
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_3-D1.T0320_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    L     206      P      51          4.915
LGA    L     207      L      52          4.540
LGA    -       -      N      53           -
LGA    Y     208      G      54          2.982
LGA    -       -      E      55           -
LGA    S     209      I      56          3.024
LGA    N     210      S      57          1.705
LGA    E     211      F      58          1.971
LGA    P     212      S      59          1.421
LGA    I     213      Y      60          1.310
LGA    C     214      N      61          1.934
LGA    G     215      G      62          2.508
LGA    L     216      G      63          4.473
LGA    Y     217      K      64          3.659
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    G     218      Q      67          1.537
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          2.554
LGA    F     221      C     214          1.531
LGA    -       -      G     215           -
LGA    T     222      L     216          4.706
LGA    S     223      Y     217          4.669
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    I     224      I     224          1.276
LGA    G     225      G     225          4.076
LGA    G     226      G     226           #
LGA    I     227      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  214    5.0     19    3.16    21.05      5.762     0.582

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.092842 * X  +  -0.096222 * Y  +  -0.991021 * Z  +  20.413506
  Y_new =  -0.918158 * X  +   0.393318 * Y  +   0.047827 * Z  +  23.768667
  Z_new =   0.385185 * X  +   0.914353 * Y  +  -0.124863 * Z  +  20.775761 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.706516   -1.435077  [ DEG:    97.7762    -82.2238 ]
  Theta =  -0.395408   -2.746185  [ DEG:   -22.6552   -157.3448 ]
  Phi   =  -1.671571    1.470022  [ DEG:   -95.7740     84.2260 ]
 
# 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_3-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_3-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   19   3.16   21.05   5.762
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_3-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      14.949  29.656  31.160  1.00  0.00              
ATOM    207  CA  LEU   207      16.087  33.676  31.676  1.00  0.00              
ATOM    208  CA  TYR   208      19.318  36.228  32.644  1.00  0.00              
ATOM    209  CA  SER   209      17.547  32.589  33.293  1.00  0.00              
ATOM    210  CA  ASN   210      20.371  30.371  32.454  1.00  0.00              
ATOM    211  CA  GLU   211      18.808  28.409  29.688  1.00  0.00              
ATOM    212  CA  PRO   212      20.941  27.352  26.770  1.00  0.00              
ATOM    213  CA  ILE   213      19.193  28.494  23.464  1.00  0.00              
ATOM    214  CA  CYS   214      19.764  28.198  20.423  1.00  0.00              
ATOM    215  CA  GLY   215      17.688  30.705  17.836  1.00  0.00              
ATOM    216  CA  LEU   216      16.970  29.056  14.890  1.00  0.00              
ATOM    217  CA  TYR   217      15.786  25.890  16.673  1.00  0.00              
ATOM    218  CA  GLY   218      13.525  27.605  19.257  1.00  0.00              
ATOM    219  CA  LYS   219      11.941  29.633  16.586  1.00  0.00              
ATOM    220  CA  GLY   220      10.964  26.726  14.420  1.00  0.00              
ATOM    221  CA  PHE   221      13.536  26.873  11.682  1.00  0.00              
ATOM    222  CA  THR   222      14.227  23.438  10.485  1.00  0.00              
ATOM    223  CA  SER   223      18.015  23.489   9.275  1.00  0.00              
ATOM    224  CA  ILE   224      19.946  20.841  11.352  1.00  0.00              
ATOM    225  CA  GLY   225      22.697  19.869   9.169  1.00  0.00              
ATOM    226  CA  GLY   226      24.012  16.374   9.407  1.00  0.00              
ATOM    227  CA  ILE   227      25.055  16.165  13.062  1.00  0.00              
TER                                                                             
END
