
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_5-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    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    L     206      L      52          3.842
LGA    L     207      N      53          3.459
LGA    Y     208      G      54          3.213
LGA    -       -      E      55           -
LGA    S     209      I      56          2.530
LGA    N     210      S      57          3.165
LGA    E     211      F      58          3.295
LGA    P     212      S      59          2.477
LGA    I     213      Y      60          1.876
LGA    C     214      N      61          1.309
LGA    G     215      G      62          2.101
LGA    L     216      G      63          4.274
LGA    Y     217      K      64          3.606
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    G     218      Q      67          1.729
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    -       -      T     104           -
LGA    -       -      V     105           -
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    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
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    K     219      P     212           #
LGA    G     220      I     213          3.267
LGA    F     221      C     214          1.869
LGA    -       -      G     215           -
LGA    T     222      L     216          4.334
LGA    S     223      Y     217          3.065
LGA    I     224      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    G     225      G     225           #
LGA    G     226      G     226           #
LGA    I     227      I     227          2.595

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  214    5.0     18    3.01    16.67      5.777     0.578

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.797417 * X  +   0.239900 * Y  +   0.553691 * Z  +  20.213984
  Y_new =   0.165179 * X  +   0.795749 * Y  +  -0.582665 * Z  +  33.508179
  Z_new =  -0.580381 * X  +   0.556085 * Y  +   0.594918 * Z  +  16.608208 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.751673   -2.389920  [ DEG:    43.0677   -136.9323 ]
  Theta =   0.619196    2.522397  [ DEG:    35.4773    144.5227 ]
  Phi   =   0.204254   -2.937339  [ DEG:    11.7029   -168.2971 ]
 
# 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_5-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_5-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   18   3.01   16.67   5.777
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_5-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      15.007  39.894  34.937  1.00  0.00              
ATOM    207  CA  LEU   207      18.522  38.223  33.894  1.00  0.00              
ATOM    208  CA  TYR   208      19.393  34.448  32.580  1.00  0.00              
ATOM    209  CA  SER   209      17.475  30.757  33.104  1.00  0.00              
ATOM    210  CA  ASN   210      20.249  28.338  32.187  1.00  0.00              
ATOM    211  CA  GLU   211      18.624  26.515  29.225  1.00  0.00              
ATOM    212  CA  PRO   212      20.632  25.676  26.198  1.00  0.00              
ATOM    213  CA  ILE   213      18.844  27.397  23.328  1.00  0.00              
ATOM    214  CA  CYS   214      20.045  27.453  19.744  1.00  0.00              
ATOM    215  CA  GLY   215      18.017  30.254  17.650  1.00  0.00              
ATOM    216  CA  LEU   216      17.026  28.626  14.289  1.00  0.00              
ATOM    217  CA  TYR   217      16.228  25.438  16.280  1.00  0.00              
ATOM    218  CA  GLY   218      14.126  26.968  19.062  1.00  0.00              
ATOM    219  CA  LYS   219      11.965  28.792  16.641  1.00  0.00              
ATOM    220  CA  GLY   220      11.187  25.751  14.555  1.00  0.00              
ATOM    221  CA  PHE   221      13.084  26.487  11.325  1.00  0.00              
ATOM    222  CA  THR   222      14.580  23.267  10.140  1.00  0.00              
ATOM    223  CA  SER   223      15.970  24.333   6.697  1.00  0.00              
ATOM    224  CA  ILE   224      19.594  24.518   7.372  1.00  0.00              
ATOM    225  CA  GLY   225      21.108  24.729   3.984  1.00  0.00              
ATOM    226  CA  GLY   226      24.694  23.890   3.523  1.00  0.00              
ATOM    227  CA  ILE   227      26.551  26.298   5.833  1.00  0.00              
TER                                                                             
END
