Contacts of the strand formed by residues 341 - 344 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329I  PRO*     3.6    10.7    -      -       -      +
    331I  MET*     3.9     7.4    -      -       -      -
    333I  ALA*     3.5    26.2    -      -       +      +
    334I  TYR      4.2     7.9    -      -       -      -
    335I  SER*     4.4     2.7    -      -       -      -
    338I  ASN*     3.7    22.1    -      -       -      +
    339I  ARG*     3.2     4.5    -      -       -      -
    340I  SER*     1.3    78.8    -      -       -      +
    342I  SER*     1.3    63.6    +      -       -      +
    343I  ILE      3.4    14.8    +      -       -      +
    344I  ARG*     4.5     7.1    +      -       -      +
    359I  ARG*     4.9     2.4    +      -       -      -
    392I  MET*     5.0     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 342 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329I  PRO*     3.4    29.0    -      -       -      +
    330I  VAL      4.8     0.7    -      -       -      -
    331I  MET      2.4    31.9    +      -       -      -
    332I  LEU*     3.4    17.7    -      -       -      +
    333I  ALA      3.6     0.2    +      -       -      -
    341I  ALA*     1.3    72.9    -      -       -      +
    343I  ILE*     1.3    61.6    +      -       -      +
    344I  ARG      4.0     0.2    -      -       -      -
    357I  GLU      3.5     0.2    -      -       -      +
    358I  VAL*     3.6     1.9    -      -       -      +
    359I  ARG*     2.7    36.2    +      -       -      +
    360I  PHE*     4.1    20.4    +      -       -      -
    410I  VAL*     5.2     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 343 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298I  ILE*     4.2    17.3    -      -       +      -
    301I  VAL*     5.1     8.3    -      -       +      -
    302I  ILE*     4.0    23.8    -      -       +      -
    332I  LEU*     4.5     6.3    -      -       +      -
    333I  ALA      3.0    26.1    +      -       -      +
    334I  TYR*     3.2    32.6    -      -       +      -
    335I  SER      3.3     3.5    +      -       -      -
    341I  ALA*     3.5     7.6    -      -       -      +
    342I  SER*     1.3    92.0    -      -       -      +
    344I  ARG*     1.3    68.5    +      -       -      +
    345I  ILE*     4.2     9.6    -      -       +      -
    356I  ILE*     4.3    10.3    -      -       +      -
    357I  GLU      3.2    10.1    -      -       -      +
    358I  VAL*     4.5    20.2    -      -       +      -
    360I  PHE*     5.5     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 344 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50H  ASP*     5.4     4.9    -      -       -      +
     64H  ASP*     3.5    23.7    +      -       -      -
    271I  HIS*     5.1     1.8    +      -       -      -
    335I  SER      3.2    11.0    -      -       -      +
    336I  ALA      4.9     9.3    +      -       -      +
    338I  ASN      4.3     9.2    -      -       -      +
    339I  ARG*     3.6    36.7    -      -       +      +
    341I  ALA      4.6     7.6    -      -       -      +
    342I  SER      4.0     1.1    -      -       -      +
    343I  ILE*     1.3    75.8    -      -       -      +
    345I  ILE*     1.3    67.2    +      -       -      +
    346I  PRO*     3.4    33.9    -      -       -      +
    357I  GLU*     2.9    61.3    +      -       -      +
    359I  ARG*     4.4    16.8    -      -       +      +
   4479I  ADP      4.0    18.0    +      -       -      -
----------------------------------------------------------
 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