
#######################################################
#                                                     #
#                        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   52 (   52),  selected   52 , name T0372TS464_4_2
# Molecule2: number of CA atoms  298 ( 2427),  selected  298 , name T0372.pdb
# PARAMETERS: T0372TS464_4_2.T0372.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K       5      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    D       6      L      62           #
LGA    I       7      A      63          3.673
LGA    T       8      Y      64          4.487
LGA    L       9      M      65          4.119
LGA    -       -      M      66           -
LGA    A     102      P      67          3.699
LGA    D     103      V      68          3.067
LGA    L     104      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    E     105      L      73          4.946
LGA    A     106      K      74           #
LGA    -       -      A      75           -
LGA    I     107      V      76          3.886
LGA    L     108      L      77          1.410
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    P     109      F      91          5.247
LGA    E     110      -       -           -
LGA    R     111      C      92          3.564
LGA    F     112      M      93          2.240
LGA    I     113      L      94          2.241
LGA    F     114      G      95          2.000
LGA    V     213      V      96           -
LGA    N     214      C      97          4.639
LGA    G     215      S      98          2.289
LGA    K     216      -       -           -
LGA    I     217      N      99          1.885
LGA    V     218      M     100          0.766
LGA    A     219      R     101          1.357
LGA    F     220      A     102          1.808
LGA    T     221      D     103          1.064
LGA    F     222      L     104          1.235
LGA    G     223      E     105          2.654
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    M     224      F     112          3.640
LGA    P     225      I     113          4.567
LGA    I     226      F     114          2.812
LGA    N     227      T     115          1.478
LGA    H     228      E     116          2.128
LGA    E     229      D     117          2.107
LGA    T     230      -       -           -
LGA    F     231      R     118           #
LGA    G     232      A     119          3.882
LGA    V     233      Y     120          1.738
LGA    H     234      A     121          4.742
LGA    V     235      D     122          2.861
LGA    E     236      Y     123           #
LGA    K     237      -       -           -
LGA    A     238      -       -           -
LGA    D     239      I     124          4.105
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    T     240      R     266          3.890
LGA    S     241      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    M     300      P     284          3.534
LGA    D     301      V     285          3.364
LGA    M     302      T     286          3.532
LGA    -       -      I     287           -
LGA    V     303      L     288          3.311
LGA    R     304      E     289           #
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52  298    5.0     38    3.23     2.63      7.310     1.141

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.416409 * X  +  -0.710219 * Y  +  -0.567620 * Z  +  62.547127
  Y_new =   0.128513 * X  +  -0.572074 * Y  +   0.810071 * Z  +  38.817623
  Z_new =  -0.900049 * X  +  -0.410268 * Y  +  -0.146945 * Z  + 126.568710 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.914729    1.226864  [ DEG:  -109.7059     70.2941 ]
  Theta =   1.119881    2.021712  [ DEG:    64.1645    115.8355 ]
  Phi   =   0.299348   -2.842244  [ DEG:    17.1514   -162.8486 ]
 
# 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: T0372TS464_4_2                                
REMARK     2: T0372.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2.T0372.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52  298   5.0   38   3.23    2.63   7.310
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  LYS     5      34.297  50.323  -7.996  1.00  0.00
ATOM      2  CA  ASP     6      33.173  48.442  -4.901  1.00  0.00
ATOM      3  CA  ILE     7      34.005  48.961  -1.255  1.00  0.00
ATOM      4  CA  THR     8      34.149  46.578   1.698  1.00  0.00
ATOM      5  CA  LEU     9      34.405  48.105   5.194  1.00  0.00
ATOM      6  CA  ALA   102      33.207  59.561   4.446  1.00  0.00
ATOM      7  CA  ASP   103      36.549  58.623   2.908  1.00  0.00
ATOM      8  CA  LEU   104      35.078  55.614   1.063  1.00  0.00
ATOM      9  CA  GLU   105      32.495  57.987  -0.363  1.00  0.00
ATOM     10  CA  ALA   106      35.223  59.760  -2.342  1.00  0.00
ATOM     11  CA  ILE   107      35.767  56.830  -4.689  1.00  0.00
ATOM     12  CA  LEU   108      32.024  56.716  -5.394  1.00  0.00
ATOM     13  CA  PRO   109      31.620  52.940  -5.237  1.00  0.00
ATOM     14  CA  GLU   110      28.688  51.359  -7.059  1.00  0.00
ATOM     15  CA  ARG   111      28.290  49.128  -4.044  1.00  0.00
ATOM     16  CA  PHE   112      29.404  49.488  -0.455  1.00  0.00
ATOM     17  CA  ILE   113      29.317  46.524   1.874  1.00  0.00
ATOM     18  CA  PHE   114      30.018  46.872   5.588  1.00  0.00
ATOM     19  CA  VAL   213      19.377  51.952  10.930  1.00  0.00
ATOM     20  CA  ASN   214      22.652  53.708  10.434  1.00  0.00
ATOM     21  CA  GLY   215      23.592  51.397   7.611  1.00  0.00
ATOM     22  CA  LYS   216      20.197  52.242   6.014  1.00  0.00
ATOM     23  CA  ILE   217      21.055  55.958   5.902  1.00  0.00
ATOM     24  CA  VAL   218      24.571  56.236   4.407  1.00  0.00
ATOM     25  CA  ALA   219      23.719  54.032   1.410  1.00  0.00
ATOM     26  CA  PHE   220      20.279  55.945   1.115  1.00  0.00
ATOM     27  CA  THR   221      22.846  58.742   0.922  1.00  0.00
ATOM     28  CA  PHE   222      25.275  56.868  -1.209  1.00  0.00
ATOM     29  CA  GLY   223      22.525  55.390  -3.415  1.00  0.00
ATOM     30  CA  MET   224      24.228  52.002  -3.190  1.00  0.00
ATOM     31  CA  PRO   225      22.405  49.167  -1.504  1.00  0.00
ATOM     32  CA  ILE   226      23.755  46.181   0.384  1.00  0.00
ATOM     33  CA  ASN   227      23.219  42.443   0.700  1.00  0.00
ATOM     34  CA  HIS   228      22.075  40.758   3.819  1.00  0.00
ATOM     35  CA  GLU   229      25.478  39.323   4.125  1.00  0.00
ATOM     36  CA  THR   230      27.223  42.630   3.918  1.00  0.00
ATOM     37  CA  PHE   231      24.829  44.013   6.447  1.00  0.00
ATOM     38  CA  GLY   232      25.507  41.201   8.904  1.00  0.00
ATOM     39  CA  VAL   233      29.208  41.294   8.479  1.00  0.00
ATOM     40  CA  HIS   234      29.417  45.024   9.038  1.00  0.00
ATOM     41  CA  VAL   235      27.114  44.710  12.022  1.00  0.00
ATOM     42  CA  GLU   236      29.338  42.097  13.422  1.00  0.00
ATOM     43  CA  LYS   237      32.484  44.203  13.408  1.00  0.00
ATOM     44  CA  ALA   238      31.479  47.741  14.233  1.00  0.00
ATOM     45  CA  ASP   239      28.412  47.443  16.412  1.00  0.00
ATOM     46  CA  THR   240      30.188  47.445  19.750  1.00  0.00
ATOM     47  CA  SER   241      27.083  47.774  22.021  1.00  0.00
ATOM     48  CA  MET   300      24.870  45.364  20.055  1.00  0.00
ATOM     49  CA  ASP   301      21.917  47.645  19.148  1.00  0.00
ATOM     50  CA  MET   302      21.870  46.872  15.329  1.00  0.00
ATOM     51  CA  VAL   303      22.844  50.461  14.509  1.00  0.00
ATOM     52  CA  ARG   304      26.401  51.303  13.385  1.00  0.00
TER
END
