Contacts of the strand formed by residues 99 - 102 (chain A) in PDB entry 4JUO


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 VAL 99 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ILE*     4.8     5.2    -      -       +      -
     45A  LEU*     4.5     9.2    -      -       +      -
     48A  MET*     4.7     3.4    -      -       +      -
     85A  MET*     4.0    29.4    -      -       +      +
     88A  MET*     3.2    31.6    +      -       +      +
     89A  SER*     3.0    29.2    -      -       -      -
     97A  ILE*     3.6     9.9    -      -       -      +
     98A  LEU*     1.3    86.1    -      -       -      +
    100A  GLU*     1.3    70.9    +      -       -      +
    101A  MET*     4.6     1.8    -      -       +      -
    121A  ALA*     4.1    15.3    -      -       +      -
    122A  ARG      3.6    11.2    -      -       -      +
    123A  LEU*     4.6     6.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  PHE*     4.7     4.5    -      -       -      +
     59A  TYR*     3.5    18.5    -      -       +      +
     89A  SER*     4.8     0.2    -      -       -      -
     97A  ILE*     4.5    13.7    -      -       +      +
     99A  VAL*     1.3    76.1    -      -       -      +
    101A  MET*     1.3    60.5    +      -       -      +
    121A  ALA*     3.2     4.9    -      -       -      +
    122A  ARG*     2.9    67.7    +      -       +      +
    123A  LEU      4.3     1.7    -      -       -      +
    124A  SER*     4.0    27.1    -      -       -      +
    125A  GLU      5.2     1.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  TYR*     4.4     3.1    -      -       -      -
     62A  SER*     4.2    12.3    -      -       -      +
     82A  TYR*     4.0     3.6    -      -       +      -
     85A  MET*     4.2    21.5    -      -       +      +
     86A  VAL*     3.7    42.4    -      -       +      -
     89A  SER*     3.8    16.6    -      -       -      +
     99A  VAL*     4.1     1.0    +      -       +      -
    100A  GLU*     1.3    75.3    -      -       -      +
    102A  HIS*     1.3    67.8    +      -       -      +
    103A  GLY      3.9     4.9    +      -       -      +
    105A  ASN*     3.8    26.9    +      -       +      +
    119A  THR*     3.8    26.5    -      -       +      -
    120A  GLU      3.2     9.6    -      -       -      +
    121A  ALA*     4.2     7.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  TYR*     3.5    44.9    +      +       +      -
    101A  MET*     1.3    75.5    -      -       -      +
    103A  GLY*     1.3    58.9    +      -       -      +
    118A  TYR      4.9     0.3    -      -       -      +
    119A  THR*     3.5     9.0    -      -       -      -
    120A  GLU*     2.7    60.2    +      -       +      +
----------------------------------------------------------
 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