Contacts of the strand formed by residues 216 - 219 (chain C) in PDB entry 5GJQ


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 216 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  LYS      3.3    13.9    -      -       -      -
     70C  HIS*     4.6     7.6    -      -       -      -
    138C  TRP*     6.0     0.2    -      -       -      -
    211C  ILE*     4.1     1.4    -      -       -      +
    212C  CYS*     4.0     1.4    -      -       -      -
    213C  ASN*     3.3    30.3    +      -       -      +
    214C  GLU      3.7     1.0    -      -       -      -
    215C  ALA*     1.3    79.2    -      -       -      +
    217C  PHE*     1.3    64.8    +      -       -      -
    218C  ARG*     3.8     4.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 217 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  LEU*     4.7     1.8    -      -       +      -
     64C  VAL*     3.7    29.2    -      -       +      -
     65C  GLU      4.0     2.0    -      -       -      -
     66C  PRO*     3.7    43.6    -      -       +      +
     68C  THR      5.2     0.9    -      -       -      +
     69C  LYS*     2.9    15.2    +      -       -      +
     70C  HIS*     4.0     4.5    -      -       -      +
     71C  ILE      3.9    20.6    -      -       -      +
     72C  GLY*     3.6    17.5    -      -       -      -
    136C  CYS*     3.6    26.2    -      -       -      -
    210C  GLY*     4.3     3.8    -      -       -      -
    211C  ILE      3.1    31.0    -      -       -      -
    212C  CYS*     3.9     5.2    -      -       +      +
    216C  GLY*     1.3    72.7    -      -       -      -
    218C  ARG*     1.3    77.7    +      -       -      +
    219C  ARG*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 218 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  GLY*     3.4     1.9    -      -       -      -
    211C  ILE*     2.9    56.2    +      -       +      +
    216C  GLY      3.8     2.4    +      -       -      +
    217C  PHE*     1.3    87.0    -      -       -      +
    219C  ARG*     1.3    76.6    +      -       -      +
    220C  LEU*     3.8    14.4    -      -       -      +
    221C  THR*     4.5     6.1    -      -       -      +
    224C  GLU*     3.0    41.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 219 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  HIS*     3.1    42.4    +      -       -      +
     64C  VAL*     2.9    31.5    +      -       +      +
     65C  GLU*     4.0     5.1    +      -       -      -
     66C  PRO*     3.7    20.8    -      -       -      +
    208C  GLU*     3.4    30.3    +      -       +      -
    209C  VAL      3.5    17.3    -      -       -      +
    210C  GLY*     4.2     2.0    -      -       -      -
    217C  PHE*     4.5     5.0    -      -       +      -
    218C  ARG*     1.3    91.0    +      -       -      +
    220C  LEU*     1.3    71.4    +      -       -      +
    221C  THR*     3.7     2.3    +      -       -      +
----------------------------------------------------------
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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