Backbone independent rotamer libraries

This page is obsolete. See the newer page.

How where the libraries built ?

The two libraries described here were built from an analysis of crystallographic protein structures from the Protein Data Bank (PDB).

The first was built in 1995 and is discussed as RC3 in Tuffery &; al., Prot. Eng., 1997, 10, pp361-372.
The second is much older and was built in 1990 and is discussed in Tuffery &; al., J. Biomol. Struct. Dynam., (1991), 6, pp1267-1289.

The main differences come from a better definition of preferential states observed for chi4 and chi5. However, some differences are also observed for side chains such as ILE, LEU or HIS. For ASN and ASP, the conformations have few significance for chi2.

Both libraries were built using a combination of dynamic clustering and segmentation methods.

The PDB structures were first cleaned up to remove steric contacts involving the side chains.
Then dynamic clustering was performed using chi1/chi2. Each cluster defined was then extracted and re-analysed by dynamic clustering introducing gradually chi3 to chi5.
Dihedrals that could not be significantly assigned from the data sets (some chi3 to chi5) or dihedrals involving hydrogens are assigned an extended conformation (180 degrees).

More information concerning side chain rotamers can also be found at The Protein Sidechain Webpage

Backbone independent rotamer library (1995) build upon a survey of 200 non redundant protein structures resolved at 2.5 Angstroms or better.

A more detailled version (including standard deviations and effectives) can be accessed here

-------------------------------------------------------------- 
       Pept  Num  NChi  Natm  Chi1   Chi2   Chi3   Chi4   Chi5 
-------------------------------------------------------------- 
    1) ALA    1    1    4    180.0 
-------------------------------------------------------------- 
    2) CYS    1    2    5    -65.0  180.0 
       CYS    2             -178.0  180.0 
       CYS    3               64.0  180.0 
-------------------------------------------------------------- 
    3) ASP    1    2    6    -73.0  -14.0 
       ASP    2             -171.0    1.0 
       ASP    3             -168.0   84.0 
       ASP    4               61.0     .0 
       ASP    5               57.0  103.0 
-------------------------------------------------------------- 
    4) GLU    1    3    9    -66.0  179.0  -23.0 
       GLU    2              -66.0  -67.0  -52.0 
       GLU    3             -172.0  177.0  -26.0 
       GLU    4              -70.0  177.0   44.0 
       GLU    5             -173.0   67.0   52.0 
       GLU    6              -68.0   75.0   22.0 
       GLU    7             -175.0  172.0   42.0 
       GLU    8               53.0 -178.0  -49.0
       GLU    9               64.0 -173.0   48.0
       GLU   10             -159.0 -114.0  -62.0
       GLU   11               58.0  -80.0   -4.0
       GLU   12               45.0   98.0    5.0
--------------------------------------------------------------
    5) PHE    1    2   14    -66.0  103.0
       PHE    2             -178.0   75.0
       PHE    3               64.0   91.0
       PHE    4              -67.0  -16.0
--------------------------------------------------------------
    6) GLY    1    0    1  
--------------------------------------------------------------
    7) HIS    1    2   11    -61.0  -74.0
       HIS    2              -64.0   98.0
       HIS    3             -177.0   70.0
       HIS    4             -172.0  -93.0
       HIS    5              -66.0  176.0
       HIS    6               60.0   82.0
       HIS    7               63.0  -81.0
       HIS    8             -162.0  173.0
       HIS    9               60.0 -161.0
--------------------------------------------------------------
    8) ILE    1    4   13    -64.0  168.0  180.0  180.0
       ILE    2              -60.0  -60.0  180.0  180.0
       ILE    3               59.0  167.0  180.0  180.0
       ILE    4             -169.0  169.0  180.0  180.0
       ILE    5              -79.0   87.0  180.0  180.0
       ILE    6             -165.0   70.0  180.0  180.0
       ILE    7               68.0   98.0  180.0  180.0
--------------------------------------------------------------
    9) LYS    1    5   16    -68.0 -179.0 -179.0  179.0  180.0
       LYS    2             -175.0  175.0  177.0  179.0  180.0
       LYS    3              -62.0 -173.0  178.0  -67.0  180.0
       LYS    4              -71.0 -178.0  175.0   67.0  180.0
       LYS    5              -60.0  -64.0  178.0 -177.0  180.0
       LYS    6              -72.0 -175.0  -77.0 -176.0  180.0
       LYS    7             -176.0 -179.0 -179.0   65.0  180.0
       LYS    8              -66.0 -179.0   63.0  176.0  180.0
       LYS    9               65.0 -176.0  179.0 -175.0  180.0
       LYS   10             -172.0  175.0  177.0  -61.0  180.0
       LYS   11             -167.0  178.0   70.0  175.0  180.0
       LYS   12             -175.0   71.0 -173.0  173.0  180.0
       LYS   13              -54.0  -60.0 -178.0  -69.0  180.0
       LYS   14              178.0   70.0  171.0   74.0  180.0
       LYS   15              -54.0  -65.0 -176.0   65.0  180.0
       LYS   16             -173.0  177.0  -67.0 -174.0  180.0
       LYS   17              -92.0   79.0 -172.0  172.0  180.0
       LYS   18             -153.0 -124.0  170.0  168.0  180.0
       LYS   19              -71.0 -173.0  -76.0  -69.0  180.0
       LYS   20               65.0 -172.0 -149.0  -56.0  180.0
       LYS   21             -172.0  170.0   57.0   61.0  180.0
       LYS   22              -69.0 -173.0  -76.0   80.0  180.0
       LYS   23               69.0  174.0 -179.0   69.0  180.0
       LYS   24             -162.0   82.0  109.0 -166.0  180.0
       LYS   25              -56.0  -60.0  -77.0 -174.0  180.0
       LYS   26               67.0 -156.0  -68.0  169.0  180.0
       LYS   27             -157.0  171.0   96.0  -83.0  180.0
       LYS   28              -99.0   88.0  174.0  -88.0  180.0
       LYS   29               58.0  177.0   60.0  171.0  180.0
       LYS   30              -46.0  -53.0  -71.0  -72.0  180.0
       LYS   31              -59.0  -86.0   73.0 -154.0  180.0
       LYS   32             -172.0   64.0 -169.0  -59.0  180.0
       LYS   33              -64.0 -176.0   63.0   64.0  180.0
       LYS   34              -73.0   87.0 -175.0   60.0  180.0
       LYS   35              -84.0  104.0   94.0 -169.0  180.0
       LYS   36             -178.0  170.0  -72.0  -65.0  180.0
       LYS   37              -78.0  100.0  -82.0  170.0  180.0
       LYS   38             -176.0 -173.0  -70.0   96.0  180.0
       LYS   39               67.0  175.0  109.0   51.0  180.0
       LYS   40             -142.0 -114.0  168.0  -61.0  180.0
       LYS   41             -107.0   60.0   60.0   64.0  180.0
       LYS   42             -178.0  -87.0  -75.0 -179.0  180.0
       LYS   43             -147.0  -80.0  176.0   81.0  180.0
       LYS   44             -147.0 -113.0  -80.0  -97.0  180.0
       LYS   45              177.0 -109.0  102.0 -170.0  180.0
       LYS   46               78.0   93.0  180.0  180.0  180.0
       LYS   47              -60.0  -75.0   99.0   74.0  180.0
       LYS   48             -120.0  103.0   91.0  -44.0  180.0
       LYS   49              -84.0  165.0   62.0  -96.0  180.0
--------------------------------------------------------------
   10) LEU    1    4   13    -65.0  175.0  180.0  180.0
       LEU    2             -179.0   64.0  180.0  180.0
       LEU    3             -105.0   30.0  180.0  180.0
       LEU    4             -152.0 -170.0  180.0  180.0
       LEU    5              -84.0   75.0  180.0  180.0
       LEU    6              -83.0  -49.0  180.0  180.0
       LEU    7             -167.0  -82.0  180.0  180.0
       LEU    8               65.0   88.0  180.0  180.0
       LEU    9               64.0  160.0  180.0  180.0
--------------------------------------------------------------
   11) MET    1    4   11    -69.0  176.0   70.0  180.0
       MET    2              -66.0 -175.0  -76.0  180.0
       MET    3              -67.0  177.0  179.0  180.0
       MET    4              -66.0  -59.0  -73.0  180.0
       MET    5              -64.0  -62.0  132.0  180.0
       MET    6             -176.0  179.0  -74.0  180.0
       MET    7             -177.0  179.0   82.0  180.0
       MET    8             -176.0  171.0 -178.0  180.0
       MET    9             -171.0   70.0   75.0  180.0
       MET   10             -165.0   71.0 -146.0  180.0
       MET   11               59.0  178.0  -65.0  180.0
       MET   12               59.0 -177.0   75.0  180.0
       MET   13             -177.0  -94.0  -77.0  180.0
       MET   14               48.0 -166.0 -174.0  180.0
       MET   15              -84.0   64.0 -156.0  180.0
       MET   16               60.0   90.0   68.0  180.0
       MET   17              -86.0   76.0  111.0  180.0
--------------------------------------------------------------
   12) ASN    1    2    8    -70.0  -40.0
       ASN    2             -167.0 -128.0
       ASN    3              -67.0  138.0
       ASN    4             -167.0    6.0
       ASN    5             -169.0   62.0
       ASN    6               65.0     .0
       ASN    7             -170.0  -46.0
       ASN    8               61.0   64.0
       ASN    9               58.0  -75.0
       ASN   10              -75.0   75.0
       ASN   11               68.0  179.0
--------------------------------------------------------------
   13) PRO    1    5    9     26.9  -29.4   21.1   -4.8  -13.8
       PRO    2              -21.8   31.2  -29.9   16.9    3.3
       PRO    3                 .3    -.8    1.0    -.9     .4
--------------------------------------------------------------
   14) GLN    1    3   11    -66.0  177.0   21.0
       GLN    2              -68.0 -179.0  -69.0
       GLN    3              -70.0 -179.0  150.0
       GLN    4             -174.0  174.0   28.0
       GLN    5             -178.0 -178.0 -157.0
       GLN    6             -173.0  174.0  -60.0
       GLN    7              -63.0  -60.0  -48.0
       GLN    8              -57.0  -62.0  126.0
       GLN    9             -177.0   63.0   52.0
       GLN   10             -177.0   60.0 -120.0
       GLN   11              -66.0   71.0   23.0
       GLN   12               60.0 -179.0   -2.0
       GLN   13               63.0 -173.0   96.0
       GLN   14               56.0 -175.0 -106.0
       GLN   15              -83.0   60.0 -121.0
       GLN   16             -175.0  -88.0  -21.0
       GLN   17              173.0 -113.0  100.0
       GLN   18               71.0  -91.0   35.0
       GLN   19               22.0   89.0  -20.0
--------------------------------------------------------------
   15) ARG    1    5   18    -70.0 -177.0  179.0  177.0  180.0
       ARG    2              -64.0 -167.0 -174.0  -97.0  180.0
       ARG    3              -65.0  175.0   60.0 -154.0  180.0
       ARG    4             -173.0  174.0  179.0  179.0  180.0
       ARG    5             -175.0  174.0  -68.0  158.0  180.0
       ARG    6              -71.0 -170.0  -66.0  -93.0  180.0
       ARG    7              -61.0 -177.0  -75.0  178.0  180.0
       ARG    8              -58.0  179.0   67.0   95.0  180.0
       ARG    9              -69.0 -177.0  178.0   90.0  180.0
       ARG   10             -176.0  179.0  177.0  -88.0  180.0
       ARG   11             -175.0  168.0   73.0 -132.0  180.0
       ARG   12             -177.0 -173.0  -64.0  -95.0  180.0
       ARG   13             -178.0  170.0   68.0   85.0  180.0
       ARG   14              -68.0 -168.0  -74.0  101.0  180.0
       ARG   15             -175.0  171.0  174.0   90.0  180.0
       ARG   16              -71.0  -60.0  -58.0  -87.0  180.0
       ARG   17              -63.0  -69.0  176.0  -95.0  180.0
       ARG   18              -62.0  -73.0  173.0 -175.0  180.0
       ARG   19             -140.0  -99.0  173.0  179.0  180.0
       ARG   20               68.0 -172.0  172.0 -167.0  180.0
       ARG   21               54.0  174.0 -177.0   94.0  180.0
       ARG   22             -115.0   93.0   91.0  150.0  180.0
       ARG   23             -179.0   76.0 -167.0  172.0  180.0
       ARG   24             -178.0   64.0 -177.0   94.0  180.0
       ARG   25             -178.0   83.0   81.0 -150.0  180.0
       ARG   26              -68.0  -62.0  -62.0  161.0  180.0
       ARG   27               62.0  178.0 -177.0  -84.0  180.0
       ARG   28             -174.0   58.0 -154.0  -90.0  180.0
       ARG   29             -119.0   69.0 -124.0 -134.0  180.0
       ARG   30               63.0 -174.0   68.0 -175.0  180.0
       ARG   31              -61.0  -65.0  178.0   92.0  180.0
       ARG   32               47.0 -179.0 -108.0  -95.0  180.0
       ARG   33              178.0   68.0   60.0   92.0  180.0
       ARG   34               59.0  176.0   74.0   91.0  180.0
       ARG   35              -70.0  -63.0   83.0   84.0  180.0
       ARG   36              178.0 -101.0  -70.0  159.0  180.0
       ARG   37               50.0  105.0   70.0  169.0  180.0
       ARG   38               57.0  165.0  -87.0 -168.0  180.0
       ARG   39              -61.0  -65.0   90.0 -163.0  180.0
--------------------------------------------------------------
   16) SER    1    2    5     62.0  180.0
       SER    2              -63.0  180.0
       SER    3             -178.0  180.0
--------------------------------------------------------------
   17) THR    1    3    8    -61.0  180.0  180.0
       THR    2               61.0  180.0  180.0
       THR    3             -172.0  180.0  180.0
--------------------------------------------------------------
   18) VAL    1    3   10    173.0  180.0  180.0
       VAL    2              -62.0  180.0  180.0
       VAL    3               66.0  180.0  180.0
--------------------------------------------------------------
   19) TRP    1    2   18    -68.0   97.0
       TRP    2             -175.0 -106.0
       TRP    3              -71.0  -10.0
       TRP    4              178.0   77.0
       TRP    5               62.0  -89.0
       TRP    6              -68.0  -87.0
       TRP    7               61.0   81.0
       TRP    8             -173.0   21.0
--------------------------------------------------------------
   20) TYR    1    3   15    179.0   70.0  180.0
       TYR    2              -64.0  -77.0  180.0
       TYR    3              -67.0   82.0  180.0
       TYR    4              -68.0  -29.0  180.0
       TYR    5             -178.0  -83.0  180.0
       TYR    6               62.0   81.0  180.0
       TYR    7               63.0  -81.0  180.0
       TYR    8              -61.0  137.0  180.0

Backbone independent rotamer library build upon a survey of 53 protein structures resolved at 2.0 Angstroms or better (1990). Chi3 poorly defined. Chi4 to Chi5 not defined.

       Pept  Num  NChi  Natm  Chi1   Chi2   Chi3   Chi4   Chi5
--------------------------------------------------------------
    1) ALA    1    1    4    180.0
--------------------------------------------------------------
    2) CYS    1    2    5    -65.0  180.0
       CYS    2             -178.0  180.0
       CYS    3               64.0  180.0
--------------------------------------------------------------
    3) ASP    1    2    6    -70.0  -32.0
       ASP    2             -171.0 -171.0
       ASP    3               62.0    4.0
--------------------------------------------------------------
    4) GLU    1    3    9    -66.0  178.0  174.0
       GLU    2              -69.0  180.0  -15.0
       GLU    3              -64.0  -65.0  -45.0
       GLU    4             -174.0  176.0 -173.0
       GLU    5              179.0  175.0    8.0
       GLU    6             -175.0   70.0   57.0
       GLU    7              -65.0   79.0    8.0
       GLU    8               72.0  178.0   41.0
       GLU    9               50.0  -87.0 -161.0
       GLU   10               65.0  176.0 -120.0
--------------------------------------------------------------
    5) PHE    1    2   14    -69.0   93.0
       PHE    2              178.0   73.0
       PHE    3               65.0   89.0
       PHE    4              -70.0  -20.0
--------------------------------------------------------------
    6) GLY    1    0    1
--------------------------------------------------------------
    7) HIS    1    2   11    -62.0  -84.0
       HIS    2             -177.0   68.0
       HIS    3              -67.0   97.0
       HIS    4             -168.0 -108.0
       HIS    5               64.0  -95.0
       HIS    6               68.0   81.0
--------------------------------------------------------------
    8) ILE    1    4   13    -62.0  163.0  180.0  180.0
       ILE    2               63.0  164.0  180.0  180.0
       ILE    3              -57.0  -59.0  180.0  180.0
       ILE    4             -168.0  161.0  180.0  180.0
       ILE    5             -156.0   72.0  180.0  180.0
--------------------------------------------------------------
    9) LYS    1    5   16    -70.0 -179.0  180.0  180.0  180.0
       LYS    2             -172.0  180.0  180.0  180.0  180.0
       LYS    3              -61.0  -71.0 -178.0  180.0  180.0
       LYS    4             -173.0 -174.0   77.0  180.0  180.0
       LYS    5             -174.0   70.0 -174.0  180.0  180.0
       LYS    6               70.0 -172.0  179.0  180.0  180.0
       LYS    7              -69.0  178.0   79.0  180.0  180.0
       LYS    8              -71.0 -172.0  -72.0  180.0  180.0
       LYS    9             -170.0 -176.0  -74.0  180.0  180.0
       LYS   10              -71.0   90.0 -168.0  180.0  180.0
       LYS   11              -70.0  -83.0  -80.0  180.0  180.0
       LYS   12               69.0 -156.0  -75.0  180.0  180.0
       LYS   13             -160.0   82.0   75.0  180.0  180.0
       LYS   14               70.0  175.0   67.0  180.0  180.0
       LYS   15              -73.0  -99.0   69.0  180.0  180.0
       LYS   16              -64.0   89.0   77.0  180.0  180.0
--------------------------------------------------------------
   10) LEU    1    4   13    -62.0  170.0  180.0  180.0
       LEU    2             -176.0   66.0  180.0  180.0
       LEU    3              -99.0   25.0  180.0  180.0
       LEU    4             -168.0 -161.0  180.0  180.0
       LEU    5              -83.0  -80.0  180.0  180.0
       LEU    6               61.0   85.0  180.0  180.0
--------------------------------------------------------------
   11) MET    1    4   11    -66.0  -67.0  -67.0  180.0
       MET    2              -68.0  180.0   74.0  180.0
       MET    3              -72.0  179.0  180.0  180.0
       MET    4              179.0  178.0   77.0  180.0
       MET    5             -169.0 -169.0 -101.0  180.0
       MET    6              -61.0  -67.0  131.0  180.0
       MET    7             -170.0   65.0   76.0  180.0
       MET    8               80.0 -172.0  180.0  180.0
       MET    9              -74.0 -173.0  -82.0  180.0
       MET   10              -66.0  -67.0  140.0  180.0
--------------------------------------------------------------
   12) ASN    1    2    8    -72.0  -44.0
       ASN    2             -171.0   12.0
       ASN    3              -69.0  131.0
       ASN    4               66.0   12.0
--------------------------------------------------------------
   13) PRO    1    5    9     26.9  -29.4   22.8   -5.5  -14.2
       PRO    2              -21.8   31.2  -30.9   17.3    3.3
       PRO    3                0.3   -0.8    1.3   -1.1    0.5
--------------------------------------------------------------
   14) GLN    1    3   11    -63.0  178.0   -3.0
       GLN    2              -68.0 -179.0 -176.0
       GLN    3              -68.0  -64.0  -42.0
       GLN    4             -173.0  180.0    1.0
       GLN    5             -172.0   68.0   32.0
       GLN    6              -66.0  -70.0  140.0
       GLN    7             -174.0 -177.0  179.0
       GLN    8             -170.0   68.0 -124.0
       GLN    9               69.0 -173.0  -10.0
       GLN   10               64.0 -169.0  116.0
--------------------------------------------------------------
   15) ARG    1    5   18   -176.0  156.0 -175.0  180.0  180.0
       ARG    2              -67.0 -176.0  -76.0  180.0  180.0
       ARG    3             -178.0  171.0   62.0  180.0  180.0
       ARG    4              -72.0  166.0   72.0  180.0  180.0
       ARG    5              -60.0  -60.0  171.0  180.0  180.0
       ARG    6               78.0  171.0  172.0  180.0  180.0
       ARG    7             -172.0 -170.0  -66.0  180.0  180.0
       ARG    8              -69.0  175.0  180.0  180.0  180.0
       ARG    9              -59.0  -74.0  -75.0  180.0  180.0
       ARG   10               66.0  158.0   74.0  180.0  180.0
       ARG   11               74.0 -169.0  -80.0  180.0  180.0
--------------------------------------------------------------
   16) SER    1    2    5     65.0  180.0
       SER    2              -63.0  180.0
       SER    3             -178.0  180.0
--------------------------------------------------------------
   17) THR    1    3    8    -61.0  180.0  180.0
       THR    2               65.0  180.0  180.0
       THR    3             -160.0  180.0  180.0
--------------------------------------------------------------
   18) VAL    1    3   10    173.0  180.0  180.0
       VAL    2              -62.0  180.0  180.0
       VAL    3               72.0  180.0  180.0
--------------------------------------------------------------
   19) TRP    1    2   18   -178.0   82.0
       TRP    2              -67.0   85.0
       TRP    3             -174.0 -101.0
       TRP    4               64.0   93.0
       TRP    5               57.0  -86.0
       TRP    6              -74.0  -86.0
       TRP    7              -73.0    4.0
--------------------------------------------------------------
   20) TYR    1    3   15    -64.0  102.0  180.0
       TYR    2              -66.0  -87.0  180.0
       TYR    3             -178.0   74.0  180.0
       TYR    4             -177.0 -103.0  180.0
       TYR    5               65.0  -96.0  180.0
       TYR    6               62.0   89.0  180.0

P. Tuffery <tuffery@urbb.jussieu.fr>

Last modified: Sat Mar 1 13:49:37 1997