
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0372AL333_3-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL333_3-D2.T0372_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    I     160      I     160          3.685
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    T     161      R     164          1.544
LGA    P     162      I     165          0.924
LGA    D     163      Q     166          0.366
LGA    R     164      E     167          0.531
LGA    I     165      C     168          0.331
LGA    Q     166      L     169          0.555
LGA    E     167      D     170          0.529
LGA    C     168      L     171          0.200
LGA    L     169      E     172          0.680
LGA    D     170      A     173          1.158
LGA    L     171      E     174          0.793
LGA    E     172      W     175          0.434
LGA    A     173      C     176          0.606
LGA    E     174      K     177          0.832
LGA    T     207      V     178          0.457
LGA    G     208      N     179          0.669
LGA    G     209      N     180           #
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    I     210      T     187          4.622
LGA    L     211      G     188          3.463
LGA    H     212      N     189          4.006
LGA    V     213      E     190          2.977
LGA    -       -      R     191           -
LGA    N     214      R     192          1.912
LGA    G     215      A     193          3.580
LGA    K     216      L     194          2.961
LGA    I     217      I     195           #
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26  172    5.0     24    2.10     4.17     11.662     1.091

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.430919 * X  +   0.378941 * Y  +   0.818970 * Z  +  57.224155
  Y_new =   0.091967 * X  +  -0.884388 * Y  +   0.457601 * Z  +   1.168607
  Z_new =   0.897692 * X  +   0.272508 * Y  +   0.346250 * Z  +   1.886808 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.666780   -2.474813  [ DEG:    38.2037   -141.7963 ]
  Theta =  -1.114503   -2.027090  [ DEG:   -63.8563   -116.1437 ]
  Phi   =   2.931326   -0.210267  [ DEG:   167.9526    -12.0474 ]
 
# 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: T0372AL333_3-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_3-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26  172   5.0   24   2.10    4.17  11.662
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_3-D2
REMARK Aligment from pdb entry: 1lva_A
ATOM    137  N   ILE   160      46.485  41.588  30.659  1.00  0.00              
ATOM    138  CA  ILE   160      47.473  40.520  30.624  1.00  0.00              
ATOM    139  C   ILE   160      48.640  40.989  29.777  1.00  0.00              
ATOM    140  O   ILE   160      48.481  41.862  28.934  1.00  0.00              
ATOM    141  N   THR   161      49.816  40.419  30.007  1.00  0.00              
ATOM    142  CA  THR   161      50.979  40.773  29.209  1.00  0.00              
ATOM    143  C   THR   161      50.844  40.037  27.887  1.00  0.00              
ATOM    144  O   THR   161      50.181  38.999  27.810  1.00  0.00              
ATOM    145  N   PRO   162      51.476  40.560  26.827  1.00  0.00              
ATOM    146  CA  PRO   162      51.403  39.924  25.507  1.00  0.00              
ATOM    147  C   PRO   162      51.719  38.429  25.544  1.00  0.00              
ATOM    148  O   PRO   162      51.001  37.614  24.958  1.00  0.00              
ATOM    149  N   ASP   163      52.805  38.086  26.229  1.00  0.00              
ATOM    150  CA  ASP   163      53.270  36.706  26.353  1.00  0.00              
ATOM    151  C   ASP   163      52.195  35.761  26.888  1.00  0.00              
ATOM    152  O   ASP   163      51.938  34.695  26.320  1.00  0.00              
ATOM    153  N   ARG   164      51.577  36.169  27.988  1.00  0.00              
ATOM    154  CA  ARG   164      50.544  35.381  28.634  1.00  0.00              
ATOM    155  C   ARG   164      49.316  35.204  27.744  1.00  0.00              
ATOM    156  O   ARG   164      48.814  34.086  27.589  1.00  0.00              
ATOM    157  N   ILE   165      48.831  36.295  27.154  1.00  0.00              
ATOM    158  CA  ILE   165      47.649  36.200  26.300  1.00  0.00              
ATOM    159  C   ILE   165      47.901  35.284  25.101  1.00  0.00              
ATOM    160  O   ILE   165      47.075  34.433  24.792  1.00  0.00              
ATOM    161  N   GLN   166      49.037  35.445  24.431  1.00  0.00              
ATOM    162  CA  GLN   166      49.330  34.608  23.272  1.00  0.00              
ATOM    163  C   GLN   166      49.281  33.130  23.631  1.00  0.00              
ATOM    164  O   GLN   166      48.788  32.301  22.859  1.00  0.00              
ATOM    165  N   GLU   167      49.783  32.809  24.817  1.00  0.00              
ATOM    166  CA  GLU   167      49.817  31.426  25.274  1.00  0.00              
ATOM    167  C   GLU   167      48.410  30.867  25.468  1.00  0.00              
ATOM    168  O   GLU   167      48.137  29.721  25.112  1.00  0.00              
ATOM    169  N   CYS   168      47.527  31.685  26.029  1.00  0.00              
ATOM    170  CA  CYS   168      46.147  31.280  26.267  1.00  0.00              
ATOM    171  C   CYS   168      45.410  31.136  24.944  1.00  0.00              
ATOM    172  O   CYS   168      44.687  30.164  24.724  1.00  0.00              
ATOM    173  N   LEU   169      45.595  32.108  24.059  1.00  0.00              
ATOM    174  CA  LEU   169      44.944  32.079  22.755  1.00  0.00              
ATOM    175  C   LEU   169      45.434  30.919  21.902  1.00  0.00              
ATOM    176  O   LEU   169      44.644  30.279  21.207  1.00  0.00              
ATOM    177  N   ASP   170      46.734  30.641  21.947  1.00  0.00              
ATOM    178  CA  ASP   170      47.262  29.548  21.157  1.00  0.00              
ATOM    179  C   ASP   170      46.743  28.230  21.692  1.00  0.00              
ATOM    180  O   ASP   170      46.486  27.301  20.925  1.00  0.00              
ATOM    181  N   LEU   171      46.578  28.148  23.007  1.00  0.00              
ATOM    182  CA  LEU   171      46.033  26.938  23.589  1.00  0.00              
ATOM    183  C   LEU   171      44.573  26.792  23.104  1.00  0.00              
ATOM    184  O   LEU   171      44.134  25.706  22.766  1.00  0.00              
ATOM    185  N   GLU   172      43.823  27.889  23.084  1.00  0.00              
ATOM    186  CA  GLU   172      42.427  27.843  22.626  1.00  0.00              
ATOM    187  C   GLU   172      42.352  27.488  21.145  1.00  0.00              
ATOM    188  O   GLU   172      41.386  26.878  20.698  1.00  0.00              
ATOM    189  N   ALA   173      43.371  27.863  20.380  1.00  0.00              
ATOM    190  CA  ALA   173      43.388  27.516  18.966  1.00  0.00              
ATOM    191  C   ALA   173      43.596  26.000  18.815  1.00  0.00              
ATOM    192  O   ALA   173      42.925  25.356  18.001  1.00  0.00              
ATOM    193  N   GLU   174      44.507  25.428  19.605  1.00  0.00              
ATOM    194  CA  GLU   174      44.772  23.983  19.550  1.00  0.00              
ATOM    195  C   GLU   174      43.557  23.164  19.972  1.00  0.00              
ATOM    196  O   GLU   174      43.320  22.079  19.451  1.00  0.00              
ATOM    197  N   THR   207      42.793  23.673  20.926  1.00  0.00              
ATOM    198  CA  THR   207      41.609  22.963  21.371  1.00  0.00              
ATOM    199  C   THR   207      40.490  23.166  20.362  1.00  0.00              
ATOM    200  O   THR   207      39.443  22.544  20.463  1.00  0.00              
ATOM    201  N   GLY   208      40.713  24.051  19.396  1.00  0.00              
ATOM    202  CA  GLY   208      39.707  24.301  18.376  1.00  0.00              
ATOM    203  C   GLY   208      38.626  25.281  18.783  1.00  0.00              
ATOM    204  O   GLY   208      37.616  25.404  18.106  1.00  0.00              
ATOM    205  N   GLY   209      38.837  25.983  19.888  1.00  0.00              
ATOM    206  CA  GLY   209      37.866  26.955  20.379  1.00  0.00              
ATOM    207  C   GLY   209      37.923  28.241  19.563  1.00  0.00              
ATOM    208  O   GLY   209      36.905  28.890  19.327  1.00  0.00              
ATOM    209  N   ILE   210      39.128  28.603  19.142  1.00  0.00              
ATOM    210  CA  ILE   210      39.341  29.800  18.343  1.00  0.00              
ATOM    211  C   ILE   210      40.146  29.412  17.117  1.00  0.00              
ATOM    212  O   ILE   210      40.780  28.366  17.098  1.00  0.00              
ATOM    213  N   LEU   211      40.106  30.264  16.100  1.00  0.00              
ATOM    214  CA  LEU   211      40.858  30.055  14.866  1.00  0.00              
ATOM    215  C   LEU   211      41.554  31.389  14.638  1.00  0.00              
ATOM    216  O   LEU   211      40.934  32.445  14.790  1.00  0.00              
ATOM    217  N   HIS   212      42.838  31.345  14.287  1.00  0.00              
ATOM    218  CA  HIS   212      43.621  32.565  14.060  1.00  0.00              
ATOM    219  C   HIS   212      43.440  33.048  12.628  1.00  0.00              
ATOM    220  O   HIS   212      43.773  32.326  11.688  1.00  0.00              
ATOM    221  N   VAL   213      42.905  34.257  12.468  1.00  0.00              
ATOM    222  CA  VAL   213      42.680  34.830  11.140  1.00  0.00              
ATOM    223  C   VAL   213      43.956  35.559  10.719  1.00  0.00              
ATOM    224  O   VAL   213      44.360  35.512   9.562  1.00  0.00              
ATOM    225  N   ASN   214      44.576  36.239  11.672  1.00  0.00              
ATOM    226  CA  ASN   214      45.856  36.896  11.460  1.00  0.00              
ATOM    227  C   ASN   214      46.443  37.186  12.838  1.00  0.00              
ATOM    228  O   ASN   214      45.825  36.856  13.863  1.00  0.00              
ATOM    229  N   GLY   215      47.640  37.761  12.874  1.00  0.00              
ATOM    230  CA  GLY   215      48.307  38.045  14.141  1.00  0.00              
ATOM    231  C   GLY   215      47.486  38.881  15.107  1.00  0.00              
ATOM    232  O   GLY   215      47.648  38.778  16.319  1.00  0.00              
ATOM    233  N   LYS   216      46.601  39.705  14.567  1.00  0.00              
ATOM    234  CA  LYS   216      45.776  40.571  15.388  1.00  0.00              
ATOM    235  C   LYS   216      44.394  40.003  15.726  1.00  0.00              
ATOM    236  O   LYS   216      43.866  40.238  16.821  1.00  0.00              
ATOM    237  N   ILE   217      43.821  39.230  14.808  1.00  0.00              
ATOM    238  CA  ILE   217      42.481  38.703  15.028  1.00  0.00              
ATOM    239  C   ILE   217      42.269  37.207  15.080  1.00  0.00              
ATOM    240  O   ILE   217      42.657  36.472  14.167  1.00  0.00              
END
