Contacts of the strand formed by residues 320 - 324 (chain I) in PDB entry 6RAR


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 320 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166I  ILE*     3.9     2.1    -      -       -      +
    167I  LYS*     3.1    20.1    +      -       -      +
    310I  ASN*     4.4     7.0    -      -       -      -
    313I  ALA*     3.3    15.7    -      -       -      +
    314I  VAL*     4.7     7.0    -      -       -      -
    318I  TYR      3.3     3.2    +      -       -      -
    319I  GLU*     1.3    79.8    -      -       -      +
    321I  VAL*     1.3    68.9    +      -       -      +
    341I  ALA      3.3    11.9    -      -       -      -
    342I  LYS*     4.6     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 321 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164I  ILE*     4.1    13.2    -      -       +      -
    165I  GLU      3.2    13.2    -      -       -      +
    166I  ILE*     4.7     4.0    -      -       +      -
    167I  LYS*     3.9     6.3    -      -       -      +
    306I  PHE*     3.9    24.2    -      -       +      -
    309I  LEU*     4.1     4.3    -      -       +      +
    310I  ASN*     3.6    28.7    -      -       +      +
    313I  ALA*     3.5    19.3    -      -       +      -
    320I  GLY*     1.3    79.3    -      -       -      +
    322I  MET*     1.3    65.3    +      -       -      +
    323I  ILE*     4.5     2.7    -      -       +      -
    340I  LYS*     3.6     2.9    -      -       -      -
    341I  ALA*     3.0    43.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 322 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  AMP      3.4    54.5    -      -       +      +
    148I  ALA*     3.8    28.5    -      -       +      -
    163I  GLN      3.6     0.7    -      -       -      +
    164I  ILE*     3.3    10.2    -      -       -      +
    165I  GLU*     2.7    36.3    +      -       +      +
    166I  ILE      4.2     0.7    -      -       -      +
    167I  LYS*     3.9    31.4    -      -       +      -
    321I  VAL*     1.3    77.4    -      -       -      +
    323I  ILE*     1.3    62.0    +      -       -      +
    324I  LYS*     4.0    18.4    -      -       +      -
    338I  TRP*     4.3    11.7    -      -       +      -
    339I  LEU      3.4    11.7    -      -       -      +
    340I  LYS*     4.0     5.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 323 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151I  SER*     3.8    23.1    -      -       -      +
    158I  MET*     3.6    33.2    -      -       +      -
    162I  LYS*     3.7    31.3    +      -       +      +
    163I  GLN      3.8     1.8    -      -       -      -
    164I  ILE*     3.6    15.7    -      -       +      -
    297I  LEU*     4.8     0.9    -      -       +      -
    306I  PHE*     3.7    28.9    -      -       +      -
    321I  VAL*     4.5     1.3    -      -       +      -
    322I  MET*     1.3    76.5    -      -       -      +
    324I  LYS*     1.3    60.2    +      -       -      +
    336I  HIS      5.0     0.2    -      -       -      +
    337I  SER      3.5     2.8    -      -       -      +
    339I  LEU*     2.7    45.2    +      -       +      +
    340I  LYS      4.3     1.1    -      -       -      -
    341I  ALA*     4.0    11.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 324 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  AMP      3.0    37.1    +      -       -      -
    162I  LYS*     3.4     7.0    -      -       -      -
    163I  GLN*     2.7    50.0    +      -       +      +
    165I  GLU*     3.3    31.0    +      -       -      +
    249I  PHE*     3.7    17.6    +      -       -      +
    266I  GLN*     3.6    28.6    -      -       -      +
    322I  MET*     4.0    11.9    -      -       +      -
    323I  ILE*     1.3    81.2    -      -       -      +
    325I  ASP*     1.3    62.2    +      -       -      +
    326I  PRO*     3.4     1.7    -      -       -      +
    337I  SER      3.1     5.2    -      -       -      +
    338I  TRP*     3.7    28.1    -      -       +      +
----------------------------------------------------------
 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