Contacts of the strand formed by residues 50 - 54 (chain C) in PDB entry 1JIQ


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 HIS 50 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  THR*     5.4     6.7    -      -       -      -
     44C  LEU      3.1     8.3    -      -       -      +
     45C  ASN*     3.3    46.6    +      -       +      +
     49C  GLY*     1.3    77.8    -      -       -      -
     51C  ILE*     1.3    62.8    +      -       -      +
    478C  VAL      3.9     0.2    -      -       -      +
    479C  PHE*     3.1     6.2    -      -       -      +
    480C  THR*     2.9    34.0    +      -       -      +
    486C  MET*     3.8     0.2    -      -       -      +
    548D  PHE*     3.8    25.8    -      +       +      -
    551D  GLN*     4.9     4.0    +      -       -      -
    552D  GLN*     3.6    24.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  LEU      3.7     1.0    -      -       -      +
     43C  THR*     3.4     2.9    -      -       -      -
     44C  LEU*     2.8    51.1    +      -       +      +
     46C  THR*     4.3    16.8    -      -       +      -
     50C  HIS*     1.3    77.7    -      -       -      +
     52C  LEU*     1.3    60.9    +      -       -      +
     53C  VAL*     3.9    23.4    +      -       +      -
    303C  MET*     4.1    25.6    -      -       +      -
    477C  ILE*     4.1    15.7    -      -       +      -
    478C  VAL      3.4     8.1    -      -       -      +
    479C  PHE*     4.4     1.8    -      -       +      -
    486C  MET*     3.6    33.2    -      -       +      -
    489C  ALA*     4.4     5.4    -      -       +      -
    490C  LEU*     4.5    11.9    -      -       +      -
    493C  MET*     5.3     2.2    -      -       -      -
    548D  PHE*     4.4     2.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  PHE*     3.9    28.3    -      -       +      -
     41C  SER*     4.0    13.0    -      -       -      -
     42C  LEU      3.4    15.5    -      -       -      +
     43C  THR*     3.9    15.7    -      -       +      +
     51C  ILE*     1.3    73.4    -      -       -      +
     53C  VAL*     1.3    60.7    +      -       -      +
     54C  ASP*     4.3     6.5    -      -       +      +
    476C  SER      3.5     1.2    -      -       -      +
    477C  ILE*     3.3     5.5    -      -       -      +
    478C  VAL*     2.7    36.9    +      -       +      +
    545D  LEU*     3.7    26.2    -      -       +      -
    548D  PHE*     3.6    46.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  SER*     3.2     3.5    -      -       -      -
     42C  LEU*     2.9    49.4    +      -       +      +
     44C  LEU*     5.1     4.3    -      -       +      -
     51C  ILE*     3.9    20.2    +      -       +      +
     52C  LEU*     1.3    72.8    -      -       -      +
     54C  ASP*     1.3    61.1    +      -       -      +
     55C  TYR*     3.6    15.1    +      -       +      +
    316C  ALA*     4.4    11.4    -      -       +      +
    319C  LEU*     6.3     1.6    -      -       +      -
    320C  LEU*     4.2    27.6    -      -       +      -
    475C  ASN*     5.8     1.1    -      -       -      +
    476C  SER      4.0     2.2    -      -       -      -
    477C  ILE*     4.5    13.2    -      -       +      -
    493C  MET*     4.4    18.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 54 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  PHE*     3.3    28.2    -      -       +      -
     40C  PHE      3.8     1.4    -      -       -      +
     41C  SER*     3.8     5.4    -      -       -      -
     52C  LEU*     3.7     3.6    -      -       +      -
     53C  VAL*     1.3    71.9    -      -       -      +
     55C  TYR*     1.3    58.8    +      -       -      +
     56C  SER*     2.6    31.8    +      -       -      -
     57C  LYS*     5.1     1.7    +      -       -      -
    474C  THR      4.5     0.9    -      -       -      +
    475C  ASN*     3.6     4.5    -      -       -      +
    476C  SER*     2.9    41.8    +      -       -      +
    541D  SER*     2.6    23.1    +      -       -      -
    545D  LEU*     3.5    22.6    -      -       +      +
----------------------------------------------------------
 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