Contacts of the strand formed by residues 164 - 169 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  LEU*     4.1     3.8    -      -       +      -
    162A  PHE*     3.5    25.6    -      -       +      -
    163A  GLY*     1.3    79.5    -      -       -      +
    165A  VAL*     1.3    64.5    +      -       -      +
    166A  ILE*     3.6    18.6    -      -       +      -
    182A  ILE*     3.7    33.0    -      -       +      -
    184A  SER      3.2    15.5    -      -       -      +
    185A  VAL*     4.3     7.6    -      -       +      +
    186A  ARG      4.6     0.7    -      -       -      +
    191A  ALA*     3.9    15.9    -      -       +      -
    197A  ILE*     4.1     7.4    -      -       +      -
    203A  LEU*     4.4     6.5    -      -       +      -
    223A  LEU*     4.3    11.0    -      -       +      -
    232A  LEU*     3.9    28.3    -      -       +      -
    242B  ALA*     3.7     2.1    -      -       -      +
    243B  VAL*     2.9    50.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  PHE*     1.3    78.1    -      -       -      +
    166A  ILE*     1.3    65.3    +      -       -      +
    182A  ILE*     3.3     8.3    -      -       -      +
    183A  THR*     2.8    44.8    +      -       -      +
    184A  SER*     2.9    27.4    +      -       -      +
    240B  GLU*     3.4    25.8    -      -       +      +
    241B  THR      3.4    14.1    -      -       -      +
    242B  ALA*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  PHE*     3.6    29.6    -      -       +      -
    165A  VAL*     1.3    75.3    -      -       -      +
    167A  ARG*     1.3    60.1    -      -       -      +
    180A  VAL*     3.9    29.2    -      -       +      -
    181A  VAL      3.4     3.1    -      -       -      +
    182A  ILE*     4.2     9.2    -      -       +      -
    183A  THR*     4.5     1.1    -      -       -      -
    203A  LEU*     4.4     4.9    -      -       +      -
    216A  HIS*     3.4    19.5    -      -       +      +
    219A  ALA*     4.3    14.8    -      -       +      -
    220A  MET*     4.4     8.5    -      -       +      +
    223A  LEU*     4.0    20.0    -      -       +      -
    240B  GLU*     3.2     6.7    -      -       -      +
    241B  THR      2.9    41.6    +      -       -      +
    243B  VAL*     4.2    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     1.3    74.3    -      -       -      +
    168A  GLY*     1.3    61.6    +      -       -      +
    178A  ARG*     5.0     1.8    -      -       -      +
    179A  PRO*     4.2     6.1    +      -       -      +
    180A  VAL*     3.3     7.2    -      -       -      +
    181A  VAL*     2.9    67.2    +      -       +      +
    183A  THR*     3.5    26.4    -      -       +      +
    216A  HIS*     4.0     2.2    -      -       -      -
   1244A  SCN      3.0    27.6    +      -       -      +
    149B  ARG*     5.2     2.9    -      -       -      +
    151B  VAL*     3.8    22.5    -      -       -      +
    152B  GLU      5.0     4.0    +      -       -      -
    153B  VAL*     5.1     0.8    -      -       -      +
    194B  GLU*     4.5     3.2    +      -       -      -
    196B  THR*     3.2    33.1    +      -       -      +
    236B  TYR*     3.4    12.0    +      -       -      -
    238B  VAL*     4.0    14.6    -      -       +      -
    239B  SER      3.1    15.0    -      -       -      +
    240B  GLU*     4.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     5.6     0.3    -      -       -      +
    167A  ARG*     1.3    78.4    -      -       -      +
    169A  GLY*     1.3    57.9    +      -       -      -
    178A  ARG*     4.0     2.2    -      -       -      -
    179A  PRO      3.6    11.0    -      -       -      -
    180A  VAL*     4.2     7.6    -      -       -      +
    216A  HIS*     2.8    33.4    +      -       -      +
   1244A  SCN      3.4    26.4    -      -       -      -
    239B  SER      3.3     8.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  GLY*     1.3    73.6    -      -       -      -
    170A  ALA*     1.3    67.3    +      -       -      -
    171A  HIS*     4.9     0.9    -      -       -      +
    177A  SER*     3.6     1.7    -      -       -      -
    178A  ARG*     2.9    36.5    +      -       -      +
    180A  VAL*     4.0    11.4    -      -       -      +
    211A  LEU      6.0     0.4    -      -       -      -
    214A  THR      3.6     8.7    -      -       -      -
    215A  THR      4.2     0.4    -      -       -      -
    216A  HIS*     3.9     9.0    -      -       -      -
   1244A  SCN      5.6     2.1    -      -       -      -
----------------------------------------------------------
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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