Contacts of the strand formed by residues 158 - 162 (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 GLU 158 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  LEU*     4.9     3.6    -      -       -      +
     92A  PRO*     6.1     0.5    -      -       -      +
     94A  VAL*     4.1     8.9    -      -       -      +
     95A  THR      4.9     0.3    +      -       -      -
     98A  ASP*     3.4    42.0    -      -       +      +
    101A  ARG*     3.9     9.0    -      -       +      +
    102A  ILE      3.0    15.0    +      -       -      +
    103A  CYS*     3.4    16.7    -      -       -      +
    104A  VAL      3.0    22.4    +      -       -      -
    157A  PHE*     1.3    71.0    -      -       -      +
    159A  CYS*     1.3    58.4    +      -       -      +
    160A  VAL*     3.7     4.2    +      -       +      +
    184A  ARG*     3.7    18.4    -      -       +      +
    208A  ARG*     2.7    46.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  VAL*     3.5     7.6    -      -       -      +
    106A  ILE*     4.8    10.1    -      -       +      -
    153A  MET*     3.6    46.9    -      -       -      -
    154A  GLY*     3.9     1.3    -      -       -      -
    157A  PHE*     3.5    11.3    +      -       -      -
    158A  GLU*     1.3    72.5    -      -       -      +
    160A  VAL*     1.3    62.7    +      -       -      +
    182A  VAL*     3.8    27.6    -      -       +      +
    183A  PHE*     3.5    12.4    -      -       +      -
    184A  ARG*     2.9    33.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  LEU*     3.9    43.3    -      -       +      -
    103A  CYS*     4.0    13.7    -      -       -      -
    104A  VAL      2.8    10.9    +      -       -      +
    105A  VAL*     4.2    16.6    -      -       +      -
    106A  ILE*     2.8    30.1    +      -       -      +
    158A  GLU*     4.1     8.7    -      -       +      +
    159A  CYS*     1.3    81.0    -      -       -      +
    161A  LEU*     1.3    72.8    +      -       -      +
    162A  PHE*     4.6     0.4    -      -       +      +
    183A  PHE*     3.6     4.0    -      -       -      -
    184A  ARG*     5.1     1.3    -      -       +      -
    185A  ALA*     3.9    14.6    -      -       +      +
    187A  LEU*     4.3    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE      3.4    15.0    -      -       -      +
    107A  ASP      4.2     2.9    -      -       -      +
    108A  LEU*     4.0    33.2    -      -       +      +
    112A  LEU*     4.9     0.9    -      -       +      -
    160A  VAL*     1.3    75.5    -      -       -      +
    162A  PHE*     1.3    54.6    +      -       -      +
    163A  THR*     4.5    16.6    -      -       +      -
    170A  ALA*     5.2     0.2    -      -       +      -
    174A  THR*     3.0    35.2    -      -       +      +
    183A  PHE*     3.5    31.6    -      -       +      -
    185A  ALA      3.1    12.6    +      -       -      +
    186A  ARG*     3.3    14.1    -      -       +      -
    187A  LEU      2.7    33.1    +      -       -      -
    188A  PHE*     4.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     4.5     4.3    -      -       +      -
    105A  VAL*     3.4    33.4    -      -       +      +
    106A  ILE      3.0     7.4    +      -       -      -
    107A  ASP*     3.6    11.3    +      -       -      -
    160A  VAL*     3.9     1.5    +      -       +      -
    161A  LEU*     1.3    74.4    -      -       -      +
    163A  THR*     1.3    64.8    +      -       -      +
    187A  LEU*     3.4    32.3    -      -       +      -
    188A  PHE      4.5     0.9    -      -       -      -
    191A  SER*     3.6    26.7    -      -       -      -
    192A  CYS*     3.6    24.0    -      -       -      -
    201A  LYS*     3.0    55.9    +      -       +      +
    202A  ASP      4.6     3.6    -      -       -      -
    203A  LEU*     4.9     2.2    -      -       +      -
    206A  LEU*     3.7    25.1    -      -       +      -
----------------------------------------------------------
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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