Contacts of the strand formed by residues 161 - 164 (chain E) in PDB entry 4WFN


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 GLY 161 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89E  LEU*     4.7     4.5    -      -       -      -
     90E  ARG*     2.9    38.2    +      -       -      +
     94E  PHE*     4.1     8.3    -      -       -      -
    107E  ILE*     5.0     1.1    -      -       -      -
    152E  ARG*     3.7    25.1    -      -       -      -
    160E  LYS*     1.3    77.7    -      -       -      +
    162E  VAL*     1.3    66.4    +      -       -      -
    163E  ARG*     3.5     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87E  LEU*     3.6    41.5    -      -       +      -
     88E  GLU      3.5     6.5    -      -       -      +
     89E  LEU*     3.6    21.1    -      -       +      -
    105E  MET*     4.7     1.6    -      -       -      -
    107E  ILE*     4.1    14.6    -      -       +      -
    131E  ILE*     5.2     0.9    -      -       +      -
    148E  VAL*     3.2    26.7    -      -       +      +
    149E  ARG*     3.7    23.1    -      -       +      +
    151E  VAL*     4.6     0.7    -      -       +      -
    152E  ARG*     3.4    11.9    +      -       -      +
    154E  PRO*     3.5    19.6    -      -       -      +
    161E  GLY*     1.3    69.6    -      -       -      -
    163E  ARG*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87E  LEU*     3.7     6.7    -      -       -      +
     88E  GLU*     2.9    45.6    +      -       +      +
     90E  ARG*     3.3    48.8    -      -       +      +
    149E  ARG*     5.5     2.0    -      -       -      -
    154E  PRO*     4.4    11.2    -      -       +      +
    158E  HIS      5.1     0.6    +      -       -      -
    159E  GLY*     3.0    29.8    +      -       -      -
    161E  GLY      3.5     1.3    +      -       -      +
    162E  VAL*     1.3    75.2    -      -       -      +
    164E  PHE*     1.3    61.8    +      -       -      +
    165E  VAL      3.4     3.3    +      -       -      +
    167E  GLU*     3.8    31.2    +      -       +      +
    168E  GLN*     4.4     1.6    -      -       -      +
    169E  ILE*     3.4    43.1    -      -       -      +
    171E  LEU*     5.5     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85E  ILE*     4.1    39.9    -      -       +      -
     86E  ASN      4.0     1.8    -      -       -      -
     87E  LEU*     3.5    20.6    -      -       +      -
    145E  ALA*     5.6     2.5    -      -       +      -
    149E  ARG*     3.2    40.7    -      -       -      +
    163E  ARG*     1.3    73.7    -      -       -      +
    165E  VAL*     1.3    85.4    +      -       +      +
    166E  GLY      3.1     0.5    +      -       -      -
    167E  GLU*     2.8    46.7    +      -       +      +
----------------------------------------------------------
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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