Contacts of the strand formed by residues 352 - 356 (chain G) in PDB entry 2HU4


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 PHE 352 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279G  SER*     3.7    10.5    -      -       -      -
    290G  VAL*     3.9    11.2    -      -       -      +
    300G  ARG*     4.1     6.1    -      -       -      +
    351G  GLY*     1.3    74.8    -      -       -      +
    353G  SER*     1.3    78.5    +      -       -      +
    354G  PHE*     3.9    22.7    -      +       -      -
    361G  TRP      5.0     0.4    -      -       -      -
    362G  ILE*     5.0     0.5    -      -       -      +
    363G  GLY*     3.9    22.7    +      -       -      +
    374G  PHE*     4.0    11.0    -      +       -      -
    376G  MET*     3.7    30.7    -      -       +      -
    407G  SER*     3.5    20.9    -      -       -      -
    408G  GLY      3.8     9.6    -      -       -      -
    409G  SER*     3.7    25.4    -      -       -      +
    422G  PHE*     3.5    41.7    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 353 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279G  SER      5.6     0.2    -      -       -      +
    281G  TYR*     3.4    20.8    +      -       -      -
    290G  VAL*     3.5    21.0    -      -       -      +
    300G  ARG*     4.9     2.6    -      -       -      -
    317G  ILE*     3.7    30.7    -      -       -      +
    352G  PHE*     1.3    86.5    +      -       -      +
    354G  PHE*     1.3    67.8    +      -       -      +
    360G  VAL*     5.2     2.5    -      -       -      -
    361G  TRP      3.4    14.4    +      -       -      -
    362G  ILE*     3.9    16.3    -      -       -      +
    383G  TRP*     5.1     2.2    -      -       -      -
    409G  SER*     5.7     0.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 354 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  LEU*     4.3     5.8    -      -       +      -
     97G  TRP*     3.6    27.4    -      +       -      -
    281G  TYR*     3.7    42.4    -      +       +      -
    352G  PHE*     3.9    20.4    -      +       -      -
    353G  SER*     1.3    73.8    -      -       -      +
    355G  LYS*     1.3    60.4    +      -       -      +
    356G  TYR*     3.9    19.6    +      -       +      -
    360G  VAL*     3.2     8.6    -      -       -      +
    361G  TRP*     2.9    38.9    +      -       +      -
    409G  SER*     3.5    17.5    -      -       -      -
    410G  PHE      4.5     2.5    -      -       -      -
    411G  VAL*     5.6     0.9    -      -       +      -
    420G  PRO*     3.6    28.7    -      -       +      -
    421G  CYS      3.4    27.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 355 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  LEU*     4.0    12.7    -      -       -      +
    281G  TYR*     3.0    19.3    +      -       -      +
    283G  ASN*     5.6     1.9    +      -       -      -
    288G  THR*     5.1     4.9    -      -       +      +
    353G  SER      4.1     0.4    +      -       -      -
    354G  PHE*     1.3    72.8    -      -       -      +
    356G  TYR*     1.3    66.7    +      -       -      +
    357G  GLY*     2.4    39.3    +      -       -      +
    358G  ASN*     4.8     2.6    +      -       -      +
    359G  GLY      3.7     5.2    -      -       -      +
    360G  VAL*     4.2     0.7    -      -       -      -
    383G  TRP*     3.3    61.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 356 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  LEU*     3.6    29.1    -      -       +      +
     92G  CYS      2.7    32.2    +      -       -      -
     93G  PRO*     4.2     8.1    -      -       +      -
     94G  ILE*     3.8    11.2    -      -       +      +
    354G  PHE*     3.9    23.5    +      +       +      -
    355G  LYS*     1.3    75.5    -      -       -      +
    357G  GLY*     1.3    59.0    -      -       -      +
    358G  ASN      3.0     0.7    +      -       -      -
    359G  GLY*     2.8    29.7    +      -       -      +
    361G  TRP*     4.2    24.9    -      +       -      -
    378G  TRP*     4.0    19.4    -      +       +      -
    420G  PRO*     3.3    21.7    -      -       -      +
----------------------------------------------------------
 Back to top of page


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