77.994  53.277  72.666  1.00  0.00              
ATOM     61  N   THR   305      78.061  55.238  71.566  1.00  0.00              
ATOM     62  CA  THR   305      79.261  54.893  70.814  1.00  0.00              
ATOM     63  C   THR   305      80.421  54.480  71.732  1.00  0.00              
ATOM     64  O   THR   305      81.142  53.513  71.446  1.00  0.00              
ATOM     65  N   VAL   306      80.586  55.235  72.806  1.00  0.00              
ATOM     66  CA  VAL   306      81.647  54.941  73.790  1.00  0.00              
ATOM     67  C   VAL   306      81.587  53.485  74.287  1.00  0.00              
ATOM     68  O   VAL   306      82.587  52.767  74.256  1.00  0.00              
ATOM     69  N   THR   307      80.403  53.055  74.725  1.00  0.00              
ATOM     70  CA  THR   307      80.197  51.689  75.213  1.00  0.00              
ATOM     71  C   THR   307      80.246  50.651  74.098  1.00  0.00              
ATOM     72  O   THR   307      80.675  49.532  74.322  1.00  0.00              
ATOM     73  N   HIS   308      79.793  51.008  72.896  1.00  0.00              
ATOM     74  CA  HIS   308      79.727  50.066  71.799  1.00  0.00              
ATOM     75  C   HIS   308      81.081  49.761  71.207  1.00  0.00              
ATOM     76  O   HIS   308      81.326  48.685  70.755  1.00  0.00              
ATOM     77  N   ILE   309      81.942  50.756  71.177  1.00  0.00              
ATOM     78  CA  ILE   309      83.166  50.728  70.402  1.00  0.00              
ATOM     79  C   ILE   309      84.439  50.496  71.211  1.00  0.00              
ATOM     80  O   ILE   309      85.452  50.172  70.654  1.00  0.00              
ATOM     81  N   THR   310      84.365  50.682  72.521  1.00  0.00              
ATOM     82  CA  THR   310      85.467  50.394  73.419  1.00  0.00              
ATOM     83  C   THR   310      85.468  48.882  73.597  1.00  0.00              
ATOM     84  O   THR   310      84.451  48.316  73.943  1.00  0.00              
ATOM     85  N   GLN   311      86.583  48.216  73.313  1.00  0.00              
ATOM     86  CA  GLN   311      86.653  46.750  73.360  1.00  0.00              
ATOM     87  C   GLN   311      86.481  46.160  74.754  1.00  0.00              
ATOM     88  O   GLN   311      85.836  45.142  74.921  1.00  0.00              
ATOM     89  N   ARG   312      87.039  46.794  75.770  1.00  0.00              
ATOM     90  CA  ARG   312      87.029  46.192  77.076  1.00  0.00              
ATOM     91  C   ARG   312      85.759  46.525  77.797  1.00  0.00              
ATOM     92  O   ARG   312      84.848  47.199  77.256  1.00  0.00              
ATOM     93  N   GLU   313      85.697  46.111  79.055  1.00  0.00              
ATOM     94  CA  GLU   313      84.561  46.458  79.893  1.00  0.00              
ATOM     95  C   GLU   313      84.485  47.945  80.132  1.00  0.00              
ATOM     96  O   GLU   313      85.443  48.564  80.628  1.00  0.00              
END
