Contacts of the strand formed by residues 50 - 54 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548A  PHE*     3.8    24.7    -      +       +      -
    551A  GLN*     5.0     3.5    +      -       -      -
    552A  GLN*     3.6    24.8    +      -       -      +
     43B  THR*     5.4     7.9    -      -       -      -
     44B  LEU      3.1     9.4    -      -       -      +
     45B  ASN*     3.4    42.1    +      -       +      +
     49B  GLY*     1.3    77.8    -      -       -      -
     51B  ILE*     1.3    62.4    +      -       -      +
     52B  LEU      4.2     0.2    -      -       -      -
    479B  PHE*     3.1     7.3    -      -       -      +
    480B  THR*     2.9    33.7    +      -       -      +
    486B  MET*     3.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548A  PHE*     4.4     1.8    -      -       -      -
     42B  LEU      3.5     1.6    -      -       -      +
     43B  THR*     3.4     3.2    -      -       -      -
     44B  LEU*     2.8    49.6    +      -       +      +
     46B  THR*     4.1    16.2    -      -       +      -
     50B  HIS*     1.3    77.2    -      -       -      +
     52B  LEU*     1.3    62.1    +      -       -      +
     53B  VAL*     3.9    21.0    +      -       +      -
    303B  MET*     3.9    27.1    -      -       +      -
    477B  ILE*     4.0    16.6    -      -       +      -
    478B  VAL      3.4     7.9    -      -       -      +
    479B  PHE*     4.3     2.2    -      -       +      -
    486B  MET*     3.6    32.3    -      -       +      -
    489B  ALA*     4.5     3.1    -      -       +      -
    490B  LEU*     4.4    12.6    -      -       +      -
    493B  MET*     5.2     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545A  LEU*     3.8    26.7    -      -       +      -
    548A  PHE*     3.7    51.0    -      -       +      -
     37B  PHE*     3.9    19.1    -      -       +      -
     41B  SER*     4.0    22.0    -      -       -      -
     42B  LEU      3.4    13.2    -      -       -      +
     43B  THR*     3.8    16.4    -      -       +      +
     51B  ILE*     1.3    72.6    -      -       -      +
     53B  VAL*     1.3    60.4    +      -       -      +
     54B  ASP*     4.3     5.8    -      -       +      +
    476B  SER      3.4     1.4    -      -       -      +
    477B  ILE*     3.3     5.5    -      -       -      +
    478B  VAL*     2.7    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  SER*     3.2     3.5    -      -       -      -
     42B  LEU*     2.8    47.0    +      -       +      +
     44B  LEU*     5.2     3.4    -      -       +      -
     51B  ILE*     4.0    20.6    -      -       +      +
     52B  LEU*     1.3    73.6    -      -       -      +
     54B  ASP*     1.3    60.6    +      -       -      +
     55B  TYR*     3.6    15.0    +      -       +      +
    316B  ALA*     4.4    21.3    -      -       +      +
    319B  LEU*     6.2     2.7    -      -       +      -
    320B  LEU*     4.1    28.7    -      -       +      -
    475B  ASN*     5.6     1.3    -      -       -      +
    476B  SER      3.9     1.8    -      -       -      -
    477B  ILE*     4.3    14.1    -      -       +      -
    493B  MET*     4.5     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  SER*     2.5    27.1    +      -       -      -
    545A  LEU*     3.5    23.3    -      -       +      +
     37B  PHE*     3.4    27.3    -      -       +      -
     40B  PHE      3.7     1.7    -      -       -      +
     41B  SER*     4.0     4.7    -      -       -      -
     52B  LEU*     3.6     3.6    -      -       +      -
     53B  VAL*     1.3    71.1    -      -       -      +
     55B  TYR*     1.3    59.8    +      -       -      +
     56B  SER*     2.7    27.4    +      -       -      -
     57B  LYS*     5.1     2.0    +      -       -      -
    474B  THR      4.4     1.0    -      -       -      +
    475B  ASN*     3.6     3.4    -      -       -      -
    476B  SER*     2.8    43.3    +      -       -      +
----------------------------------------------------------
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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