
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0372AL044_3-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_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           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    R     118      G     188          1.202
LGA    A     119      N     189          2.080
LGA    Y     120      E     190          1.979
LGA    A     121      R     191          1.656
LGA    D     122      R     192          1.960
LGA    Y     123      A     193          1.466
LGA    I     124      L     194          1.013
LGA    Y     125      I     195          1.989
LGA    L     126      Y     196          2.315
LGA    -       -      A     197           -
LGA    R     127      L     198          4.039
LGA    S     128      H     199          4.768
LGA    D     129      N     200          4.562
LGA    L     130      F     201          2.094
LGA    A     131      E     202          2.479
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    T     132      G     205          3.306
LGA    L     133      L     206          0.208
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)   16  172    5.0     16    2.62     6.25      7.034     0.588

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.785191 * X  +   0.124569 * Y  +   0.606595 * Z  +  28.057600
  Y_new =   0.123460 * X  +  -0.928403 * Y  +   0.350464 * Z  +  47.700401
  Z_new =   0.606822 * X  +   0.350072 * Y  +   0.713594 * Z  + -12.543793 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.456079   -2.685513  [ DEG:    26.1314   -153.8686 ]
  Theta =  -0.652056   -2.489537  [ DEG:   -37.3601   -142.6399 ]
  Phi   =   2.985633   -0.155959  [ DEG:   171.0642     -8.9358 ]
 
# 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: T0372AL044_3-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_3-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  172   5.0   16   2.62    6.25   7.034
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_3-D2
REMARK Aligment from pdb entry: 1sqe_A
ATOM    149  N   ARG   118      41.675  31.572  11.498  1.00  0.00              
ATOM    150  CA  ARG   118      43.020  31.444  12.060  1.00  0.00              
ATOM    151  C   ARG   118      43.782  32.738  11.822  1.00  0.00              
ATOM    152  O   ARG   118      44.540  33.186  12.683  1.00  0.00              
ATOM    153  N   ALA   119      43.571  33.329  10.648  1.00  0.00              
ATOM    154  CA  ALA   119      44.212  34.587  10.282  1.00  0.00              
ATOM    155  C   ALA   119      43.842  35.618  11.316  1.00  0.00              
ATOM    156  O   ALA   119      44.693  36.353  11.800  1.00  0.00              
ATOM    157  N   TYR   120      42.557  35.666  11.650  1.00  0.00              
ATOM    158  CA  TYR   120      42.053  36.612  12.640  1.00  0.00              
ATOM    159  C   TYR   120      42.701  36.386  14.011  1.00  0.00              
ATOM    160  O   TYR   120      43.123  37.336  14.668  1.00  0.00              
ATOM    161  N   ALA   121      42.765  35.128  14.443  1.00  0.00              
ATOM    162  CA  ALA   121      43.361  34.802  15.732  1.00  0.00              
ATOM    163  C   ALA   121      44.825  35.236  15.770  1.00  0.00              
ATOM    164  O   ALA   121      45.307  35.716  16.793  1.00  0.00              
ATOM    165  N   ASP   122      45.524  35.071  14.651  1.00  0.00              
ATOM    166  CA  ASP   122      46.927  35.464  14.574  1.00  0.00              
ATOM    167  C   ASP   122      47.039  36.967  14.785  1.00  0.00              
ATOM    168  O   ASP   122      47.981  37.454  15.406  1.00  0.00              
ATOM    169  N   TYR   123      46.068  37.699  14.252  1.00  0.00              
ATOM    170  CA  TYR   123      46.014  39.147  14.398  1.00  0.00              
ATOM    171  C   TYR   123      45.890  39.482  15.887  1.00  0.00              
ATOM    172  O   TYR   123      46.595  40.349  16.407  1.00  0.00              
ATOM    173  N   ILE   124      45.000  38.774  16.572  1.00  0.00              
ATOM    174  CA  ILE   124      44.790  38.993  17.998  1.00  0.00              
ATOM    175  C   ILE   124      46.054  38.716  18.809  1.00  0.00              
ATOM    176  O   ILE   124      46.319  39.390  19.800  1.00  0.00              
ATOM    177  N   TYR   125      46.828  37.724  18.380  1.00  0.00              
ATOM    178  CA  TYR   125      48.059  37.336  19.076  1.00  0.00              
ATOM    179  C   TYR   125      49.320  38.016  18.537  1.00  0.00              
ATOM    180  O   TYR   125      50.428  37.690  18.954  1.00  0.00              
ATOM    181  N   LEU   126      49.155  38.961  17.622  1.00  0.00              
ATOM    182  CA  LEU   126      50.301  39.646  17.038  1.00  0.00              
ATOM    183  C   LEU   126      50.837  40.785  17.895  1.00  0.00              
ATOM    184  O   LEU   126      50.186  41.247  18.836  1.00  0.00              
ATOM    185  N   ARG   127      52.040  41.237  17.560  1.00  0.00              
ATOM    186  CA  ARG   127      52.640  42.327  18.293  1.00  0.00              
ATOM    187  C   ARG   127      51.962  43.626  17.897  1.00  0.00              
ATOM    188  O   ARG   127      51.742  44.484  18.743  1.00  0.00              
ATOM    189  N   SER   128      51.612  43.768  16.618  1.00  0.00              
ATOM    190  CA  SER   128      50.937  44.985  16.160  1.00  0.00              
ATOM    191  C   SER   128      49.619  45.178  16.897  1.00  0.00              
ATOM    192  O   SER   128      49.169  46.306  17.087  1.00  0.00              
ATOM    193  N   ASP   129      49.002  44.072  17.305  1.00  0.00              
ATOM    194  CA  ASP   129      47.748  44.127  18.044  1.00  0.00              
ATOM    195  C   ASP   129      48.068  44.504  19.488  1.00  0.00              
ATOM    196  O   ASP   129      47.398  45.352  20.080  1.00  0.00              
ATOM    197  N   LEU   130      49.095  43.865  20.047  1.00  0.00              
ATOM    198  CA  LEU   130      49.517  44.134  21.418  1.00  0.00              
ATOM    199  C   LEU   130      49.957  45.588  21.553  1.00  0.00              
ATOM    200  O   LEU   130      49.503  46.299  22.448  1.00  0.00              
ATOM    201  N   ALA   131      50.848  46.021  20.667  1.00  0.00              
ATOM    202  CA  ALA   131      51.325  47.399  20.683  1.00  0.00              
ATOM    203  C   ALA   131      50.116  48.335  20.699  1.00  0.00              
ATOM    204  O   ALA   131      50.010  49.213  21.560  1.00  0.00              
ATOM    205  N   THR   132      49.203  48.140  19.751  1.00  0.00              
ATOM    206  CA  THR   132      47.994  48.954  19.678  1.00  0.00              
ATOM    207  C   THR   132      47.184  48.632  20.927  1.00  0.00              
ATOM    208  O   THR   132      47.697  47.994  21.848  1.00  0.00              
ATOM    209  N   LEU   133      45.925  49.059  20.970  1.00  0.00              
ATOM    210  CA  LEU   133      45.092  48.777  22.139  1.00  0.00              
ATOM    211  C   LEU   133      45.772  49.245  23.424  1.00  0.00              
ATOM    212  O   LEU   133      46.459  48.466  24.095  1.00  0.00              
END
