
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_1-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    L     206      Y      17          2.765
LGA    L     207      L      18          3.846
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    Y     208      D      21          3.411
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    S     209      I      27          3.054
LGA    N     210      A      28          1.104
LGA    E     211      S      29          3.806
LGA    P     212      T      30          3.653
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    I     213      I      34          0.363
LGA    C     214      R      35          3.474
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    G     215      R      38          0.812
LGA    L     216      K      39          4.388
LGA    -       -      Y      40           -
LGA    Y     217      L      41          4.783
LGA    G     218      L      42          4.570
LGA    K     219      S      43          3.966
LGA    G     220      E      44          1.810
LGA    F     221      I      45          1.675
LGA    T     222      F      46          1.692
LGA    S     223      V      47           #
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    I     224      S      50          3.507
LGA    G     225      P      51          1.701
LGA    G     226      L      52          4.299
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    I     227      F      58          3.428
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    -       -      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     21    3.23     9.52      5.651     0.632

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.501684 * X  +   0.815477 * Y  +   0.288635 * Z  +   7.475424
  Y_new =   0.265603 * X  +   0.462754 * Y  +  -0.845762 * Z  +  22.773766
  Z_new =  -0.823267 * X  +  -0.347643 * Y  +  -0.448750 * Z  +  28.728228 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.482475    0.659118  [ DEG:  -142.2353     37.7647 ]
  Theta =   0.967142    2.174450  [ DEG:    55.4132    124.5868 ]
  Phi   =   2.654684   -0.486909  [ DEG:   152.1022    -27.8978 ]
 
# 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_1-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_1-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   21   3.23    9.52   5.651
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_1-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      -0.054  20.919  22.701  1.00  0.00              
ATOM    207  CA  LEU   207      -3.344  18.895  22.395  1.00  0.00              
ATOM    208  CA  TYR   208      -6.669  16.640  23.613  1.00  0.00              
ATOM    209  CA  SER   209      -3.715  16.028  21.096  1.00  0.00              
ATOM    210  CA  ASN   210      -1.701  13.551  23.050  1.00  0.00              
ATOM    211  CA  GLU   211       1.578  15.363  23.303  1.00  0.00              
ATOM    212  CA  PRO   212       3.654  15.265  26.383  1.00  0.00              
ATOM    213  CA  ILE   213       4.169  18.737  27.748  1.00  0.00              
ATOM    214  CA  CYS   214       6.188  19.164  30.915  1.00  0.00              
ATOM    215  CA  GLY   215       5.569  22.127  32.955  1.00  0.00              
ATOM    216  CA  LEU   216       8.540  23.509  34.934  1.00  0.00              
ATOM    217  CA  TYR   217       6.681  24.306  38.254  1.00  0.00              
ATOM    218  CA  GLY   218       4.877  20.981  38.235  1.00  0.00              
ATOM    219  CA  LYS   219       8.118  19.112  37.603  1.00  0.00              
ATOM    220  CA  GLY   220      10.057  20.784  40.379  1.00  0.00              
ATOM    221  CA  PHE   221      12.136  23.360  38.421  1.00  0.00              
ATOM    222  CA  THR   222      12.346  26.485  40.242  1.00  0.00              
ATOM    223  CA  SER   223      11.992  29.316  37.577  1.00  0.00              
ATOM    224  CA  ILE   224      15.430  30.434  36.120  1.00  0.00              
ATOM    225  CA  GLY   225      14.556  33.822  34.745  1.00  0.00              
ATOM    226  CA  GLY   226      16.330  34.708  31.541  1.00  0.00              
ATOM    227  CA  ILE   227      16.187  31.740  29.021  1.00  0.00              
TER                                                                             
END
