Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 4HZF


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 SER 47 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ILE*     5.0     0.7    -      -       -      -
     46A  GLY*     1.3    73.4    -      -       -      -
     48A  VAL*     1.3    65.7    +      -       -      +
     65A  LEU      3.2     5.6    -      -       -      -
     66A  ASN*     3.1    26.5    -      -       -      -
     90A  LYS*     2.8    52.4    +      -       -      +
     91A  THR*     3.4    17.3    +      -       -      +
     93A  CYS*     3.3    10.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LEU*     4.2    13.0    -      -       +      -
     43A  ILE*     3.9    16.6    -      -       +      -
     47A  SER*     1.3    81.2    -      -       -      +
     49A  ALA*     1.3    61.6    +      -       -      +
     64A  TYR*     3.3     9.7    -      -       -      +
     65A  LEU*     2.8    57.5    +      -       +      +
     71A  ILE*     4.6     1.1    -      -       +      -
     87A  VAL*     3.5    28.7    -      -       +      -
     88A  ARG      3.2    14.1    -      -       -      +
     89A  ALA*     4.2     4.3    -      -       -      -
     90A  LYS*     4.0     7.2    -      -       -      +
     93A  CYS*     3.9    16.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  VAL*     1.3    74.7    -      -       -      +
     50A  VAL*     1.3    62.0    +      -       -      +
     51A  LEU*     3.7    20.6    -      -       +      +
     61A  ILE*     4.4    10.8    -      -       +      -
     63A  SER      3.5     6.3    -      -       -      +
     64A  TYR*     3.9    21.1    -      -       +      -
     87A  VAL*     3.3     3.9    -      -       -      -
     88A  ARG*     2.9    33.9    +      -       +      +
     90A  LYS*     4.8     6.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  VAL*     4.9     0.4    -      -       +      -
     49A  ALA*     1.3    73.5    -      -       -      +
     51A  LEU*     1.3    57.7    +      -       -      +
     61A  ILE*     3.5     6.1    -      -       -      +
     62A  LEU*     2.8    35.6    +      -       +      -
     63A  SER*     2.8    22.5    +      -       -      +
     65A  LEU*     3.7    31.4    -      -       +      -
     85A  ALA*     3.7    16.2    -      -       +      -
     86A  TRP      3.3     4.7    -      -       -      +
     87A  VAL*     4.4     9.2    -      -       +      -
    301A  CMP      3.5    48.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ALA*     3.7    31.6    -      -       +      +
     50A  VAL*     1.3    76.4    -      -       -      +
     52A  ILE*     1.3    64.7    +      -       -      +
     53A  LYS*     5.5     2.7    -      -       -      -
     59A  GLU*     3.1    44.4    -      -       +      +
     60A  MET      3.4     4.7    -      -       -      +
     61A  ILE*     3.8    23.8    -      -       +      -
     62A  LEU*     5.0     0.9    -      -       -      -
     85A  ALA*     3.4     5.4    -      -       -      +
     86A  TRP*     2.8    50.5    +      -       +      +
     88A  ARG*     4.1    18.4    -      -       +      -
    175A  GLN*     4.7     2.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLN*     4.1     8.1    -      -       -      +
     51A  LEU*     1.3    79.6    -      -       -      +
     53A  LYS*     1.3    70.4    +      -       -      +
     59A  GLU*     3.3     2.8    -      -       -      +
     60A  MET*     2.9    49.7    +      -       +      +
     62A  LEU*     3.7    24.9    -      -       +      -
     84A  SER      4.1     9.9    -      -       -      +
     85A  ALA*     3.9    10.5    -      -       +      -
     86A  TRP*     4.2     4.9    -      -       -      -
    129B  SER*     3.8    17.3    -      -       -      +
    130B  GLU*     5.4     2.0    -      -       -      -
    133B  GLY*     3.6    31.6    -      -       -      +
    137B  PHE*     4.3     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLN*     5.3     0.6    -      -       -      +
     51A  LEU*     5.4     3.1    -      -       +      -
     52A  ILE*     1.3    83.5    -      -       -      +
     54A  ASP*     1.3    67.4    -      -       -      +
     57A  GLY*     4.5    11.9    -      -       -      +
     58A  LYS      3.1    11.4    -      -       -      +
     59A  GLU*     3.6    29.5    +      -       +      +
     86A  TRP*     3.7    60.7    -      -       +      +
    137B  PHE*     3.6    12.2    -      -       -      -
----------------------------------------------------------
 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