Contacts of the strand formed by residues 341 - 344 (chain F) in PDB entry 1FPY


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 ALA 341 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329F  PRO*     3.6    11.7    -      -       -      +
    331F  MET*     3.9     6.7    -      -       -      -
    333F  ALA*     3.5    26.5    -      -       +      +
    334F  TYR      4.2     8.1    -      -       -      -
    335F  SER*     4.3     2.9    -      -       -      +
    338F  ASN*     3.7    21.0    -      -       -      +
    339F  ARG      4.3     4.0    -      -       -      -
    340F  SER*     1.3    78.2    -      -       -      +
    342F  SER*     1.3    62.9    +      -       -      +
    343F  ILE      3.4    14.0    +      -       -      +
    344F  ARG*     4.5     8.2    +      -       -      +
    359F  ARG*     4.9     2.1    +      -       -      -
    392F  MET*     5.0     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 342 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329F  PRO*     3.4    29.5    -      -       -      +
    330F  VAL      4.8     0.7    -      -       -      -
    331F  MET      2.4    30.9    +      -       -      -
    332F  LEU*     3.4    18.7    -      -       -      +
    333F  ALA      3.6     0.2    +      -       -      -
    341F  ALA*     1.3    73.3    -      -       -      +
    343F  ILE*     1.3    60.0    +      -       -      +
    344F  ARG      4.0     0.4    -      -       -      -
    357F  GLU      3.5     0.3    -      -       -      +
    358F  VAL*     3.6     2.1    -      -       -      +
    359F  ARG*     2.7    35.9    +      -       -      +
    360F  PHE*     4.1    20.2    -      -       -      -
    410F  VAL*     5.2     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 343 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298F  ILE*     4.2    22.4    -      -       +      -
    301F  VAL*     5.1     9.0    -      -       +      -
    302F  ILE*     4.0    22.9    -      -       +      -
    332F  LEU*     4.5     6.3    -      -       +      -
    333F  ALA      3.0    26.3    +      -       -      +
    334F  TYR*     3.2    33.2    -      -       +      -
    335F  SER      3.3     3.3    +      -       -      -
    341F  ALA*     3.5     7.8    -      -       -      +
    342F  SER*     1.3    90.8    -      -       -      +
    344F  ARG*     1.3    68.4    +      -       -      +
    345F  ILE*     4.2     3.8    -      -       +      -
    356F  ILE*     4.3    11.2    -      -       +      -
    357F  GLU      3.2    10.1    -      -       -      +
    358F  VAL*     4.5    19.7    -      -       +      -
    360F  PHE*     5.5     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 344 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ASP*     5.4     4.6    -      -       -      +
     64A  ASP*     3.3    25.4    +      -       -      -
    271F  HIS*     5.1     1.6    +      -       -      -
    335F  SER      3.2    11.4    -      -       -      +
    336F  ALA      4.9     8.7    +      -       -      +
    338F  ASN      4.3     9.0    -      -       -      +
    339F  ARG*     3.6    36.0    -      -       +      +
    341F  ALA      4.6     7.9    -      -       -      +
    342F  SER      4.0     1.2    -      -       -      +
    343F  ILE*     1.3    75.6    -      -       -      +
    345F  ILE*     1.3    68.5    +      -       -      +
    346F  PRO*     3.4    33.2    -      -       -      +
    357F  GLU*     2.9    59.8    +      -       +      +
    359F  ARG*     4.4    16.2    -      -       +      +
   4476F  ADP      4.0    18.2    +      -       -      -
----------------------------------------------------------
 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