
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0338AL509_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338AL509_1-D2.T0338_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      E     144           -
LGA    Y     184      H     145          2.017
LGA    -       -      P     146           -
LGA    -       -      H     147           -
LGA    -       -      T     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      K     152           -
LGA    -       -      C     153           -
LGA    -       -      T     154           -
LGA    -       -      Q     155           -
LGA    -       -      L     156           -
LGA    -       -      V     157           -
LGA    -       -      R     158           -
LGA    -       -      A     159           -
LGA    -       -      S     160           -
LGA    -       -      K     161           -
LGA    -       -      D     162           -
LGA    -       -      L     163           -
LGA    -       -      A     164           -
LGA    -       -      Q     165           -
LGA    -       -      T     166           -
LGA    -       -      S     167           -
LGA    -       -      Y     168           -
LGA    -       -      F     169           -
LGA    -       -      M     170           -
LGA    -       -      A     171           -
LGA    -       -      T     172           -
LGA    -       -      N     173           -
LGA    -       -      S     174           -
LGA    -       -      L     175           -
LGA    -       -      H     176           -
LGA    -       -      L     177           -
LGA    -       -      T     178           -
LGA    -       -      T     179           -
LGA    -       -      F     180           -
LGA    -       -      C     181           -
LGA    -       -      L     182           -
LGA    -       -      Q     183           -
LGA    -       -      Y     184           -
LGA    -       -      K     185           -
LGA    K     185      P     186          0.567
LGA    P     186      T     187          0.262
LGA    T     187      V     188          0.499
LGA    V     188      I     189          0.630
LGA    I     189      A     190          0.465
LGA    A     190      C     191          0.272
LGA    C     191      V     192          0.259
LGA    V     192      C     193          0.250
LGA    C     193      I     194          0.268
LGA    I     194      H     195          0.102
LGA    H     195      L     196          0.091
LGA    L     196      A     197          0.119
LGA    A     197      C     198          0.330
LGA    C     198      K     199          0.419
LGA    K     199      W     200          0.370
LGA    W     200      S     201          0.437
LGA    -       -      N     202           -
LGA    -       -      W     203           -
LGA    -       -      E     204           -
LGA    -       -      I     205           -
LGA    -       -      P     206           -
LGA    -       -      V     207           -
LGA    -       -      S     208           -
LGA    -       -      T     209           -
LGA    -       -      D     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      H     213           -
LGA    -       -      W     214           -
LGA    -       -      W     215           -
LGA    -       -      E     216           -
LGA    -       -      Y     217           -
LGA    -       -      V     218           -
LGA    -       -      D     219           -
LGA    -       -      P     220           -
LGA    -       -      T     221           -
LGA    -       -      V     222           -
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      E     225           -
LGA    -       -      L     226           -
LGA    -       -      L     227           -
LGA    -       -      D     228           -
LGA    -       -      E     229           -
LGA    -       -      L     230           -
LGA    -       -      T     231           -
LGA    -       -      H     232           -
LGA    -       -      E     233           -
LGA    -       -      F     234           -
LGA    -       -      L     235           -
LGA    -       -      Q     236           -
LGA    -       -      I     237           -
LGA    -       -      L     238           -
LGA    -       -      E     239           -
LGA    -       -      K     240           -
LGA    -       -      T     241           -
LGA    -       -      P     242           -
LGA    -       -      N     243           -
LGA    -       -      R     244           -
LGA    -       -      L     245           -
LGA    -       -      K     246           -
LGA    -       -      K     247           -
LGA    -       -      I     248           -
LGA    -       -      R     249           -
LGA    -       -      N     250           -
LGA    -       -      W     251           -
LGA    -       -      R     252           -
LGA    -       -      A     253           -
LGA    -       -      N     254           -
LGA    -       -      Q     255           -
LGA    -       -      A     256           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  113    5.0     17    0.61     0.00     14.908     2.408

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.668490 * X  +  -0.231237 * Y  +   0.706859 * Z  + -20.652628
  Y_new =  -0.150613 * X  +   0.972835 * Y  +   0.175809 * Z  + -16.292336
  Z_new =  -0.728311 * X  +   0.011064 * Y  +  -0.685158 * Z  + 118.668213 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.125445   -0.016147  [ DEG:   179.0748     -0.9252 ]
  Theta =   0.815853    2.325739  [ DEG:    46.7449    133.2551 ]
  Phi   =  -2.919990    0.221603  [ DEG:  -167.3031     12.6969 ]
 
# 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: T0338AL509_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338AL509_1-D2.T0338_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  113   5.0   17   0.61    0.00  14.908
REMARK  ---------------------------------------------------------- 
MOLECULE T0338AL509_1-D2
REMARK Aligment from pdb entry: 1vin
ATOM    177  N   TYR   184     -26.002  18.300  62.612  1.00  0.00              
ATOM    178  CA  TYR   184     -25.191  17.178  63.068  1.00  0.00              
ATOM    179  C   TYR   184     -25.673  15.786  62.623  1.00  0.00              
ATOM    180  O   TYR   184     -26.865  15.554  62.473  1.00  0.00              
ATOM    181  N   LYS   185     -24.711  14.873  62.476  1.00  0.00              
ATOM    182  CA  LYS   185     -25.002  13.489  62.115  1.00  0.00              
ATOM    183  C   LYS   185     -25.412  12.800  63.396  1.00  0.00              
ATOM    184  O   LYS   185     -25.047  13.252  64.477  1.00  0.00              
ATOM    185  N   PRO   186     -26.236  11.740  63.292  1.00  0.00              
ATOM    186  CA  PRO   186     -26.686  10.994  64.467  1.00  0.00              
ATOM    187  C   PRO   186     -25.550  10.499  65.372  1.00  0.00              
ATOM    188  O   PRO   186     -25.721  10.474  66.583  1.00  0.00              
ATOM    189  N   THR   187     -24.420  10.064  64.807  1.00  0.00              
ATOM    190  CA  THR   187     -23.277   9.546  65.595  1.00  0.00              
ATOM    191  C   THR   187     -22.661  10.629  66.512  1.00  0.00              
ATOM    192  O   THR   187     -22.191  10.342  67.606  1.00  0.00              
ATOM    193  N   VAL   188     -22.605  11.838  65.969  1.00  0.00              
ATOM    194  CA  VAL   188     -22.092  12.992  66.676  1.00  0.00              
ATOM    195  C   VAL   188     -22.999  13.373  67.843  1.00  0.00              
ATOM    196  O   VAL   188     -22.528  13.586  68.958  1.00  0.00              
ATOM    197  N   ILE   189     -24.306  13.402  67.597  1.00  0.00              
ATOM    198  CA  ILE   189     -25.265  13.750  68.627  1.00  0.00              
ATOM    199  C   ILE   189     -25.264  12.681  69.683  1.00  0.00              
ATOM    200  O   ILE   189     -25.374  12.989  70.881  1.00  0.00              
ATOM    201  N   ALA   190     -25.136  11.429  69.269  1.00  0.00              
ATOM    202  CA  ALA   190     -25.088  10.316  70.196  1.00  0.00              
ATOM    203  C   ALA   190     -23.819  10.416  71.075  1.00  0.00              
ATOM    204  O   ALA   190     -23.851  10.091  72.277  1.00  0.00              
ATOM    205  N   CYS   191     -22.701  10.833  70.480  1.00  0.00              
ATOM    206  CA  CYS   191     -21.443  10.957  71.216  1.00  0.00              
ATOM    207  C   CYS   191     -21.539  12.067  72.263  1.00  0.00              
ATOM    208  O   CYS   191     -21.213  11.838  73.421  1.00  0.00              
ATOM    209  N   VAL   192     -22.070  13.223  71.847  1.00  0.00              
ATOM    210  CA  VAL   192     -22.219  14.365  72.737  1.00  0.00              
ATOM    211  C   VAL   192     -23.170  14.004  73.859  1.00  0.00              
ATOM    212  O   VAL   192     -22.883  14.249  75.037  1.00  0.00              
ATOM    213  N   CYS   193     -24.241  13.305  73.494  1.00  0.00              
ATOM    214  CA  CYS   193     -25.272  12.882  74.436  1.00  0.00              
ATOM    215  C   CYS   193     -24.726  11.907  75.471  1.00  0.00              
ATOM    216  O   CYS   193     -25.063  12.007  76.667  1.00  0.00              
ATOM    217  N   ILE   194     -23.871  10.985  75.024  1.00  0.00              
ATOM    218  CA  ILE   194     -23.233   9.994  75.912  1.00  0.00              
ATOM    219  C   ILE   194     -22.223  10.677  76.861  1.00  0.00              
ATOM    220  O   ILE   194     -22.248  10.464  78.081  1.00  0.00              
ATOM    221  N   HIS   195     -21.338  11.494  76.305  1.00  0.00              
ATOM    222  CA  HIS   195     -20.374  12.202  77.140  1.00  0.00              
ATOM    223  C   HIS   195     -21.093  12.987  78.229  1.00  0.00              
ATOM    224  O   HIS   195     -20.823  12.822  79.413  1.00  0.00              
ATOM    225  N   LEU   196     -22.060  13.793  77.808  1.00  0.00              
ATOM    226  CA  LEU   196     -22.803  14.651  78.699  1.00  0.00              
ATOM    227  C   LEU   196     -23.514  13.882  79.791  1.00  0.00              
ATOM    228  O   LEU   196     -23.477  14.270  80.965  1.00  0.00              
ATOM    229  N   ALA   197     -24.109  12.760  79.412  1.00  0.00              
ATOM    230  CA  ALA   197     -24.833  11.941  80.369  1.00  0.00              
ATOM    231  C   ALA   197     -23.826  11.348  81.362  1.00  0.00              
ATOM    232  O   ALA   197     -24.094  11.322  82.567  1.00  0.00              
ATOM    233  N   CYS   198     -22.699  10.856  80.838  1.00  0.00              
ATOM    234  CA  CYS   198     -21.630  10.287  81.670  1.00  0.00              
ATOM    235  C   CYS   198     -21.114  11.321  82.673  1.00  0.00              
ATOM    236  O   CYS   198     -21.075  11.062  83.874  1.00  0.00              
ATOM    237  N   LYS   199     -20.776  12.502  82.165  1.00  0.00              
ATOM    238  CA  LYS   199     -20.265  13.595  82.964  1.00  0.00              
ATOM    239  C   LYS   199     -21.258  14.027  84.031  1.00  0.00              
ATOM    240  O   LYS   199     -20.876  14.139  85.192  1.00  0.00              
ATOM    241  N   TRP   200     -22.522  14.235  83.662  1.00  0.00              
ATOM    242  CA  TRP   200     -23.522  14.655  84.635  1.00  0.00              
ATOM    243  C   TRP   200     -23.743  13.650  85.769  1.00  0.00              
ATOM    244  O   TRP   200     -23.914  14.030  86.924  1.00  0.00              
END
