
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_2-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      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
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    -       -      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    L     206      A     160          3.541
LGA    L     207      I     161          5.188
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    Y     208      T     181          2.926
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    S     209      F     188          2.054
LGA    N     210      M     189          1.741
LGA    E     211      R     190          3.336
LGA    P     212      L     191          2.205
LGA    I     213      Q     192          1.081
LGA    C     214      P     193          2.353
LGA    G     215      L     194          2.659
LGA    -       -      L     195           -
LGA    L     216      H     196          3.571
LGA    Y     217      W     197          4.104
LGA    G     218      -       -           -
LGA    K     219      -       -           -
LGA    G     220      D     198          3.359
LGA    F     221      L     199          4.268
LGA    T     222      T     200          1.904
LGA    S     223      N     201          1.109
LGA    I     224      I     202          2.883
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    G     225      F     205          1.344
LGA    G     226      L     206          2.542
LGA    -       -      L     207           -
LGA    I     227      Y     208          4.274
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    3.03    10.00      5.916     0.639

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.014737 * X  +  -0.565075 * Y  +  -0.824908 * Z  +  14.128281
  Y_new =   0.324134 * X  +  -0.783147 * Y  +   0.530677 * Z  +  24.235523
  Z_new =  -0.945896 * X  +  -0.259560 * Y  +   0.194701 * Z  +  23.302822 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.927219    2.214374  [ DEG:   -53.1257    126.8743 ]
  Theta =   1.240346    1.901246  [ DEG:    71.0666    108.9334 ]
  Phi   =   1.616230   -1.525362  [ DEG:    92.6032    -87.3968 ]
 
# 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_2-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_2-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   3.03   10.00   5.916
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_2-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      23.330  26.631  32.134  1.00  0.00              
ATOM    207  CA  LEU   207      25.608  23.219  32.597  1.00  0.00              
ATOM    208  CA  TYR   208      27.808  21.513  35.778  1.00  0.00              
ATOM    209  CA  SER   209      25.435  24.354  34.935  1.00  0.00              
ATOM    210  CA  ASN   210      22.317  23.633  37.040  1.00  0.00              
ATOM    211  CA  GLU   211      19.926  23.429  34.146  1.00  0.00              
ATOM    212  CA  PRO   212      17.013  20.976  34.139  1.00  0.00              
ATOM    213  CA  ILE   213      17.272  19.376  31.375  1.00  0.00              
ATOM    214  CA  CYS   214      14.113  17.301  29.298  1.00  0.00              
ATOM    215  CA  GLY   215      14.648  16.142  26.507  1.00  0.00              
ATOM    216  CA  LEU   216      11.669  15.018  24.141  1.00  0.00              
ATOM    217  CA  TYR   217      12.883  15.576  20.569  1.00  0.00              
ATOM    218  CA  GLY   218      16.422  14.249  21.207  1.00  0.00              
ATOM    219  CA  LYS   219      15.024  10.899  22.360  1.00  0.00              
ATOM    220  CA  GLY   220      12.957  10.538  19.209  1.00  0.00              
ATOM    221  CA  PHE   221       9.397  11.390  20.296  1.00  0.00              
ATOM    222  CA  THR   222       8.018  13.756  17.761  1.00  0.00              
ATOM    223  CA  SER   223       5.101  15.347  19.554  1.00  0.00              
ATOM    224  CA  ILE   224       6.045  19.003  19.240  1.00  0.00              
ATOM    225  CA  GLY   225       2.593  20.508  18.487  1.00  0.00              
ATOM    226  CA  GLY   226       3.580  23.017  15.831  1.00  0.00              
ATOM    227  CA  ILE   227       3.318  26.344  17.466  1.00  0.00              
TER                                                                             
END
