Contacts of the strand formed by residues 158 - 162 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  LEU*     4.4     3.5    -      -       -      +
     92B  PRO*     6.0     1.9    -      -       -      +
     93B  GLU      5.3     0.2    -      -       -      +
     94B  VAL*     4.4    13.1    -      -       -      +
     95B  THR      5.2     0.5    +      -       -      -
     98B  ASP*     3.8    27.8    -      -       +      +
    101B  ARG*     3.9     8.4    -      -       +      +
    102B  ILE      3.0    11.5    +      -       -      +
    103B  CYS*     3.5    20.3    +      -       -      +
    104B  VAL      2.9    25.1    +      -       -      -
    157B  PHE*     1.3    74.7    -      -       -      +
    159B  CYS*     1.3    59.4    +      -       -      +
    160B  VAL*     4.7     4.3    -      -       +      -
    184B  ARG*     3.6    26.3    -      -       +      +
    208B  ARG*     2.3    40.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  VAL*     3.6     8.1    -      -       -      +
    106B  ILE*     4.4    10.5    -      -       +      -
    153B  MET*     3.6    45.1    -      -       -      -
    154B  GLY*     3.9     4.0    -      -       -      -
    157B  PHE*     3.6    10.2    +      -       -      -
    158B  GLU*     1.3    75.4    -      -       -      +
    160B  VAL*     1.3    64.1    +      -       -      +
    182B  VAL*     3.7    23.3    +      -       +      +
    183B  PHE*     3.4    14.0    -      -       +      -
    184B  ARG*     2.9    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  LEU*     3.6    44.6    -      -       +      -
    103B  CYS*     4.1    11.2    -      -       -      -
    104B  VAL      3.0     8.7    +      -       -      +
    105B  VAL*     3.4    16.0    -      -       +      -
    106B  ILE*     2.8    26.9    +      -       -      +
    158B  GLU*     4.4     9.2    -      -       +      +
    159B  CYS*     1.3    83.3    -      -       -      +
    161B  LEU*     1.3    72.3    +      -       -      +
    162B  PHE*     4.3     1.6    -      -       +      +
    183B  PHE*     3.6     3.8    -      -       -      -
    184B  ARG*     5.0     1.3    -      -       +      -
    185B  ALA*     3.5    19.5    -      -       +      +
    187B  LEU*     4.4    10.5    -      -       +      -
    206B  LEU*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  ILE      3.5    13.0    -      -       -      +
    107B  ASP      4.5     2.5    -      -       -      +
    108B  LEU*     4.2    32.1    -      -       +      +
    112B  LEU*     4.8     0.9    -      -       +      -
    160B  VAL*     1.3    74.1    -      -       -      +
    162B  PHE*     1.3    54.5    +      -       -      +
    163B  THR*     3.9    23.3    -      -       +      -
    170B  ALA*     4.8     2.2    -      -       +      -
    174B  THR*     3.7    22.0    -      -       +      +
    183B  PHE*     3.3    39.3    -      -       +      -
    185B  ALA      3.1    10.1    +      -       -      +
    186B  ARG*     3.4     9.5    -      -       +      -
    187B  LEU      2.5    34.3    +      -       -      +
    188B  PHE*     4.3    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  LEU*     5.0     3.1    -      -       +      -
    105B  VAL*     3.1    31.8    -      -       +      +
    106B  ILE      3.0    16.8    +      -       -      +
    107B  ASP*     3.6     2.1    -      -       -      -
    160B  VAL*     3.4     3.6    +      -       +      -
    161B  LEU*     1.3    74.7    -      -       -      +
    163B  THR*     1.3    65.5    +      -       -      +
    187B  LEU*     3.6    26.7    -      -       +      -
    188B  PHE      4.1     1.8    -      -       -      -
    191B  SER*     3.2    40.8    -      -       -      -
    192B  CYS*     3.5    23.1    -      -       -      -
    201B  LYS*     3.0    52.2    +      -       +      +
    202B  ASP      4.3     9.2    -      -       -      -
    203B  LEU*     5.3     1.8    -      -       +      -
    206B  LEU*     4.4    16.6    -      -       +      -
----------------------------------------------------------
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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