Contacts of the strand formed by residues 161 - 166 (chain s) in PDB entry 6FF7


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 ILE 161 (chain s).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17s  LEU*     6.1     3.4    -      -       +      -
     18s  LYS      3.5     9.2    -      -       -      +
     19s  THR*     4.4     4.3    -      -       -      +
     49s  TYR*     3.3    28.7    -      -       +      +
     50s  ASP*     3.6     1.9    -      -       -      +
     51s  ASN*     3.4    22.5    +      -       -      -
     52s  THR*     3.2    12.3    +      -       -      +
    160s  LYS*     1.3    72.1    -      -       -      +
    162s  LYS*     1.3    62.4    -      -       -      +
    163s  SER      4.9     7.2    -      -       -      +
    164s  CYS*     6.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 162 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18s  LYS*     2.7    20.5    +      -       +      +
     19s  THR*     5.3     3.6    -      -       -      -
     20s  THR      5.8     0.2    -      -       -      +
     50s  ASP*     4.8    10.5    -      -       -      +
    160s  LYS      3.6     4.2    +      -       -      +
    161s  ILE*     1.3    73.2    -      -       -      +
    163s  SER*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 163 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17s  LEU*     3.7     2.3    -      -       -      +
     18s  LYS*     3.1    36.1    +      -       -      +
     50s  ASP*     6.1     2.0    -      -       -      +
    161s  ILE*     3.6     5.9    -      -       -      +
    162s  LYS*     1.3    79.6    +      -       -      +
    164s  CYS*     1.3    65.2    +      -       -      +
    165s  GLU*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 164 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16s  LEU      3.4     8.7    -      -       -      +
     17s  LEU*     5.0     5.2    -      -       +      -
     44s  CYS*     3.6    41.2    -      -       +      +
     47s  ALA*     5.8     5.0    -      -       -      +
     49s  TYR*     5.4    13.0    -      -       +      +
    163s  SER*     1.3    77.4    -      -       -      +
    165s  GLU*     1.3    62.5    +      -       -      +
    166s  VAL*     4.2     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 165 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15s  VAL*     3.3     7.8    -      -       -      +
     16s  LEU*     2.8    47.6    +      -       +      +
     44s  CYS*     5.4     2.0    -      -       -      +
    163s  SER*     4.2     2.3    -      -       -      -
    164s  CYS*     1.3    76.1    -      -       -      +
    166s  VAL*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14s  LYS      4.4     0.4    -      -       -      -
     15s  VAL*     4.3     8.3    -      -       +      +
     41s  ILE*     6.0     4.5    -      -       +      +
     44s  CYS*     5.8     7.0    -      -       +      -
     45s  LEU*     5.9     8.5    -      -       +      -
    164s  CYS      4.2     0.6    +      -       -      +
    165s  GLU*     1.3    75.4    -      -       -      +
    167s  LEU*     1.3    63.7    +      -       -      +
    168s  PHE      3.6     8.5    -      -       -      +
    169s  ASN*     5.0    11.8    -      -       +      +
----------------------------------------------------------
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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