Contacts of the strand formed by residues 438 - 442 (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 GLN 438 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    433K  LYS*     4.1     0.7    -      -       -      -
    434K  ILE*     3.3    36.1    +      -       +      +
    435K  SER      5.0     1.6    -      -       -      +
    436K  GLY*     4.4     4.5    -      -       -      +
    437K  GLY*     1.3    77.8    -      -       -      +
    439K  TRP*     1.3    77.1    +      -       -      +
    440K  PHE*     3.6    27.8    -      -       +      -
    449K  SER*     3.5    20.6    +      -       -      -
    450K  ILE      3.8    12.1    +      -       -      +
    451K  SER*     5.7     0.2    -      -       -      +
     48M  TYR*     6.3     0.2    -      -       +      -
     50M  PHE*     5.9     1.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 439 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384K  THR*     5.7     4.3    -      -       +      -
    413K  LEU*     4.1    28.3    -      -       +      -
    414K  ILE      4.1    14.4    -      -       -      -
    415K  GLY*     4.3     0.7    -      -       -      -
    416K  ILE*     4.7     5.2    -      -       +      -
    431K  PHE*     3.7    18.6    -      -       +      -
    432K  CYS*     3.5    24.5    -      -       -      -
    433K  LYS*     3.4    50.2    -      -       +      +
    437K  GLY      3.9     6.9    +      -       -      -
    438K  GLN*     1.3    92.7    +      -       -      +
    440K  PHE*     1.3    70.9    +      -       -      +
    449K  SER*     3.7     0.3    -      -       -      -
    450K  ILE*     3.4    31.4    +      -       +      +
    451K  SER      4.4     0.7    -      -       -      +
    452K  GLN*     3.4    44.3    -      -       +      +
    455K  VAL*     4.1    26.2    -      -       +      -
    456K  LEU*     5.9     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 440 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136K  LEU*     3.9    27.4    -      -       +      -
    431K  PHE*     3.5    14.9    -      -       -      +
    432K  CYS      3.3    22.5    +      -       -      +
    434K  ILE*     3.6    38.6    -      -       +      -
    438K  GLN*     3.6    29.4    -      -       +      -
    439K  TRP*     1.3    84.5    -      -       -      +
    441K  LYS*     1.3    60.7    +      -       -      +
    442K  PHE*     3.7    24.6    +      +       +      -
    447K  VAL*     5.5     0.9    -      -       +      -
    448K  SER      3.3    11.0    -      -       -      +
    449K  SER*     3.6    29.6    -      -       -      +
    450K  ILE*     3.9     7.5    -      -       -      +
     48M  TYR*     4.5    17.0    -      +       -      -
     58M  ILE*     4.1    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 441 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429K  ILE*     4.6    23.3    -      -       +      +
    431K  PHE*     3.6    28.3    -      -       +      -
    440K  PHE*     1.3    70.9    -      -       -      +
    442K  PHE*     1.3    60.1    +      -       -      +
    443K  ASN*     4.5    19.1    -      -       -      +
    446K  MET*     3.1    23.5    -      -       +      +
    447K  VAL*     3.5     2.4    -      -       -      -
    448K  SER*     2.5    40.4    +      -       -      +
    449K  SER      4.9     0.2    -      -       -      +
    450K  ILE*     4.2    13.6    -      -       +      +
     54M  GLY*     5.0    10.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 442 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136K  LEU*     3.8    19.3    -      -       +      -
    137K  SER      5.9     0.7    -      -       -      -
    150K  SER*     5.6     2.4    -      -       -      -
    153K  GLN*     3.4    38.1    -      -       +      +
    157K  HIS*     3.3    40.4    -      +       -      -
    428K  TYR      5.4     0.2    -      -       -      +
    429K  ILE*     4.3     2.9    -      -       -      -
    430K  ALA*     3.0    45.0    +      -       +      +
    431K  PHE      5.2     0.2    -      -       -      -
    432K  CYS*     3.6    31.6    -      -       +      -
    434K  ILE*     5.2     1.3    -      -       +      -
    440K  PHE*     3.7    21.3    +      +       +      -
    441K  LYS*     1.3    75.0    -      -       -      +
    443K  ASN*     1.3    63.6    +      -       -      +
    446K  MET      4.4     0.4    -      -       -      -
    447K  VAL*     4.1    22.2    -      -       +      -
----------------------------------------------------------
 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