Contacts of the strand formed by residues 167 - 172 (chain A) in PDB entry 2VWJ


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 167 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  TYR*     4.1     2.9    -      -       -      +
    163A  ALA*     3.2     4.0    -      -       -      -
    164A  ASP*     2.7    41.9    +      -       -      +
    165A  GLU      3.3     1.2    -      -       -      -
    166A  GLU*     1.3    75.0    -      -       -      +
    168A  ALA*     1.3    62.1    +      -       -      -
    169A  ARG*     5.3     2.4    -      -       -      +
    201A  LYS*     5.7     0.2    +      -       -      -
    317A  LYS*     6.1     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  TYR      3.3     6.1    -      -       -      +
    163A  ALA*     3.6    18.4    -      -       +      -
    167A  GLY*     1.3    74.1    -      -       -      -
    169A  ARG*     1.3    73.8    +      -       -      +
    180A  TYR*     3.6    15.3    -      -       -      +
    313A  MET*     3.6    44.5    -      -       +      +
    316A  ALA*     4.8     0.4    -      -       +      -
    317A  LYS*     4.3    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  SER*     3.5     4.0    -      -       -      -
    162A  TYR*     3.0    67.7    +      -       +      +
    167A  GLY      5.3     1.8    -      -       -      +
    168A  ALA*     1.3    86.7    +      -       -      +
    170A  VAL*     1.3    67.7    +      -       -      +
    179A  PRO      3.2    27.0    +      -       -      -
    180A  TYR*     3.1    24.6    -      -       -      +
    181A  VAL      4.3     1.8    +      -       -      -
    182A  ASP*     3.0    32.4    +      -       -      +
    313A  MET*     4.9     1.2    -      -       -      +
    316A  ALA*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  MET*     3.8    37.7    -      -       +      -
    160A  ILE      3.7     4.9    -      -       -      +
    161A  SER*     4.1     5.8    -      -       -      -
    169A  ARG*     1.3    80.7    -      -       -      +
    171A  ILE*     1.3    65.9    +      -       -      +
    172A  THR*     4.1     5.2    -      -       +      -
    180A  TYR*     2.8    16.4    +      -       +      +
    181A  VAL*     3.4    13.8    -      -       +      +
    182A  ASP*     2.6    36.7    +      -       -      +
    309A  ALA*     3.9     9.2    -      -       +      +
    312A  SER*     4.1     2.5    -      -       -      +
    313A  MET*     3.7    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  MET*     3.3     2.3    -      -       -      -
    160A  ILE*     2.8    37.4    +      -       +      +
    162A  TYR*     3.9    27.8    -      -       +      -
    170A  VAL*     1.3    76.7    -      -       -      +
    172A  THR*     1.3    62.8    +      -       -      +
    182A  ASP*     3.6    17.7    -      -       +      +
    184A  VAL*     4.3     7.0    -      -       +      -
    190A  MET*     3.2    39.5    -      -       +      +
    193A  ARG*     4.0    21.5    -      -       +      -
    194A  PHE*     3.5    38.6    -      -       +      +
    197A  VAL*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  LEU      2.9    21.1    +      -       -      -
    159A  MET*     3.8    15.4    -      -       -      +
    170A  VAL*     4.1     3.3    -      -       +      -
    171A  ILE*     1.3    75.8    -      -       -      +
    173A  TRP*     1.3    58.8    +      -       -      +
    174A  ARG      3.4    21.7    +      -       -      +
    176A  ILE*     3.8    13.7    -      -       +      +
    181A  VAL*     3.7    26.5    -      -       +      -
    182A  ASP      3.2     4.8    +      -       -      +
    183A  VAL*     3.4     3.7    -      -       -      -
    184A  VAL*     3.1    26.3    +      -       -      -
    190A  MET*     4.2     2.2    -      -       -      -
    299A  TRP*     4.0    13.5    -      -       -      -
----------------------------------------------------------
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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