Contacts of the strand formed by residues 189 - 192 (chain C) in PDB entry 5GAG


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 189 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  LYS      3.5    20.7    +      -       -      +
     69C  ARG      3.5    18.7    +      -       -      -
     70C  ASN*     4.4    10.1    +      -       -      +
     72C  ASP*     2.7    36.5    +      -       -      -
    118C  SER*     4.1     7.1    -      -       -      -
    119C  GLY*     4.2     8.6    -      -       -      +
    120C  VAL      5.3     0.2    -      -       -      +
    129C  THR*     3.6    26.4    -      -       +      +
    130C  LEU*     3.3    15.3    -      -       -      +
    131C  PRO*     4.5    11.0    -      -       +      +
    132C  MET*     4.5     0.9    -      -       -      -
    143C  ASN      3.7     3.8    -      -       -      +
    144C  VAL*     3.8     1.4    -      -       -      +
    145C  GLU*     3.1    48.0    +      -       +      +
    149C  GLY*     6.0     1.8    -      -       -      +
    187C  ASP      4.9     3.4    -      -       -      +
    188C  CYS*     1.3    77.1    -      -       -      +
    190C  ALA*     1.3    60.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 190 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  ASN      4.1     0.3    -      -       -      +
    129C  THR*     3.2     6.6    -      -       -      +
    130C  LEU*     3.0    31.8    +      -       -      +
    132C  MET*     3.9    17.0    -      -       -      +
    135C  ILE*     4.3     6.7    -      -       +      +
    141C  VAL*     3.7    33.2    -      -       +      -
    142C  HIS      3.9     3.8    -      -       -      +
    143C  ASN      3.7     7.0    -      -       -      -
    144C  VAL*     4.1     6.3    -      -       +      -
    188C  CYS      4.0     0.6    +      -       -      -
    189C  ARG*     1.3    75.9    -      -       -      +
    191C  THR*     1.3    64.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 191 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  ARG*     3.8     8.4    +      -       -      +
    107C  PRO*     5.5     0.4    -      -       +      -
    127C  GLY*     3.6    26.5    -      -       -      +
    128C  ASN      3.6     2.2    -      -       -      -
    129C  THR*     3.1    23.5    +      -       -      +
    141C  VAL*     3.2     4.9    -      -       -      +
    142C  HIS*     2.8    64.9    +      -       +      +
    143C  ASN*     3.4    22.5    +      -       -      -
    190C  ALA*     1.3    74.5    -      -       -      +
    192C  LEU*     1.3    65.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 192 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107C  PRO*     4.2     1.4    -      -       -      +
    124C  ILE*     3.9    26.0    -      -       +      -
    125C  LYS      3.2    28.0    -      -       -      +
    126C  PRO*     3.7     7.1    -      -       +      +
    127C  GLY      3.3    12.8    +      -       -      -
    128C  ASN*     2.9    29.0    +      -       +      +
    130C  LEU*     3.6    24.7    -      -       +      -
    135C  ILE*     4.2    16.8    -      -       +      -
    139C  SER*     4.4     7.6    -      -       -      -
    140C  THR      3.8     8.1    -      -       -      +
    141C  VAL*     3.7    19.3    -      -       +      -
    142C  HIS*     3.2    16.5    +      -       -      -
    190C  ALA      5.3     0.2    -      -       -      +
    191C  THR*     1.3    73.7    -      -       -      +
    193C  GLY*     1.3    57.9    +      -       -      +
----------------------------------------------------------
 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