Contacts of the strand formed by residues 85 - 88 (chain K) in PDB entry 6T9L


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 PHE 85 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  CYS*     4.6     0.7    -      -       -      -
      6K  HIS*     3.7    28.5    -      -       +      -
      7K  ILE*     3.6    37.7    -      -       +      -
     10K  VAL*     5.6     4.9    -      -       +      -
     61K  LEU*     3.4    49.0    +      -       +      +
     74K  PHE*     4.7     4.1    -      -       -      -
     83K  HIS*     3.3     5.6    -      -       -      +
     84K  ILE*     1.3   106.3    -      -       +      +
     86K  GLY*     1.3    59.3    +      -       -      +
     87K  ILE*     5.7     0.3    -      -       -      +
     94K  LEU*     3.8    23.8    -      -       +      -
     95K  PHE      3.5     5.4    -      -       -      -
     96K  CYS*     4.2    13.2    -      -       +      -
    103K  ILE*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 86 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58K  PHE*     4.3     8.5    -      -       -      -
     59K  MET      3.5    10.5    -      -       -      -
     74K  PHE*     3.8    18.0    -      -       -      -
     84K  ILE      3.8     1.6    +      -       -      -
     85K  PHE*     1.3    73.7    -      -       -      +
     87K  ILE*     1.3    64.7    +      -       -      -
     88K  ASN      4.0     0.6    +      -       -      -
     93K  LEU      3.7     0.7    -      -       -      +
     94K  LEU*     3.4     2.8    -      -       -      +
     95K  PHE*     3.0    36.7    +      -       -      +
     97K  PHE*     5.7     0.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 87 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24K  CYS*     5.1    17.3    -      -       +      -
     27K  ALA*     5.3    10.3    -      -       +      -
     28K  ARG*     5.9     4.3    -      -       +      +
     31K  LEU*     6.3     2.9    -      -       +      -
     58K  PHE*     3.4     2.8    -      -       -      -
     59K  MET*     3.0    57.7    +      -       +      +
     61K  LEU*     5.3    11.7    -      -       +      -
     86K  GLY*     1.3    72.8    -      -       -      -
     88K  ASN*     1.3    73.4    +      -       -      +
     89K  SER*     3.5     1.0    +      -       -      -
     92K  GLY*     3.8    19.1    -      -       -      +
     93K  LEU      3.3    16.6    -      -       -      +
     94K  LEU*     3.7    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 88 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56K  ALA*     4.2     5.2    -      -       -      +
     57K  THR      3.2    16.3    +      -       -      +
     58K  PHE*     3.6    26.4    -      -       +      -
     86K  GLY      4.0     0.6    +      -       -      -
     87K  ILE*     1.3    71.6    -      -       -      +
     89K  SER*     1.3    64.5    +      -       -      +
     90K  ASN*     3.1    35.7    +      -       -      +
     91K  ASN*     3.3    28.3    +      -       -      +
     92K  GLY*     2.7    33.8    +      -       -      -
     93K  LEU      3.1    10.6    +      -       -      +
    102K  TYR*     4.1    12.5    +      -       +      +
     25M  GLN*     5.2     7.1    +      -       -      +
     26M  ASP*     5.5     1.4    -      -       -      +
----------------------------------------------------------
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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