Contacts of the strand formed by residues 118 - 121 (chain A) in PDB entry 4WNC


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 ARG 118 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLU      3.3     3.3    +      -       -      +
     94A  TYR*     3.3    42.5    +      -       +      -
     95A  VAL*     3.0    24.1    +      -       -      +
    112A  LEU*     4.5     0.4    -      -       -      -
    116A  ALA*     3.7     1.9    -      -       -      +
    117A  LYS*     1.3    86.0    -      -       +      +
    119A  VAL*     1.3    69.8    +      -       -      +
    120A  ILE*     4.7     5.2    -      -       +      -
    140A  TYR*     3.2    23.7    +      -       -      -
    142A  ASN*     2.9    45.2    +      -       -      +
    144A  LEU      2.8    32.9    +      -       -      -
    145A  LYS*     3.1    23.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  VAL*     3.3    11.2    -      -       +      +
     97A  GLU*     3.9    22.9    -      -       +      -
    108A  ALA*     3.7    29.6    -      -       +      +
    111A  HIS*     3.8    28.3    -      -       +      -
    112A  LEU*     4.2    15.0    -      -       +      -
    116A  ALA*     5.0     0.4    -      -       +      -
    118A  ARG*     1.3    80.0    -      -       -      +
    120A  ILE*     1.3    67.5    +      -       -      +
    121A  ILE*     4.0     2.0    -      -       +      +
    145A  LYS      2.8     8.1    +      -       -      +
    146A  ILE*     3.4    13.7    -      -       +      -
    147A  ILE*     2.9    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  TYR*     4.0    20.9    -      -       +      -
     95A  VAL      2.8    15.8    +      -       -      +
     96A  VAL*     3.4     8.5    -      -       +      +
     97A  GLU      2.8    25.2    +      -       -      -
    118A  ARG*     4.7     3.4    -      -       +      -
    119A  VAL*     1.3    79.5    -      -       -      +
    121A  ILE*     1.3    71.0    +      -       -      +
    122A  SER      3.5     0.9    +      -       -      -
    147A  ILE*     3.5    20.9    -      -       +      +
    149A  ASN*     4.4     8.5    -      -       +      +
    324A  VAL*     4.5    17.0    -      -       +      +
    327A  LEU*     4.2    22.9    -      -       +      -
    328A  MET*     3.6    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLU*     3.8    12.8    -      -       +      +
    102A  PHE      4.4     3.4    -      -       -      +
    103A  THR*     3.5    46.0    -      -       +      +
    104A  THR      4.3     2.0    -      -       -      +
    108A  ALA*     3.8    30.5    -      -       +      -
    119A  VAL*     4.6     0.9    -      -       +      -
    120A  ILE*     1.3    72.4    -      -       -      +
    122A  SER*     1.3    59.2    +      -       -      +
    123A  ALA*     3.0    28.6    +      -       +      +
    125A  SER*     4.1     2.0    -      -       -      +
    128A  ALA*     3.9    13.9    -      -       +      -
    146A  ILE*     3.9    16.6    -      -       +      -
    147A  ILE      2.8    17.9    +      -       -      +
    148A  SER*     3.5     2.5    -      -       -      -
    149A  ASN*     3.1    24.3    +      -       -      +
----------------------------------------------------------
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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