
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0372AL044_5-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_5-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    R     118      S     128          1.448
LGA    A     119      D     129          1.631
LGA    Y     120      L     130          1.473
LGA    A     121      A     131          2.765
LGA    -       -      T     132           -
LGA    D     122      L     133          0.812
LGA    Y     123      K     134           #
LGA    I     124      -       -           -
LGA    Y     125      -       -           -
LGA    L     126      G     135           #
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    R     127      N     143          0.334
LGA    S     128      H     144          0.584
LGA    D     129      I     145          1.220
LGA    L     130      N     146          1.238
LGA    A     131      R     147          0.765
LGA    T     132      F     148          0.554
LGA    L     133      R     149          0.816
LGA    K     134      N     150          0.874
LGA    G     135      T     151          3.118
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    K     136      D     154          4.370
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    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      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)   19  172    5.0     15    1.82     6.67      7.339     0.780

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.595949 * X  +  -0.381776 * Y  +  -0.706465 * Z  +  67.524879
  Y_new =  -0.391831 * X  +   0.906166 * Y  +  -0.159161 * Z  +  47.801998
  Z_new =   0.700938 * X  +   0.181963 * Y  +  -0.689620 * Z  +  47.520477 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.883613   -0.257980  [ DEG:   165.2189    -14.7811 ]
  Theta =  -0.776712   -2.364881  [ DEG:   -44.5023   -135.4977 ]
  Phi   =  -2.559969    0.581623  [ DEG:  -146.6754     33.3246 ]
 
# 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_5-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_5-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  172   5.0   15   1.82    6.67   7.339
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_5-D2
REMARK Aligment from pdb entry: 1x7v_A
ATOM    141  N   ARG   118      26.905  51.878  30.788  1.00  0.00              
ATOM    142  CA  ARG   118      25.725  51.368  31.485  1.00  0.00              
ATOM    143  C   ARG   118      25.571  49.873  31.244  1.00  0.00              
ATOM    144  O   ARG   118      25.209  49.135  32.162  1.00  0.00              
ATOM    145  N   ALA   119      25.880  49.434  30.027  1.00  0.00              
ATOM    146  CA  ALA   119      25.836  47.996  29.722  1.00  0.00              
ATOM    147  C   ALA   119      26.875  47.231  30.520  1.00  0.00              
ATOM    148  O   ALA   119      26.564  46.198  31.128  1.00  0.00              
ATOM    149  N   TYR   120      28.096  47.756  30.590  1.00  0.00              
ATOM    150  CA  TYR   120      29.139  47.150  31.432  1.00  0.00              
ATOM    151  C   TYR   120      28.751  47.126  32.911  1.00  0.00              
ATOM    152  O   TYR   120      28.991  46.140  33.617  1.00  0.00              
ATOM    153  N   ALA   121      28.178  48.213  33.387  1.00  0.00              
ATOM    154  CA  ALA   121      27.733  48.314  34.789  1.00  0.00              
ATOM    155  C   ALA   121      26.659  47.271  35.116  1.00  0.00              
ATOM    156  O   ALA   121      26.744  46.555  36.095  1.00  0.00              
ATOM    157  N   ASP   122      25.694  47.115  34.229  1.00  0.00              
ATOM    158  CA  ASP   122      24.710  46.034  34.365  1.00  0.00              
ATOM    159  C   ASP   122      25.355  44.612  34.388  1.00  0.00              
ATOM    160  O   ASP   122      24.995  43.746  35.177  1.00  0.00              
ATOM    161  N   TYR   123      26.302  44.356  33.506  1.00  0.00              
ATOM    162  CA  TYR   123      27.039  43.094  33.525  1.00  0.00              
ATOM    163  C   TYR   123      27.563  42.699  34.915  1.00  0.00              
ATOM    164  O   TYR   123      27.447  41.542  35.336  1.00  0.00              
ATOM    165  N   ILE   124      28.045  43.669  35.673  1.00  0.00              
ATOM    166  CA  ILE   124      28.616  43.354  36.998  1.00  0.00              
ATOM    167  C   ILE   124      27.616  43.115  38.114  1.00  0.00              
ATOM    168  O   ILE   124      27.976  42.667  39.244  1.00  0.00              
ATOM    169  N   TYR   125      26.355  43.405  37.821  1.00  0.00              
ATOM    170  CA  TYR   125      25.310  43.112  38.757  1.00  0.00              
ATOM    171  C   TYR   125      24.616  41.808  38.461  1.00  0.00              
ATOM    172  O   TYR   125      23.716  41.441  39.171  1.00  0.00              
ATOM    173  N   LEU   126      25.072  41.096  37.425  1.00  0.00              
ATOM    174  CA  LEU   126      24.419  39.861  37.037  1.00  0.00              
ATOM    175  C   LEU   126      24.823  38.781  37.994  1.00  0.00              
ATOM    176  O   LEU   126      25.876  38.859  38.618  1.00  0.00              
ATOM    177  N   ARG   127      23.975  37.756  38.023  1.00  0.00              
ATOM    178  CA  ARG   127      24.142  36.520  38.770  1.00  0.00              
ATOM    179  C   ARG   127      25.411  35.778  38.368  1.00  0.00              
ATOM    180  O   ARG   127      26.198  35.434  39.213  1.00  0.00              
ATOM    181  N   SER   128      25.602  35.573  37.069  1.00  0.00              
ATOM    182  CA  SER   128      26.799  34.895  36.556  1.00  0.00              
ATOM    183  C   SER   128      28.083  35.616  36.924  1.00  0.00              
ATOM    184  O   SER   128      29.054  34.986  37.382  1.00  0.00              
ATOM    185  N   ASP   129      28.096  36.930  36.784  1.00  0.00              
ATOM    186  CA  ASP   129      29.271  37.670  37.097  1.00  0.00              
ATOM    187  C   ASP   129      29.594  37.596  38.597  1.00  0.00              
ATOM    188  O   ASP   129      30.765  37.439  39.003  1.00  0.00              
ATOM    189  N   LEU   130      28.574  37.742  39.430  1.00  0.00              
ATOM    190  CA  LEU   130      28.811  37.675  40.879  1.00  0.00              
ATOM    191  C   LEU   130      29.161  36.267  41.352  1.00  0.00              
ATOM    192  O   LEU   130      29.940  36.126  42.284  1.00  0.00              
ATOM    193  N   ALA   131      28.640  35.232  40.691  1.00  0.00              
ATOM    194  CA  ALA   131      29.069  33.856  40.989  1.00  0.00              
ATOM    195  C   ALA   131      30.565  33.596  40.736  1.00  0.00              
ATOM    196  O   ALA   131      31.201  32.790  41.456  1.00  0.00              
ATOM    197  N   THR   132      31.126  34.282  39.746  1.00  0.00              
ATOM    198  CA  THR   132      32.545  34.170  39.483  1.00  0.00              
ATOM    199  C   THR   132      33.336  34.771  40.670  1.00  0.00              
ATOM    200  O   THR   132      34.328  34.175  41.164  1.00  0.00              
ATOM    201  N   LEU   133      32.832  35.905  41.161  1.00  0.00              
ATOM    202  CA  LEU   133      33.406  36.596  42.310  1.00  0.00              
ATOM    203  C   LEU   133      33.352  35.773  43.585  1.00  0.00              
ATOM    204  O   LEU   133      34.219  35.942  44.452  1.00  0.00              
ATOM    205  N   LYS   134      32.360  34.901  43.707  1.00  0.00              
ATOM    206  CA  LYS   134      32.085  34.188  44.957  1.00  0.00              
ATOM    207  C   LYS   134      32.893  32.916  45.136  1.00  0.00              
ATOM    208  O   LYS   134      32.472  31.814  44.776  1.00  0.00              
ATOM    209  N   GLY   135      34.052  33.086  45.741  1.00  0.00              
ATOM    210  CA  GLY   135      34.814  31.968  46.222  1.00  0.00              
ATOM    211  C   GLY   135      36.070  31.731  45.420  1.00  0.00              
ATOM    212  O   GLY   135      36.873  30.902  45.809  1.00  0.00              
ATOM    213  N   LYS   136      41.195  32.724  45.794  1.00  0.00              
ATOM    214  CA  LYS   136      42.422  31.934  45.970  1.00  0.00              
ATOM    215  C   LYS   136      42.946  31.316  44.672  1.00  0.00              
ATOM    216  O   LYS   136      44.117  30.931  44.604  1.00  0.00              
END
