Contacts of the strand formed by residues 178 - 185 (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 ARG 178 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     5.3    11.0    -      -       -      +
    168B  GLY*     4.6     4.9    -      -       -      -
    169B  GLY*     2.8    38.9    +      -       -      +
    176B  LYS      3.6    10.1    +      -       -      +
    177B  SER*     1.3    79.4    -      -       -      +
    179B  PRO*     1.3    75.7    -      -       +      +
    180B  VAL*     4.8     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     3.6     5.3    +      -       -      +
    168B  GLY*     3.4    11.4    -      -       -      -
    177B  SER      4.6     1.1    -      -       -      +
    178B  ARG*     1.3    93.2    -      -       +      +
    180B  VAL*     1.3    62.4    +      -       -      +
    181B  VAL*     3.4    17.8    +      -       +      +
    202B  ARG*     3.9    45.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ILE*     4.0    32.5    -      -       +      -
    167B  ARG      3.2    10.1    -      -       -      +
    168B  GLY      4.3     2.7    -      -       -      +
    169B  GLY*     4.2    19.1    -      -       -      +
    178B  ARG      4.8     0.2    -      -       -      +
    179B  PRO*     1.3    71.1    -      -       -      +
    181B  VAL*     1.3    60.5    +      -       -      +
    202B  ARG*     3.6     9.7    -      -       -      +
    203B  LEU*     2.9    41.1    +      -       +      +
    211B  LEU*     4.1    35.0    -      -       +      +
    214B  THR*     4.8     3.4    -      -       -      +
    219B  ALA*     4.4    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ILE*     3.3     4.9    -      -       -      -
    167B  ARG*     2.9    71.5    +      -       +      +
    179B  PRO*     3.7    21.8    -      -       +      +
    180B  VAL*     1.3    78.4    -      -       -      +
    182B  ILE*     1.3    75.9    +      -       -      +
    183B  THR*     3.6     2.6    -      -       +      +
    200B  GLY*     3.9    17.7    -      -       -      +
    201B  ASP      3.6    10.5    -      -       -      +
    202B  ARG*     4.7     8.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  PHE*     3.9    33.0    -      -       +      -
    165B  VAL      3.3    11.2    -      -       -      +
    166B  ILE*     4.2     4.7    -      -       +      +
    181B  VAL*     1.3    73.1    -      -       -      +
    183B  THR*     1.3    59.1    +      -       -      +
    184B  SER      3.8    16.4    -      -       -      +
    185B  VAL*     4.3     2.7    -      -       +      -
    197B  ILE*     3.4    45.3    -      -       +      -
    198B  LYS      4.2     9.4    -      -       -      +
    199B  PRO*     3.3     0.3    -      -       -      +
    200B  GLY*     2.7    33.6    +      -       -      -
    201B  ASP*     2.9    19.7    +      -       +      +
    203B  LEU*     4.6    11.2    -      -       +      -
    234B  ILE*     4.3    15.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  VAL*     2.9    33.9    +      -       -      +
    166B  ILE      4.5     0.2    -      -       -      -
    167B  ARG*     3.5    48.7    -      -       +      +
    181B  VAL*     3.6     7.6    -      -       +      +
    182B  ILE*     1.3    73.8    -      -       -      +
    184B  SER*     1.3    64.3    +      -       -      +
    199B  PRO*     3.6    16.6    -      -       -      +
    200B  GLY      4.8     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  PHE*     3.2     8.3    -      -       -      +
    165B  VAL*     3.0    30.5    +      -       -      -
    182B  ILE*     3.7     3.4    -      -       -      +
    183B  THR*     1.3    85.8    +      -       -      +
    185B  VAL*     1.3    67.6    +      -       -      +
    199B  PRO*     4.1     8.5    -      -       -      +
   1245B  EDO      2.8    31.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  GLY      3.7     7.2    -      -       -      +
    164B  PHE*     4.3     3.4    -      -       +      -
    182B  ILE*     4.3     1.6    -      -       +      -
    184B  SER*     1.3    83.8    +      -       -      +
    186B  ARG*     1.3    63.1    +      -       -      +
    187B  PRO*     3.5     8.5    -      -       -      +
    191B  ALA*     4.1     5.2    -      -       +      +
    192B  ASP*     3.5    41.9    -      -       +      +
    197B  ILE*     3.8    41.3    -      -       +      +
    198B  LYS*     6.0     0.2    -      -       +      -
    199B  PRO*     4.3    16.3    -      -       +      +
   1245B  EDO      3.7     4.3    +      -       -      -
----------------------------------------------------------
 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