Contacts of the strand formed by residues 160 - 166 (chain F) in PDB entry 3LUE


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 160 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  PRO*     3.2     6.8    -      -       -      +
    110F  LEU*     3.4     0.2    -      -       -      +
    153F  MET*     3.5    19.3    -      -       -      -
    154F  ASP      3.1    12.6    -      -       -      +
    155F  SER*     2.9    19.5    +      -       -      +
    159F  VAL*     1.3    73.1    -      -       -      +
    161F  HIS*     1.3    63.3    +      -       -      +
    162F  THR*     5.3     1.1    -      -       +      -
    177F  ARG*     3.3     3.8    -      -       -      -
    178F  LEU*     2.7    44.7    +      -       +      -
    180F  LEU      2.8    22.5    +      -       -      -
    261F  LEU*     5.0     0.5    -      -       -      +
    274F  ILE*     3.4    28.1    -      -       +      +
    277F  THR*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  PRO*     1.6    39.9    -      -       +      +
    110F  LEU*     2.1    39.9    +      -       -      -
    136F  ILE*     4.2    22.5    -      -       +      +
    138F  ALA*     4.7     0.3    -      -       -      +
    152F  VAL      3.7     1.2    -      -       -      +
    153F  MET*     3.5     2.6    -      -       -      -
    154F  ASP*     2.9    34.3    +      -       +      +
    160F  THR*     1.3    75.3    -      -       -      +
    162F  THR*     1.3    64.0    +      -       -      +
    163F  VAL*     3.9    15.0    +      -       +      -
    175F  ILE*     3.3    22.3    -      -       +      +
    176F  LEU      3.0    17.9    -      -       -      -
    177F  ARG*     3.3    14.8    -      -       +      +
    277F  THR*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151F  ILE*     4.3     4.9    -      -       +      -
    152F  VAL      3.4     4.9    -      -       -      +
    153F  MET*     3.6    19.5    -      -       +      -
    160F  THR*     5.3     1.8    -      -       +      -
    161F  HIS*     1.3    75.6    -      -       -      +
    163F  VAL*     1.3    59.5    +      -       -      +
    164F  PRO*     4.3     0.2    -      -       -      -
    175F  ILE*     3.3     6.1    -      -       -      -
    176F  LEU*     3.0    29.1    +      -       -      +
    274F  ILE*     4.9     1.3    -      -       +      +
    277F  THR*     3.4    25.3    +      -       +      +
    278F  THR*     3.4    38.6    -      -       -      +
    281F  SER*     3.0    25.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136F  ILE*     5.4     2.5    -      -       +      -
    138F  ALA*     5.0     6.7    -      -       +      -
    139F  VAL*     3.6    33.4    -      -       +      -
    151F  ILE*     3.2    23.3    -      -       -      +
    152F  VAL*     3.2    16.2    +      -       +      +
    161F  HIS*     3.9    20.2    -      -       +      +
    162F  THR*     1.3    77.3    -      -       -      +
    164F  PRO*     1.3    61.1    -      -       -      +
    165F  ILE*     3.8    16.8    +      -       +      +
    170F  ALA*     3.8    23.6    -      -       +      -
    175F  ILE*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150F  GLY      3.8     5.8    -      -       -      +
    151F  ILE*     4.0     6.7    -      -       +      -
    162F  THR      4.1     0.2    -      -       -      +
    163F  VAL*     1.3    82.6    -      -       -      +
    165F  ILE*     1.3    54.3    +      -       -      +
    170F  ALA*     3.5     2.1    -      -       -      -
    171F  LEU*     2.7    43.0    +      -       +      +
    174F  ALA*     3.5    31.6    -      -       +      +
    175F  ILE*     4.1     2.5    -      -       +      +
    281F  SER*     3.8    14.1    -      -       -      -
    285F  CYS*     3.2    37.0    -      -       -      -
    293F  LEU*     3.8    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  VAL*     2.1    19.7    -      -       -      +
     44D  MET*     1.3   111.1    -      -       +      +
     61D  LYS*     3.1     5.4    -      -       -      -
    139F  VAL*     5.3     4.5    -      -       +      -
    142F  LEU*     1.5    58.1    -      -       +      -
    148F  THR      3.4     1.1    -      -       -      +
    149F  THR*     3.2     0.5    -      -       -      +
    150F  GLY      2.9    17.0    +      -       -      +
    152F  VAL*     4.1     5.4    -      -       +      -
    163F  VAL*     3.9    20.6    -      -       +      +
    164F  PRO*     1.3    75.3    -      -       -      +
    166F  TYR*     1.3    56.1    +      -       -      +
    169F  TYR      3.2     5.6    -      -       -      +
    170F  ALA*     3.8    13.2    -      -       +      -
    171F  LEU*     4.7     0.9    -      -       -      -
    293F  LEU*     4.1     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  TYR*     3.0     2.9    -      -       -      -
     57D  GLU      2.1    27.8    -      -       -      -
     58D  ALA*     1.5    49.6    -      -       +      +
     61D  LYS*     0.8   353.3    -      -       +      +
     64D  ILE*     3.0    20.0    -      -       +      +
     65D  LEU*     2.3    43.3    -      -       +      +
    165F  ILE*     1.3    62.3    -      -       -      +
    167F  GLU*     1.3    71.6    +      -       +      +
    168F  GLY      3.4     0.4    -      -       -      -
    169F  TYR*     2.9    26.5    +      -       -      +
    289F  ILE*     3.8     2.2    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il