Contacts of the strand formed by residues 181 - 188 (chain A) in PDB entry 2QBX


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 GLY 181 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  PHE*     3.7    12.1    -      -       -      -
     86A  ILE      3.1    14.1    -      -       -      -
     88A  ARG      3.9     5.4    -      -       -      -
    125A  GLU*     3.4     6.8    -      -       -      +
    126A  ALA      3.0    24.0    +      -       -      +
    177A  VAL*     5.7     0.4    -      -       -      -
    179A  ARG*     2.9     6.6    +      -       -      +
    180A  SER*     1.3    84.6    +      -       -      +
    182A  PHE*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     4.4     2.0    -      -       +      -
     85A  PHE*     3.7     4.8    -      -       -      -
     86A  ILE*     2.7    78.1    +      -       +      +
     87A  ARG      4.4     7.4    -      -       -      -
     88A  ARG*     4.4     6.7    -      -       +      -
     94A  ILE*     3.8    41.7    -      -       +      -
    123A  TYR*     5.0     2.5    -      -       +      -
    124A  TYR      3.3    16.2    -      -       -      +
    125A  GLU*     3.9    12.1    -      -       +      +
    126A  ALA      4.6     0.9    -      -       -      +
    174A  PHE*     4.2     6.7    -      +       -      -
    177A  VAL*     4.1    15.7    -      -       +      -
    181A  GLY*     1.3    78.6    -      -       -      +
    183A  TYR*     1.3    67.3    +      -       -      +
    184A  LEU*     3.9    20.2    -      -       +      -
    200A  VAL*     3.8    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ARG*     4.2     8.1    -      -       +      -
     83A  THR*     3.4    24.9    -      -       -      +
     84A  LYS*     4.1     0.9    -      -       -      -
     85A  PHE*     3.5    38.1    -      +       +      -
     86A  ILE*     4.9     0.2    -      -       -      -
    123A  TYR*     3.2     8.8    -      -       -      +
    124A  TYR*     2.8    53.1    +      +       -      +
    126A  ALA*     4.3    14.4    -      -       +      -
    129A  ASP*     2.5    25.9    +      -       -      -
    130A  SER*     3.1     6.0    +      -       -      -
    131A  ALA*     2.8    41.4    +      -       +      +
    136A  PRO*     5.4     1.3    -      -       +      -
    143A  TRP*     3.5    21.3    -      +       +      -
    182A  PHE*     1.3    74.7    -      -       -      +
    184A  LEU*     1.4    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ARG*     3.3     8.7    -      -       -      +
     83A  THR*     3.1    45.5    +      -       +      -
     86A  ILE*     4.3     6.5    -      -       +      -
     96A  VAL*     3.6    33.0    -      -       +      -
    121A  LEU*     4.4     4.9    -      -       +      -
    122A  TYR      3.3     7.2    -      -       -      +
    123A  TYR*     3.9    13.5    -      -       +      -
    143A  TRP*     3.6     2.2    -      -       -      -
    174A  PHE*     4.0    13.5    -      -       +      -
    182A  PHE*     3.9    17.7    -      -       +      -
    183A  TYR*     1.4    81.6    -      -       -      +
    185A  ALA*     1.3    60.4    +      -       -      +
    186A  PHE*     4.1    11.4    -      -       +      -
    198A  VAL*     4.1     9.4    -      -       +      -
    200A  VAL*     3.7    20.4    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     80A  TRP*     3.5    37.2    -      -       +      -
     81A  LEU      3.1     9.9    -      -       -      +
     82A  ARG*     4.9     0.4    -      -       +      -
    120A  ASN      3.8     0.3    -      -       -      +
    121A  LEU*     3.3     9.2    -      -       -      +
    122A  TYR*     2.9    34.7    +      -       +      -
    143A  TRP*     3.6    20.6    -      -       +      -
    184A  LEU*     1.3    75.0    -      -       -      +
    186A  PHE*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  TRP*     4.2     5.4    -      +       -      -
     51A  TRP*     3.4    23.4    +      -       +      -
     80A  TRP*     3.5     1.7    -      -       -      +
     81A  LEU*     2.8    50.6    +      -       +      +
     83A  THR*     3.9    23.6    -      -       +      -
     98A  MET*     4.3    17.3    -      -       +      -
    119A  PHE*     4.1    17.5    -      +       +      -
    120A  ASN      3.4     5.4    -      -       -      +
    121A  LEU*     3.5    30.3    -      -       +      -
    184A  LEU*     4.1    10.5    -      -       +      -
    185A  ALA*     1.3    75.3    -      -       -      +
    187A  GLN*     1.3    60.3    +      -       -      +
    195A  LEU*     3.8    26.2    -      -       +      -
    198A  VAL*     3.9    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  TRP*     4.6     1.3    -      -       -      -
     78A  ASN*     3.0    30.3    +      -       -      +
     79A  ASN      3.3     3.8    -      -       -      -
     80A  TRP*     3.6    30.3    -      -       +      +
    119A  PHE*     3.4     9.5    -      -       -      +
    120A  ASN*     2.9    44.8    +      -       +      +
    122A  TYR*     2.5    42.2    +      -       +      -
    185A  ALA      4.2     0.4    -      -       -      -
    186A  PHE*     1.3    73.5    -      -       -      +
    188A  ASP*     1.3    63.6    +      -       -      +
    189A  TYR*     3.7    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  TRP*     4.0    10.4    -      -       +      +
     69A  VAL*     3.6    30.9    -      -       +      +
     71A  ASN      5.3     1.4    +      -       -      -
     77A  GLN*     4.4     0.3    -      -       -      +
     78A  ASN*     3.5     2.9    -      -       -      -
     79A  ASN*     2.8    62.5    +      -       +      +
    118A  THR      4.9     1.5    -      -       -      +
    119A  PHE*     4.8     2.9    -      -       -      -
    187A  GLN*     1.3    76.0    -      -       -      +
    189A  TYR*     1.3    66.8    +      -       -      +
    190A  GLY*     3.2     9.6    +      -       -      -
    191A  GLY*     2.7    34.9    +      -       -      +
    193A  MET*     3.7    11.6    -      -       +      +
----------------------------------------------------------
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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