Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 4FDI


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 ASN 32 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PRO      3.7     1.4    +      -       -      +
     31A  PRO*     1.3    75.1    -      -       -      +
     33A  ILE*     1.3    61.9    +      -       -      +
    133A  TYR*     4.4     0.2    -      -       -      -
    221A  ALA*     5.8     1.1    -      -       -      +
    224A  HIS      4.2     1.7    -      -       -      +
    225A  PRO*     3.6     9.0    -      -       -      +
    226A  PHE*     3.2    61.7    +      -       +      +
    277A  VAL*     3.3    23.2    -      -       -      +
    280A  ASN*     2.8    19.2    +      -       -      +
    281A  THR*     2.8    25.7    +      -       +      +
    282A  PHE*     2.8    26.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO      3.7     4.9    -      -       -      +
     32A  ASN*     1.3    79.0    -      -       -      +
     34A  LEU*     1.3    61.9    +      -       -      +
     35A  LEU*     4.1    12.3    -      -       +      -
    128A  LEU*     4.3     9.4    -      -       +      -
    133A  TYR*     3.9    24.7    -      -       +      +
    226A  PHE*     2.8    14.1    +      -       -      +
    227A  PHE*     3.2    25.6    -      -       +      -
    228A  LEU      2.9    25.3    +      -       -      -
    282A  PHE*     3.5    10.3    -      -       +      +
    349A  SER*     3.5    50.3    -      -       -      +
    352A  LEU*     4.3    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ASN      4.2     0.2    -      -       -      -
     33A  ILE*     1.3    72.9    -      -       -      +
     35A  LEU*     1.3    67.3    +      -       -      +
     36A  LEU*     3.4    34.8    +      -       +      +
    217A  ILE*     4.1    13.0    -      -       +      -
    226A  PHE*     4.3     9.6    -      -       +      -
    228A  LEU*     3.5    31.9    -      -       +      +
    230A  TRP*     4.6     0.9    -      -       +      -
    268A  ILE*     3.8    17.7    -      -       +      -
    272A  LEU*     3.8    29.2    -      -       +      -
    281A  THR*     4.5     2.9    -      -       +      +
    282A  PHE      2.8     8.9    +      -       -      +
    283A  VAL*     3.3    17.4    -      -       +      +
    284A  PHE      2.9    27.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ILE*     4.1    11.4    -      -       +      -
     34A  LEU*     1.3    75.4    -      -       -      +
     36A  LEU*     1.3    61.5    +      -       -      +
     37A  LEU*     3.6     2.3    +      -       +      +
     86A  LEU*     4.0    28.7    -      -       +      -
    124A  LEU*     4.2     9.4    -      -       +      -
    227A  PHE*     3.6    28.7    -      -       +      -
    228A  LEU      2.8    13.3    +      -       -      +
    229A  TYR*     3.7    11.4    -      -       +      -
    230A  TRP*     2.8    32.7    +      -       -      +
    282A  PHE*     5.1     4.5    -      -       +      -
    284A  PHE*     3.7    26.7    -      -       +      +
    345A  LEU*     4.4    22.7    -      -       +      -
    349A  SER*     4.4     8.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     3.4    30.7    -      -       +      +
     35A  LEU*     1.3    70.3    -      -       -      +
     37A  LEU*     1.3    60.1    +      -       -      +
     38A  MET*     4.0     8.5    -      -       +      -
     62A  MET*     4.5    10.1    -      -       +      -
    230A  TRP*     3.6    31.2    -      -       +      -
    265A  ILE*     3.9    33.9    -      -       +      -
    268A  ILE*     4.6     8.7    -      -       +      -
    269A  LEU*     5.4     3.8    -      -       +      -
    283A  VAL*     5.2     5.8    -      -       +      -
    284A  PHE      2.8    15.1    +      -       -      +
    285A  PHE*     3.5    24.9    -      -       +      -
    286A  THR*     3.0    29.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.6     2.3    +      -       +      -
     36A  LEU*     1.3    72.3    -      -       -      +
     38A  MET*     1.3    69.9    +      -       -      +
     83A  ARG*     3.8    27.7    +      -       +      +
     86A  LEU*     3.8    16.6    -      -       +      -
    229A  TYR*     3.3    38.4    -      -       +      +
    230A  TRP      3.0    18.6    +      -       -      +
    231A  ALA*     3.4    13.5    -      -       -      +
    232A  VAL      3.6     6.1    +      -       -      +
    286A  THR*     3.8    19.7    -      -       +      -
    287A  SER      3.7    29.6    -      -       -      -
    288A  ASP*     3.8     4.0    -      -       +      +
    342A  ILE*     3.8    12.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     4.0    17.7    -      -       +      -
     37A  LEU*     1.3    84.6    -      -       -      +
     39A  ASP*     1.3    61.7    +      -       -      +
     41A  MET*     3.6    25.6    -      -       +      +
     83A  ARG*     3.9     1.4    +      -       -      -
    230A  TRP*     4.3     6.1    -      -       +      -
    232A  VAL*     3.8    21.5    -      -       +      -
    235A  THR*     5.0     0.2    -      -       -      +
    261A  ILE*     3.5    30.5    -      -       +      -
    265A  ILE*     4.2     3.6    -      -       +      -
    285A  PHE*     3.4    37.7    -      -       +      -
    286A  THR      2.9    17.0    +      -       -      +
    287A  SER*     3.9    13.0    -      -       -      -
    288A  ASP*     3.1    27.2    +      -       -      +
----------------------------------------------------------
 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