Contacts of the strand formed by residues 167 - 171 (chain B) in PDB entry 3EXG


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 VAL 167 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  ILE*     3.3     7.9    +      -       -      +
    113B  VAL*     3.2     8.0    -      -       +      +
    114B  PHE*     2.9    27.6    +      -       -      -
    143B  LYS*     3.2    28.9    -      -       +      +
    145B  VAL*     4.9     5.8    -      -       +      -
    160B  ALA*     3.4    31.0    -      -       +      +
    163B  ASP*     4.0    24.7    -      -       +      +
    165B  ASN      3.5    15.0    -      -       -      +
    166B  PRO*     1.3    74.3    -      -       -      +
    168B  VAL*     1.3    63.5    +      -       -      +
    169B  VAL*     4.1     6.7    -      -       +      -
    195B  ILE*     4.5     7.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  PHE*     3.5    29.8    -      -       +      -
     93B  VAL*     4.6     1.8    -      -       +      -
    114B  PHE*     3.3    23.6    -      -       +      -
    136B  TYR*     4.2    23.8    -      -       +      -
    142B  LEU*     4.1    26.2    -      -       +      -
    143B  LYS      2.9     5.9    +      -       -      +
    144B  VAL*     3.4     8.8    -      -       +      +
    145B  VAL      3.0    25.3    +      -       -      +
    167B  VAL*     1.3    75.3    -      -       -      +
    169B  VAL*     1.3    62.4    +      -       -      +
    170B  LEU*     3.9    15.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  PHE*     3.4    14.1    -      -       -      -
    113B  VAL*     3.9    25.6    -      -       +      -
    114B  PHE      2.7    11.0    +      -       -      +
    115B  ARG*     3.4    14.5    -      -       +      -
    116B  GLY      3.5     1.4    +      -       -      +
    145B  VAL*     3.3    21.5    -      -       +      -
    147B  PRO*     4.3    13.0    -      -       +      -
    156B  LEU*     5.0     1.8    -      -       +      +
    157B  ILE*     4.3    20.4    -      -       +      +
    160B  ALA*     4.3     4.9    -      -       +      -
    167B  VAL*     4.1    11.7    -      -       +      -
    168B  VAL*     1.3    76.6    -      -       -      +
    170B  LEU*     1.3    61.4    -      -       -      +
    171B  GLU*     3.4    23.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  PHE*     3.6    36.3    -      -       +      -
    116B  GLY      4.0     2.2    -      -       -      -
    118B  ASN*     3.5    26.7    -      -       -      +
    132B  PHE*     4.6     1.6    -      -       +      -
    133B  ALA*     3.6    34.3    -      -       +      -
    136B  TYR*     4.6     8.1    -      -       +      -
    144B  VAL*     3.7    19.1    -      -       +      -
    145B  VAL      2.8    15.6    +      -       -      +
    146B  SER*     3.7    19.1    +      -       -      +
    147B  PRO*     3.2    18.5    -      -       -      +
    168B  VAL*     3.9    10.8    -      -       +      -
    169B  VAL*     1.3    71.8    -      -       -      +
    171B  GLU*     1.3    65.4    +      -       -      +
    213B  SER*     4.8     2.8    +      -       -      -
    241B  ILE*     4.7     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ILE*     3.4    31.4    -      -       +      +
    115B  ARG*     2.6    45.2    +      -       -      +
    116B  GLY      2.9    25.1    +      -       -      +
    117B  PRO*     3.7     2.5    -      -       -      -
    118B  ASN*     2.9    23.7    +      -       -      +
    147B  PRO*     4.3    13.7    -      -       +      -
    157B  ILE*     4.4     0.5    -      -       -      +
    169B  VAL*     4.3    15.4    -      -       +      +
    170B  LEU*     1.3    78.5    -      -       -      +
    172B  ASN*     1.3    62.7    +      -       -      +
    176B  TYR*     2.6    35.4    +      -       +      +
    213B  SER*     5.1     0.2    +      -       -      -
----------------------------------------------------------
 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