Contacts of the strand formed by residues 465 - 470 (chain A) in PDB entry 4R2G


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 ILE 465 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  LYS*     4.1     2.2    +      -       -      +
    358A  THR*     2.9    36.1    -      -       +      +
    360A  VAL*     3.9    26.2    -      -       +      -
    394A  THR*     6.2     0.9    -      -       +      -
    463A  SER*     2.9    30.6    +      -       -      +
    464A  GLU*     1.3    84.7    -      -       +      +
    466A  GLU*     1.3    80.4    +      -       -      +
    467A  ILE*     4.4     8.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  PHE*     3.9    21.0    -      -       +      -
    357A  LYS*     3.5    34.4    +      -       +      +
    358A  THR      2.9     5.2    +      -       -      +
    359A  ILE*     3.3    14.7    -      -       +      +
    360A  VAL      2.9    26.0    +      -       -      +
    456A  ARG*     3.1    40.0    +      -       -      +
    458A  GLY*     4.3    10.5    +      -       -      -
    463A  SER*     5.2     0.5    +      -       -      -
    465A  ILE*     1.3    83.2    -      -       -      +
    467A  ILE*     1.3    67.1    +      -       -      +
    468A  PHE*     3.7    19.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  VAL*     3.3    20.2    -      -       +      +
    362A  THR*     3.4    30.1    -      -       -      +
    456A  ARG*     3.1    23.7    -      -       -      +
    457A  ASP*     3.1    41.9    +      -       +      +
    458A  GLY      5.6     0.2    -      -       -      +
    463A  SER*     6.6     0.2    -      -       -      -
    465A  ILE*     4.7     9.2    -      -       +      +
    466A  GLU*     1.3    82.3    +      -       -      +
    468A  PHE*     1.3    63.6    +      -       -      +
    469A  ARG*     4.7     5.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  ILE*     3.6    23.3    -      -       +      -
    349A  LEU*     3.6    39.7    -      -       +      -
    353A  PHE*     3.6    17.3    -      +       -      -
    359A  ILE*     3.8    14.6    -      -       +      -
    360A  VAL      2.9    11.2    +      -       -      -
    361A  PHE*     3.5    24.3    -      +       +      -
    362A  THR      3.0    21.7    +      -       -      +
    391A  PHE*     5.1     0.9    -      -       -      +
    454A  LEU*     4.6    16.3    -      -       +      +
    455A  THR      3.5     4.7    -      -       -      +
    456A  ARG*     3.5    35.0    -      -       +      -
    466A  GLU*     3.7    27.4    -      -       +      -
    467A  ILE*     1.3    73.2    -      -       -      +
    469A  ARG*     1.3    62.3    +      -       -      +
    470A  PRO*     4.6     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  THR*     3.4    22.2    -      -       -      +
    363A  HIS*     3.3    31.6    +      -       -      +
    364A  SER*     4.3     2.4    +      -       -      -
    365A  SER*     3.2    41.3    -      -       -      +
    454A  LEU*     3.4     5.7    -      -       -      -
    455A  THR*     2.9    39.4    +      -       -      +
    457A  ASP*     2.8    41.3    +      -       -      +
    467A  ILE*     4.7     6.4    -      -       +      +
    468A  PHE*     1.3    80.1    -      -       -      +
    470A  PRO*     1.3    76.1    -      -       +      +
     48L  PRO*     3.6    15.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  GLN*     3.7    41.7    -      -       +      +
    362A  THR      3.2    17.0    -      -       -      +
    363A  HIS*     4.7     0.9    -      -       -      -
    364A  SER*     3.9    26.1    +      -       -      +
    371A  ILE      4.8     1.0    -      -       -      +
    387A  SER*     4.2     3.1    -      -       -      +
    391A  PHE*     4.0    30.3    -      -       +      -
    453A  LEU      3.4     7.9    -      -       -      +
    454A  LEU*     3.9     5.3    -      -       +      -
    455A  THR*     4.6     2.9    +      -       -      -
    469A  ARG*     1.3    94.7    -      -       +      +
    471A  GLY*     1.3    58.3    +      -       -      +
----------------------------------------------------------
 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