Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 3VAS


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 LEU 191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  GLN      3.0    12.4    +      -       -      +
    163A  VAL*     3.3     9.4    -      -       +      +
    164A  TYR*     2.7    35.2    +      -       -      +
    185A  SER*     3.9     1.8    -      -       -      -
    190A  LYS*     1.3    75.5    -      -       -      +
    192A  PHE*     1.3    53.1    +      -       -      +
    193A  CYS*     3.9    21.8    -      -       -      -
    217A  ASN*     3.5    24.5    -      -       +      -
    218A  ILE*     4.2    19.1    -      -       +      -
    309A  ILE*     5.5     0.2    -      -       +      -
    312A  TYR*     4.8    12.1    -      -       +      -
    313A  ILE*     4.0    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  TYR*     3.7    25.4    -      +       +      -
    166A  ILE*     3.7    35.0    -      -       +      -
    181A  ILE*     4.3     2.0    -      -       +      -
    182A  ALA*     3.8    29.4    -      -       +      -
    185A  SER*     3.5    13.9    +      -       -      +
    191A  LEU*     1.3    72.7    -      -       -      +
    193A  CYS*     1.3    70.5    +      -       -      +
    194A  PHE*     4.1     6.7    -      +       +      -
    212A  MET*     3.4    34.8    -      -       +      -
    215A  TYR      3.6    17.5    -      -       -      +
    216A  SER*     3.5    28.2    -      -       -      -
    217A  ASN*     2.8    36.5    +      -       -      +
    218A  ILE      3.3     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  VAL*     4.5     3.6    -      -       -      -
    164A  TYR      2.8    20.6    +      -       -      +
    165A  TYR*     3.5    20.7    -      -       +      -
    166A  ILE      3.1    25.5    +      -       -      +
    191A  LEU*     3.9    28.0    -      -       -      -
    192A  PHE*     1.3    80.2    -      -       -      +
    194A  PHE*     1.3    60.6    +      -       -      +
    218A  ILE*     3.4    22.4    -      -       -      +
    220A  PHE*     4.3     6.5    -      -       +      -
    309A  ILE*     4.0    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  TYR*     5.1     0.4    -      -       -      -
    166A  ILE      3.3    13.9    -      -       -      -
    168A  GLY*     3.6    30.7    -      -       -      -
    171A  ILE*     4.3    10.1    -      -       +      -
    178A  MET*     4.0     8.1    -      -       +      -
    192A  PHE*     4.1     3.1    -      +       +      -
    193A  CYS*     1.3    74.9    -      -       -      +
    195A  ASN*     1.3    67.2    +      -       -      +
    196A  LEU*     4.2     7.6    -      -       +      -
    209A  VAL*     4.1    26.2    -      -       +      -
    212A  MET*     3.7    42.6    -      -       +      -
    213A  ILE*     4.3    10.8    -      -       +      -
    216A  SER*     3.1    29.2    -      -       -      +
    218A  ILE      2.9     7.4    +      -       -      +
    219A  VAL*     3.3    12.3    -      -       +      +
    220A  PHE*     2.8    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  TYR*     3.0    30.1    +      -       +      +
    166A  ILE      3.5     6.7    +      -       -      -
    167A  ALA*     4.1     7.0    -      -       +      -
    168A  GLY*     2.7    31.0    +      -       -      -
    194A  PHE*     1.3    81.3    -      -       -      +
    196A  LEU*     1.3    62.6    +      -       -      +
    197A  SER*     2.9    34.6    +      -       -      +
    220A  PHE*     3.5    26.8    -      -       +      +
    221A  GLY*     4.7     0.7    -      -       -      -
    225A  GLU*     4.2     5.0    -      -       -      +
    301A  GLY*     4.6    10.9    +      -       -      -
    302A  ASP*     5.2     3.9    +      -       -      -
    305A  ALA*     4.4     5.5    -      -       -      +
----------------------------------------------------------
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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