Contacts of the strand formed by residues 164 - 169 (chain B) in PDB entry 2JIL


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 PHE 164 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  LEU*     4.0     2.9    -      -       +      -
    162B  PHE*     3.4    27.3    -      -       +      +
    163B  GLY*     1.3    78.0    +      -       -      +
    165B  VAL*     1.3    60.4    +      -       -      +
    166B  ILE*     3.6    25.6    +      -       +      +
    182B  ILE*     3.9    31.9    -      -       +      -
    184B  SER      3.2    15.5    -      -       -      +
    185B  VAL*     4.3     6.7    -      -       +      -
    191B  ALA*     3.8    15.9    -      -       +      -
    197B  ILE*     4.3     6.5    -      -       +      -
    203B  LEU*     4.3     6.3    -      -       +      -
    223B  LEU*     4.1    21.3    -      -       +      -
    232B  LEU*     3.9    28.5    -      -       +      -
   1245B  EDO      3.6    11.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  PHE*     1.3    73.9    -      -       -      +
    166B  ILE*     1.3    73.6    +      -       -      +
    182B  ILE*     3.3     8.5    -      -       -      +
    183B  THR*     2.9    44.1    +      -       +      +
    184B  SER*     3.0    13.4    +      -       -      +
   1245B  EDO      3.1    37.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  PHE*     3.6    30.2    +      -       +      -
    165B  VAL*     1.3    87.2    -      -       -      +
    167B  ARG*     1.3    59.8    -      -       -      +
    180B  VAL*     4.0    29.2    -      -       +      -
    181B  VAL      3.3     8.5    -      -       -      +
    182B  ILE*     4.2     7.0    -      -       +      -
    183B  THR*     4.5     0.7    -      -       -      -
    203B  LEU*     4.4     4.9    -      -       +      -
    216B  HIS*     3.4    29.3    -      -       +      +
    219B  ALA*     4.4     5.8    -      -       +      -
    220B  MET*     4.3    21.5    -      -       +      +
    223B  LEU*     4.0    20.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ILE*     1.3    75.0    -      -       -      +
    168B  GLY*     1.3    62.4    +      -       -      +
    178B  ARG*     5.3    12.3    -      -       -      +
    179B  PRO*     4.4     7.5    +      -       -      +
    180B  VAL*     3.2     7.7    -      -       -      +
    181B  VAL*     2.9    68.0    +      -       +      +
    183B  THR*     3.5    26.8    -      -       +      +
    216B  HIS*     4.0     6.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     1.3    80.3    -      -       -      +
    169B  GLY*     1.3    57.3    +      -       -      -
    178B  ARG*     4.0     9.6    -      -       -      -
    179B  PRO      3.4    13.7    -      -       -      -
    180B  VAL*     4.3     6.6    -      -       -      +
    216B  HIS*     2.7    33.8    +      -       -      +
    219B  ALA*     5.5     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  GLY*     1.3    73.8    -      -       -      -
    170B  ALA*     1.3    65.7    +      -       -      -
    171B  HIS*     5.0     0.9    -      -       -      +
    176B  LYS      4.9     0.2    -      -       -      +
    177B  SER*     3.6     1.1    -      -       -      -
    178B  ARG*     2.8    37.7    +      -       -      +
    179B  PRO      4.2     0.2    +      -       -      -
    180B  VAL*     4.2     9.9    -      -       -      +
    214B  THR      3.6    10.5    -      -       -      -
    215B  THR      4.2     0.2    -      -       -      -
    216B  HIS*     3.9     8.5    -      -       -      -
----------------------------------------------------------
 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