Contacts of the strand formed by residues 301 - 306 (chain D) in PDB entry 3IFS


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 301 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268C  ILE*     3.8    28.9    -      -       +      -
    270C  MSE      4.0    17.0    -      -       -      -
    301C  PHE*     4.5     2.7    -      +       -      -
    303C  SER*     3.6    32.5    -      -       -      -
    314C  LEU*     5.0    11.9    -      -       +      -
    317C  TYR*     3.8    34.5    -      +       +      +
    318C  VAL*     5.9     0.9    -      -       +      -
    325C  LEU*     3.8    19.5    -      -       +      -
    267D  THR      2.9    18.3    +      -       -      +
    268D  ILE*     3.5    14.2    -      -       +      +
    269D  GLU      3.0    24.1    +      -       -      -
    299D  GLY      3.4     3.0    +      -       -      -
    300D  ILE*     1.3    69.6    -      -       -      +
    302D  PRO*     1.4    82.6    -      -       +      +
    303D  SER*     3.5     9.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 302 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314C  LEU*     3.8    18.8    -      -       +      +
    317C  TYR*     4.3    10.3    -      -       +      -
    258D  ARG*     5.9     0.9    -      -       -      +
    269D  GLU      3.8     4.0    -      -       -      +
    285D  TRP*     3.6    24.0    -      -       +      -
    286D  LYS*     3.6    26.5    -      -       -      +
    289D  PHE*     4.6     5.8    -      -       +      -
    290D  GLY*     3.7    28.3    -      -       -      +
    300D  ILE*     3.3    11.2    -      -       +      +
    301D  PHE*     1.4    99.1    -      -       +      +
    303D  SER*     1.3    59.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 303 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301C  PHE*     3.5    23.6    -      -       -      -
    303C  SER*     4.9     3.7    +      -       -      -
    268D  ILE*     4.1    12.6    -      -       -      -
    269D  GLU      2.8    14.6    +      -       -      +
    270D  MSE      3.9    16.2    -      -       -      +
    271D  LEU      3.0    17.5    +      -       -      -
    285D  TRP*     3.3     9.4    -      -       -      -
    286D  LYS*     4.2     6.3    -      -       -      +
    301D  PHE*     3.5     8.4    +      -       -      -
    302D  PRO*     1.3    75.0    -      -       -      +
    304D  SER*     1.3    74.9    +      -       -      +
    314D  LEU*     5.7     1.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 304 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286C  LYS*     5.1     7.6    +      -       -      -
    270D  MSE      4.4     5.1    -      -       -      +
    271D  LEU*     3.2    19.1    -      -       -      +
    282D  ALA*     3.9    26.8    -      -       -      +
    283D  GLU*     4.4     2.9    +      -       -      -
    286D  LYS*     3.9    22.7    +      -       -      +
    303D  SER*     1.3    85.9    +      -       -      +
    305D  ALA*     1.3    65.5    +      -       -      +
    306D  ASN*     5.5     1.8    +      -       -      -
    310D  ASP*     4.8     0.3    -      -       -      +
    314D  LEU*     5.3     4.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270D  MSE      3.6    24.9    -      -       +      -
    271D  LEU      3.0     7.2    +      -       -      +
    272D  ILE*     3.4     8.7    -      -       +      +
    273D  ASN*     3.3    23.4    +      -       -      -
    304D  SER*     1.3    77.7    -      -       -      +
    306D  ASN*     1.3    68.4    +      -       -      +
    307D  PHE*     3.7    19.8    +      -       +      -
    310D  ASP*     3.4    15.0    -      -       +      +
    314D  LEU*     5.2     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 306 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283C  GLU*     6.4     0.4    -      -       -      -
    273D  ASN*     2.9    35.0    +      -       -      +
    276D  PRO*     5.5     7.6    -      -       +      -
    279D  GLN*     3.9    38.7    +      -       -      +
    282D  ALA*     5.4     3.1    -      -       -      +
    304D  SER*     5.5     1.4    +      -       -      -
    305D  ALA*     1.3    75.6    +      -       -      +
    307D  PHE*     1.3    62.9    +      -       -      +
    309D  THR*     3.3    11.4    -      -       +      +
    310D  ASP*     2.8    40.1    +      -       -      +
----------------------------------------------------------
 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