Contacts of the strand formed by residues 162 - 167 (chain F) in PDB entry 6NMY


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 162 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124F  TRP*     2.9    22.9    +      -       +      -
    126F  VAL*     5.7     1.6    -      -       -      +
    135F  GLN*     2.7    30.2    +      -       -      +
    136F  TYR*     3.1    31.4    +      -       -      +
    137F  ASP*     2.8    29.1    +      -       -      -
    150F  GLU*     5.5     0.6    +      -       -      -
    154F  TYR*     3.4    55.2    -      -       +      +
    155F  LYS      3.6     5.4    -      -       -      +
    156F  THR*     5.6     4.9    -      -       +      -
    160F  GLY      5.1     0.7    -      -       -      +
    161F  THR*     1.3    76.8    -      -       -      +
    163F  ILE*     1.3    59.0    +      -       -      +
    187F  ARG*     3.8    16.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 163 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123F  SER*     3.8     2.4    -      -       -      -
    124F  TRP*     3.0    55.3    +      -       -      +
    125F  ALA*     4.7     8.1    -      -       +      -
    126F  VAL*     5.2     7.4    -      -       +      +
    155F  LYS*     3.0    43.2    +      -       +      +
    156F  THR      4.2     9.4    -      -       -      +
    157F  ASP*     4.3    18.6    -      -       +      +
    161F  THR*     3.8     0.8    +      -       -      +
    162F  ARG*     1.3    73.5    -      -       -      +
    164F  GLY*     1.3    61.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 164 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  CYS      3.3    11.9    -      -       -      -
    123F  SER*     4.2     4.0    -      -       -      -
    124F  TRP*     3.2    14.6    -      -       -      -
    154F  TYR*     3.5     8.1    -      -       -      +
    155F  LYS*     3.2    32.3    +      -       -      +
    163F  ILE*     1.3    84.9    +      -       -      +
    165F  CYS*     1.3    63.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  SER*     3.3     5.2    -      -       -      -
    122F  CYS*     2.9    30.2    +      -       +      +
    124F  TRP*     4.1     2.5    -      -       +      -
    138F  LEU*     4.0    20.9    -      -       +      -
    151F  CYS*     2.0    49.4    -      -       +      -
    153F  HIS      3.7     9.4    -      -       -      -
    154F  TYR*     4.3     0.9    -      -       +      -
    155F  LYS*     4.2     2.9    -      -       -      +
    164F  GLY*     1.3    76.1    -      -       -      +
    166F  ARG*     1.3    71.8    +      -       -      +
    167F  PHE*     3.7    23.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115F  HIS*     4.3     7.9    -      -       -      +
    119F  PHE*     4.1    21.0    -      -       +      -
    120F  LEU      3.3     7.6    -      -       -      +
    121F  SER*     3.2    23.3    -      -       -      +
    151F  CYS*     4.6     0.9    -      -       -      -
    152F  LEU      5.2     0.9    +      -       -      -
    153F  HIS*     3.3    52.3    +      -       +      +
    165F  CYS*     1.3    83.2    -      -       -      +
    167F  PHE*     1.3    65.2    +      -       -      +
    168F  ASP*     2.5    37.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 167 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118F  ASP      4.2     0.2    -      -       -      +
    119F  PHE*     3.6     5.5    -      -       -      -
    120F  LEU*     2.8    52.7    +      -       +      +
    121F  SER*     5.9     0.2    -      -       -      -
    122F  CYS*     5.3     4.9    -      -       -      -
    138F  LEU*     3.4    34.8    -      -       +      -
    140F  LEU*     3.7    36.6    -      -       +      -
    149F  TYR*     4.3    12.1    -      -       +      -
    150F  GLU      4.1     7.4    -      -       -      -
    151F  CYS*     3.9    25.4    -      -       -      -
    152F  LEU*     5.6     1.8    -      -       +      +
    165F  CYS*     3.7    11.7    -      -       -      -
    166F  ARG*     1.3    73.3    -      -       -      +
    168F  ASP*     1.3    63.4    +      -       -      +
    169F  ASP      3.7     0.4    -      -       -      -
    170F  ILE*     4.5     3.8    +      -       +      -
    173F  LEU*     3.6    28.5    -      -       +      -
----------------------------------------------------------
 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