
#######################################################
#                                                     #
#                        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   22 (   22),  selected   22 , name T0320TS599_4-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_4-D1.T0320_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    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    L     206      E      44          5.158
LGA    L     207      I      45           #
LGA    Y     208      F      46          4.670
LGA    S     209      V      47          1.088
LGA    N     210      R      48          2.184
LGA    E     211      W      49          2.181
LGA    P     212      S      50          4.095
LGA    I     213      P      51          4.446
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    C     214      S      57          1.543
LGA    G     215      F      58          2.514
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    L     216      T     104          1.896
LGA    Y     217      V     105          4.345
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    G     218      L     129          2.036
LGA    K     219      S     130          1.756
LGA    G     220      L     131          1.289
LGA    F     221      Y     132          0.835
LGA    T     222      E     133          2.235
LGA    S     223      S     134          5.015
LGA    I     224      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    G     225      A     145          4.463
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    G     226      F     148          2.503
LGA    I     227      R     149          2.925
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  214    5.0     20    3.17     5.00      5.577     0.611

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.833051 * X  +   0.290913 * Y  +  -0.470527 * Z  +  22.401411
  Y_new =  -0.461248 * X  +  -0.104316 * Y  +  -0.881118 * Z  +  32.209866
  Z_new =  -0.305412 * X  +   0.951046 * Y  +   0.047282 * Z  +  30.744871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.521121   -1.620471  [ DEG:    87.1538    -92.8462 ]
  Theta =   0.310372    2.831221  [ DEG:    17.7830    162.2170 ]
  Phi   =  -0.505668    2.635925  [ DEG:   -28.9726    151.0274 ]
 
# 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: T0320TS599_4-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_4-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  214   5.0   20   3.17    5.00   5.577
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_4-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      12.425  25.759  37.554  1.00  0.00              
ATOM    207  CA  LEU   207      10.566  29.075  38.544  1.00  0.00              
ATOM    208  CA  TYR   208       8.103  27.834  41.666  1.00  0.00              
ATOM    209  CA  SER   209      11.050  25.833  42.168  1.00  0.00              
ATOM    210  CA  ASN   210      13.915  28.189  42.683  1.00  0.00              
ATOM    211  CA  GLU   211      16.262  27.017  39.948  1.00  0.00              
ATOM    212  CA  PRO   212      18.336  29.908  38.336  1.00  0.00              
ATOM    213  CA  ILE   213      17.777  29.545  34.469  1.00  0.00              
ATOM    214  CA  CYS   214      19.749  31.885  32.130  1.00  0.00              
ATOM    215  CA  GLY   215      18.736  32.116  28.473  1.00  0.00              
ATOM    216  CA  LEU   216      21.717  32.898  26.188  1.00  0.00              
ATOM    217  CA  TYR   217      19.802  33.866  23.053  1.00  0.00              
ATOM    218  CA  GLY   218      17.119  35.961  24.815  1.00  0.00              
ATOM    219  CA  LYS   219      19.677  37.994  26.825  1.00  0.00              
ATOM    220  CA  GLY   220      22.055  38.501  23.984  1.00  0.00              
ATOM    221  CA  PHE   221      24.729  35.978  24.718  1.00  0.00              
ATOM    222  CA  THR   222      25.600  33.766  21.785  1.00  0.00              
ATOM    223  CA  SER   223      27.202  30.702  22.927  1.00  0.00              
ATOM    224  CA  ILE   224      30.397  30.796  24.743  1.00  0.00              
ATOM    225  CA  GLY   225      31.411  27.366  25.910  1.00  0.00              
ATOM    226  CA  GLY   226      32.745  27.861  29.376  1.00  0.00              
ATOM    227  CA  ILE   227      35.726  30.216  28.899  1.00  0.00              
TER                                                                             
END
