Contacts of the strand formed by residues 169 - 174 (chain G) in PDB entry 6V3O


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 THR 169 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167G  ASN      4.1     2.6    +      -       -      -
    168G  GLN*     1.3    75.7    +      -       -      +
    170G  VAL*     1.3    73.4    +      -       -      +
    171G  ASP*     4.8     4.3    -      -       +      +
    281G  SER*     3.0    25.8    +      -       -      +
    282G  LEU      3.7     1.3    -      -       -      -
    284G  ARG*     3.8    40.0    +      -       +      +
    666G  GLY      2.7    19.7    +      -       -      +
    667G  SER*     3.5     9.0    +      -       -      +
    668G  ILE      3.4    18.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 170 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168G  GLN*     4.1     9.6    -      -       -      +
    169G  THR*     1.3    77.6    -      -       -      +
    171G  ASP*     1.3    62.2    +      -       -      +
    172G  LEU*     3.8    25.8    -      -       +      -
    282G  LEU      3.1    11.3    +      -       -      +
    283G  ILE*     3.2    12.6    -      -       +      +
    284G  ARG      2.8    25.3    +      -       -      +
    668G  ILE*     3.7    16.8    -      -       +      +
    670G  VAL*     5.3     1.8    -      -       +      -
    694G  PHE*     3.8    30.3    -      -       +      +
    695G  THR*     4.9     1.6    -      -       -      +
    698G  THR*     3.5    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 171 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169G  THR*     5.0     6.1    -      -       +      -
    170G  VAL*     1.3    74.9    -      -       -      +
    172G  LEU*     1.3    66.4    +      -       -      +
    173G  VAL*     4.0     1.1    +      -       -      +
    284G  ARG*     3.3    28.0    +      -       +      +
    285G  PHE      3.7     0.3    -      -       -      -
    286G  SER*     2.9    25.5    +      -       -      -
    452G  LYS*     4.2     8.8    +      -       -      -
    668G  ILE      3.1     6.9    +      -       -      +
    669G  ARG*     2.9    42.0    +      -       +      +
    670G  VAL      3.1    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 172 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170G  VAL*     3.8    24.9    -      -       +      -
    171G  ASP*     1.3    74.9    -      -       -      +
    173G  VAL*     1.3    60.1    +      -       -      +
    174G  PHE*     4.1     3.0    +      -       +      -
    283G  ILE*     4.8     6.1    -      -       +      -
    284G  ARG      3.0     8.7    +      -       -      +
    285G  PHE*     3.3    26.6    -      -       +      +
    286G  SER      2.9    25.1    +      -       -      +
    670G  VAL*     3.5    11.2    -      -       +      +
    672G  VAL*     3.8    15.3    -      -       +      -
    681G  PHE*     4.0    26.0    -      -       +      -
    691G  LEU*     4.4    11.0    -      -       +      -
    694G  PHE*     4.0    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 173 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171G  ASP      4.0     7.0    -      -       -      +
    172G  LEU*     1.3    76.2    -      -       -      +
    174G  PHE*     1.3    67.0    +      -       -      +
    175G  THR*     4.8     3.4    -      -       +      -
    286G  SER*     3.4    13.2    -      -       -      +
    288G  TRP*     3.6    36.3    -      -       +      +
    454G  ASP*     4.2     2.5    -      -       -      +
    638G  PHE*     3.6    28.0    -      -       +      -
    669G  ARG*     3.7    25.1    -      -       -      +
    670G  VAL      2.9    14.2    +      -       -      +
    671G  THR*     3.6     4.3    -      -       -      +
    672G  VAL*     2.7    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 174 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172G  LEU*     4.8     1.6    -      -       +      -
    173G  VAL*     1.3    74.0    -      -       -      +
    175G  THR*     1.3    61.6    +      -       -      +
    244G  GLY*     5.4     7.2    -      -       -      +
    245G  MET*     5.1     6.5    -      -       +      -
    247G  TYR*     5.7     4.3    -      -       +      -
    248G  ILE*     4.0    30.1    -      -       +      -
    252G  VAL*     5.0     5.4    -      -       +      -
    285G  PHE*     3.5    39.0    -      +       +      -
    286G  SER      2.9    20.2    +      -       -      +
    287G  SER*     4.7     2.9    -      -       -      +
    288G  TRP*     3.1    26.2    +      -       -      +
    289G  MET*     3.6    18.1    -      -       +      +
    451G  VAL*     4.9     2.2    -      -       +      -
    672G  VAL*     3.9    15.9    -      -       +      -
    677G  ILE*     3.8    34.5    -      -       +      -
    681G  PHE*     4.1    20.9    -      +       -      -
----------------------------------------------------------
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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