Contacts of the strand formed by residues 183 - 187 (chain A) in PDB entry 2Q5E


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 183 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE*     4.4    12.1    -      -       +      -
    112A  LEU*     4.1    15.5    -      -       +      -
    150A  LEU*     4.1    26.9    -      -       +      -
    159A  CYS*     3.5    16.4    -      -       +      -
    160A  VAL      3.6    15.7    -      -       -      -
    161A  LEU*     3.5    31.2    -      -       +      -
    174A  THR*     3.8    26.5    -      -       +      -
    177A  LEU*     4.6     4.9    -      -       +      -
    178A  ASP*     2.9    40.8    +      -       +      +
    181A  GLY      3.8     7.8    -      -       -      +
    182A  VAL*     1.3    70.7    -      -       +      +
    184A  ARG*     1.3    63.4    +      -       -      +
    185A  ALA      3.6    12.0    +      -       -      +
    186A  ARG*     4.6    10.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  PRO*     4.5    10.5    -      -       +      +
     95A  THR*     6.0     3.1    -      -       +      -
     97A  GLU*     4.1    20.5    +      -       -      -
     98A  ASP*     3.6    32.9    +      -       -      +
    101A  ARG*     3.8    10.7    -      -       -      +
    154A  GLY*     3.2    29.7    +      -       -      -
    157A  PHE      4.0     4.0    +      -       -      -
    158A  GLU*     3.7    20.1    -      -       +      +
    159A  CYS      2.9    19.7    +      -       -      +
    160A  VAL*     5.1     1.8    -      -       +      -
    181A  GLY      3.9    12.9    +      -       -      -
    182A  VAL*     3.5    19.0    +      -       -      +
    183A  PHE*     1.3    73.0    -      -       -      +
    185A  ALA*     1.3    62.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  LEU*     3.6    31.2    -      -       +      -
     92A  PRO*     4.4    14.6    -      -       +      -
    159A  CYS      4.3     1.0    +      -       -      -
    160A  VAL*     3.9     7.1    -      -       +      -
    161A  LEU      3.1    23.0    +      -       -      -
    183A  PHE*     3.3     5.0    +      -       -      +
    184A  ARG*     1.3    81.4    -      -       +      +
    186A  ARG*     1.3    70.3    +      -       -      +
    187A  LEU*     5.1     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     3.3    17.9    -      -       +      +
    171A  ASP*     3.0    44.7    +      -       -      +
    174A  THR*     3.7    21.9    +      -       +      +
    175A  ASP*     2.6    42.4    +      -       -      +
    178A  ASP*     5.0     6.3    +      -       -      +
    183A  PHE*     4.6     9.9    +      -       +      +
    185A  ALA*     1.3    82.5    -      -       -      +
    187A  LEU*     1.3    67.6    +      -       -      +
    188A  PHE*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     3.7    31.4    -      -       +      +
     91A  LEU*     4.0    20.2    -      -       +      -
     92A  PRO*     6.1     0.2    -      -       +      -
    160A  VAL*     4.3     4.7    -      -       +      -
    161A  LEU      2.7    15.2    +      -       -      +
    162A  PHE*     3.6    29.4    -      -       +      -
    163A  THR*     3.0    28.2    +      -       -      +
    185A  ALA*     5.1     1.8    -      -       +      -
    186A  ARG*     1.3    82.0    -      -       -      +
    188A  PHE*     1.3    63.3    +      -       -      +
    191A  SER*     4.0    16.2    -      -       -      +
    206A  LEU*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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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