
#######################################################
#                                                     #
#                        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 (   26),  selected   26 , name T0289TS599_5-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected  233 , name T0289_D1.pdb
# PARAMETERS: T0289TS599_5-D1.T0289_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      C       4           -
LGA    -       -      V       5           -
LGA    -       -      A       6           -
LGA    -       -      E       7           -
LGA    -       -      E       8           -
LGA    -       -      P       9           -
LGA    -       -      I      10           -
LGA    -       -      K      11           -
LGA    -       -      K      12           -
LGA    -       -      I      13           -
LGA    G     211      A      14          4.953
LGA    K     212      I      15          3.603
LGA    E     213      F      16          1.847
LGA    F     214      G      17          3.871
LGA    P     215      G      18          2.003
LGA    -       -      T      19           -
LGA    P     216      H      20          0.940
LGA    -       -      G      21           -
LGA    -       -      N      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      V      27           -
LGA    -       -      F      28           -
LGA    -       -      L      29           -
LGA    -       -      V      30           -
LGA    -       -      T      31           -
LGA    -       -      H      32           -
LGA    -       -      W      33           -
LGA    -       -      L      34           -
LGA    -       -      K      35           -
LGA    -       -      N      36           -
LGA    -       -      G      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      V      40           -
LGA    -       -      H      41           -
LGA    -       -      R      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      L      45           -
LGA    -       -      E      46           -
LGA    -       -      V      47           -
LGA    -       -      K      48           -
LGA    -       -      P      49           -
LGA    -       -      F      50           -
LGA    -       -      I      51           -
LGA    -       -      T      52           -
LGA    -       -      N      53           -
LGA    -       -      P      54           -
LGA    -       -      R      55           -
LGA    -       -      A      56           -
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      C      60           -
LGA    -       -      T      61           -
LGA    -       -      R      62           -
LGA    C     217      Y      63          3.456
LGA    -       -      I      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      D      67           -
LGA    A     218      L      68          2.627
LGA    I     219      N      69          3.723
LGA    -       -      R      70           -
LGA    D     220      V      71          3.237
LGA    V     221      F      72          2.148
LGA    Y     222      D      73          2.039
LGA    K     223      L      74          1.593
LGA    T     298      E      75           -
LGA    -       -      N      76           -
LGA    -       -      L      77           -
LGA    -       -      S      78           -
LGA    -       -      K      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      S      82           -
LGA    -       -      E      83           -
LGA    -       -      D      84           -
LGA    K     299      L      85           #
LGA    L     300      P      86          4.973
LGA    T     301      Y      87          4.073
LGA    -       -      E      88           -
LGA    L     302      V      89          2.007
LGA    N     303      R      90          3.345
LGA    -       -      R      91           -
LGA    -       -      A      92           -
LGA    A     304      Q      93          3.461
LGA    K     305      E      94          2.097
LGA    S     306      I      95          1.144
LGA    I     307      N      96          2.373
LGA    R     308      H      97          1.408
LGA    S     309      L      98          1.920
LGA    T     310      F      99          4.054
LGA    -       -      G     100           -
LGA    -       -      P     101           -
LGA    -       -      K     102           -
LGA    -       -      N     103           -
LGA    -       -      S     104           -
LGA    -       -      D     105           -
LGA    -       -      D     106           -
LGA    -       -      A     107           -
LGA    -       -      Y     108           -
LGA    -       -      D     109           -
LGA    -       -      V     110           -
LGA    -       -      V     111           -
LGA    -       -      F     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      H     115           -
LGA    -       -      N     116           -
LGA    -       -      T     117           -
LGA    -       -      T     118           -
LGA    -       -      S     119           -
LGA    -       -      N     120           -
LGA    -       -      M     121           -
LGA    -       -      G     122           -
LGA    -       -      C     123           -
LGA    -       -      T     124           -
LGA    -       -      L     125           -
LGA    -       -      I     126           -
LGA    -       -      L     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      S     130           -
LGA    -       -      R     131           -
LGA    -       -      N     132           -
LGA    -       -      D     133           -
LGA    -       -      F     134           -
LGA    -       -      L     135           -
LGA    -       -      I     136           -
LGA    -       -      Q     137           -
LGA    -       -      M     138           -
LGA    -       -      F     139           -
LGA    -       -      H     140           -
LGA    -       -      Y     141           -
LGA    -       -      I     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      C     145           -
LGA    -       -      M     146           -
LGA    -       -      A     147           -
LGA    -       -      P     148           -
LGA    -       -      L     149           -
LGA    -       -      P     150           -
LGA    -       -      C     151           -
LGA    -       -      S     152           -
LGA    -       -      V     153           -
LGA    -       -      Y     154           -
LGA    -       -      L     155           -
LGA    -       -      I     156           -
LGA    -       -      E     157           -
LGA    -       -      H     158           -
LGA    -       -      P     159           -
LGA    -       -      S     160           -
LGA    -       -      L     161           -
LGA    -       -      K     162           -
LGA    -       -      Y     163           -
LGA    -       -      A     164           -
LGA    -       -      T     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      S     168           -
LGA    -       -      I     169           -
LGA    -       -      A     170           -
LGA    -       -      K     171           -
LGA    -       -      Y     172           -
LGA    -       -      P     173           -
LGA    -       -      V     174           -
LGA    -       -      G     175           -
LGA    -       -      I     176           -
LGA    -       -      E     177           -
LGA    -       -      V     178           -
LGA    -       -      G     179           -
LGA    -       -      P     180           -
LGA    -       -      Q     181           -
LGA    -       -      P     182           -
LGA    -       -      H     183           -
LGA    -       -      G     184           -
LGA    -       -      V     185           -
LGA    -       -      L     186           -
LGA    -       -      R     187           -
LGA    -       -      A     188           -
LGA    -       -      D     189           -
LGA    -       -      I     190           -
LGA    -       -      L     191           -
LGA    -       -      D     192           -
LGA    -       -      Q     193           -
LGA    -       -      M     194           -
LGA    -       -      R     195           -
LGA    -       -      R     196           -
LGA    -       -      M     197           -
LGA    -       -      L     198           -
LGA    -       -      K     199           -
LGA    -       -      H     200           -
LGA    -       -      A     201           -
LGA    -       -      L     202           -
LGA    -       -      D     203           -
LGA    -       -      F     204           -
LGA    -       -      I     205           -
LGA    -       -      Q     206           -
LGA    -       -      R     207           -
LGA    -       -      F     208           -
LGA    -       -      N     209           -
LGA    -       -      E     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      E     213           -
LGA    -       -      F     214           -
LGA    -       -      P     215           -
LGA    -       -      P     216           -
LGA    -       -      C     217           -
LGA    -       -      A     218           -
LGA    -       -      I     219           -
LGA    -       -      D     220           -
LGA    -       -      V     221           -
LGA    -       -      Y     222           -
LGA    -       -      K     223           -
LGA    -       -      T     298           -
LGA    -       -      K     299           -
LGA    -       -      L     300           -
LGA    -       -      T     301           -
LGA    -       -      L     302           -
LGA    -       -      N     303           -
LGA    -       -      A     304           -
LGA    -       -      K     305           -
LGA    -       -      S     306           -
LGA    -       -      I     307           -
LGA    -       -      R     308           -
LGA    -       -      S     309           -
LGA    -       -      T     310           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26  233    5.0     24    3.01     0.00      6.458     0.772

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.608881 * X  +   0.784911 * Y  +   0.114799 * Z  +   5.059347
  Y_new =  -0.153542 * X  +  -0.258594 * Y  +   0.953705 * Z  +  28.338158
  Z_new =   0.778260 * X  +   0.563067 * Y  +   0.277970 * Z  +  -7.833543 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.112225   -2.029368  [ DEG:    63.7258   -116.2742 ]
  Theta =  -0.891890   -2.249703  [ DEG:   -51.1015   -128.8985 ]
  Phi   =  -2.894572    0.247020  [ DEG:  -165.8468     14.1532 ]
 
# 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: T0289TS599_5-D1                               
REMARK     2: T0289_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS599_5-D1.T0289_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26  233   5.0   24   3.01    0.00   6.458
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS599_5-D1
PFRMAT TS                                                                       
TARGET T0289                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLY   211      25.518  37.532  -1.872  1.00  0.00              
ATOM    212  CA  LYS   212      23.837  40.240   0.175  1.00  0.00              
ATOM    213  CA  GLU   213      20.246  41.741  -1.435  1.00  0.00              
ATOM    214  CA  PHE   214      17.616  41.880   1.139  1.00  0.00              
ATOM    215  CA  PRO   215      16.706  44.787   3.348  1.00  0.00              
ATOM    216  CA  PRO   216      17.724  44.649   6.975  1.00  0.00              
ATOM    217  CA  CYS   217      14.158  44.391   8.365  1.00  0.00              
ATOM    218  CA  ALA   218      12.844  41.628   6.194  1.00  0.00              
ATOM    219  CA  ILE   219      11.593  38.495   7.826  1.00  0.00              
ATOM    220  CA  ASP   220      11.312  35.269   5.766  1.00  0.00              
ATOM    221  CA  VAL   221       9.705  32.169   7.287  1.00  0.00              
ATOM    222  CA  TYR   222      10.243  28.835   5.672  1.00  0.00              
ATOM    223  CA  LYS   223       8.434  25.864   7.157  1.00  0.00              
ATOM    298  CA  THR   298       6.539  39.488  16.632  1.00  0.00              
ATOM    299  CA  LYS   299       4.903  39.882  13.258  1.00  0.00              
ATOM    300  CA  LEU   300       6.662  38.207  10.518  1.00  0.00              
ATOM    301  CA  THR   301       6.576  39.686   7.005  1.00  0.00              
ATOM    302  CA  LEU   302       6.766  37.452   4.000  1.00  0.00              
ATOM    303  CA  ASN   303       6.892  38.991   0.501  1.00  0.00              
ATOM    304  CA  ALA   304       5.085  36.897  -2.098  1.00  0.00              
ATOM    305  CA  LYS   305       7.446  37.612  -5.010  1.00  0.00              
ATOM    306  CA  SER   306      10.476  36.623  -2.891  1.00  0.00              
ATOM    307  CA  ILE   307       8.752  33.407  -1.802  1.00  0.00              
ATOM    308  CA  ARG   308       7.812  32.403  -5.305  1.00  0.00              
ATOM    309  CA  SER   309      11.378  33.006  -6.560  1.00  0.00              
ATOM    310  CA  THR   310      12.574  30.650  -3.309  1.00  0.00              
TER                                                                             
END
