Contacts of the strand formed by residues 94 - 102 (chain B) 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 ILE 94 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  LEU*     3.8    26.5    -      -       +      -
     88B  ARG*     5.2     0.7    -      -       +      -
     91B  ALA*     3.8    20.2    -      -       +      -
     93B  ARG*     1.3    74.5    -      -       -      +
     95B  HIS*     1.3    67.0    +      -       -      +
     96B  VAL*     4.3     0.4    -      -       +      -
    172B  ARG      4.0     0.2    -      -       -      +
    173B  SER*     3.2     5.9    -      -       -      -
    174B  PHE*     3.0    72.2    +      -       +      -
    177B  VAL*     3.7    22.4    -      -       +      -
    182B  PHE*     3.8    15.9    -      -       +      -
    200B  VAL*     3.6    26.2    -      -       +      -
    201B  PHE      3.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  ARG*     4.0    10.3    -      -       +      +
     94B  ILE*     1.3    74.9    -      -       -      +
     96B  VAL*     1.3    61.6    +      -       -      +
     97B  GLU      4.0     0.4    -      -       -      -
    171B  VAL*     4.5     7.5    -      -       +      +
    172B  ARG      3.6     3.1    +      -       -      +
    173B  SER*     3.4    26.2    -      -       -      -
    200B  VAL*     3.3     4.5    -      -       -      +
    201B  PHE*     2.6    79.9    +      +       +      +
    202B  TYR*     4.0    11.4    -      -       -      -
    203B  ARG*     3.7    16.9    -      -       -      -
    401B  SO4      2.6    40.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  ILE*     4.3     4.0    -      -       +      -
     95B  HIS*     1.3    76.7    -      -       -      +
     97B  GLU*     1.3    60.0    +      -       -      +
     98B  MET*     3.7    18.6    -      -       +      +
    121B  LEU*     4.4    17.5    -      -       +      -
    171B  VAL*     3.4     5.6    -      -       -      -
    172B  ARG      2.7    36.4    +      -       -      +
    174B  PHE*     3.7    31.4    -      -       +      -
    184B  LEU*     3.6    29.8    -      -       +      -
    198B  VAL*     3.8    18.8    -      -       +      -
    199B  ARG      3.5     2.7    -      -       -      +
    200B  VAL*     4.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  HIS      4.0     1.4    -      -       -      -
     96B  VAL*     1.3    70.7    -      -       -      +
     98B  MET*     1.3    64.5    +      -       -      +
     99B  LYS*     3.4    20.2    +      -       +      -
    169B  THR*     3.3    25.1    -      -       +      +
    170B  GLU      3.8     2.5    -      -       -      -
    171B  VAL*     3.7    22.8    -      -       +      +
    197B  ALA      3.7     0.9    -      -       -      +
    198B  VAL*     3.2     6.6    -      -       -      +
    199B  ARG*     2.7    77.4    +      -       +      +
    201B  PHE*     4.4     8.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  VAL*     3.7    22.7    -      -       +      +
     97B  GLU*     1.3    77.2    -      -       -      +
     99B  LYS*     1.3    61.6    +      -       -      +
    100B  PHE*     4.0    14.2    -      -       +      -
    119B  PHE*     4.1    25.8    -      -       -      -
    121B  LEU*     4.0    20.4    -      -       +      -
    149B  ILE*     3.7    24.0    -      -       +      -
    168B  ASN      3.7     0.9    -      -       -      +
    169B  THR*     3.3     6.8    -      -       -      +
    170B  GLU*     2.9    49.8    +      -       +      +
    172B  ARG*     4.0    13.0    -      -       +      -
    186B  PHE*     4.2    15.0    -      -       +      -
    195B  LEU*     4.5     9.6    -      -       +      -
    197B  ALA      3.4     5.6    -      -       -      +
    198B  VAL*     4.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ASP*     6.1     3.1    -      -       +      -
     59B  GLU*     3.1    33.2    +      -       +      -
     97B  GLU*     3.4    24.0    +      -       -      +
     98B  MET*     1.3    75.0    -      -       -      +
    100B  PHE*     1.3    62.7    +      -       -      +
    167B  ILE*     4.2    10.3    -      -       +      -
    168B  ASN      3.3     4.9    -      -       -      +
    169B  THR*     2.5    39.7    +      -       +      +
    195B  LEU*     3.8     2.4    -      -       -      +
    196B  ILE*     2.8    31.1    +      -       +      -
    197B  ALA*     2.9    36.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  MET*     4.0    11.2    -      -       +      -
     99B  LYS*     1.3    76.3    -      -       -      +
    101B  SER*     1.3    65.6    +      -       -      +
    102B  VAL*     3.9    20.9    -      -       +      -
    119B  PHE*     3.9    22.7    -      +       +      -
    149B  ILE*     3.8    19.3    -      -       +      -
    150B  ALA*     3.9    12.3    -      -       -      -
    151B  ALA*     3.9    18.8    -      -       +      -
    167B  ILE*     3.5     4.9    -      -       -      +
    168B  ASN*     2.9    59.0    +      -       +      +
    170B  GLU*     3.7    26.2    -      -       +      -
    193B  MET*     5.9     2.0    -      -       +      -
    194B  SER      3.2    14.1    -      -       -      +
    195B  LEU*     4.2    12.1    -      -       +      -
    196B  ILE*     4.0     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     1.3    70.8    +      -       -      +
    102B  VAL*     1.3    63.0    +      -       -      +
    165B  MET*     4.4     0.7    -      -       -      +
    166B  LYS      3.0    23.0    +      -       -      -
    167B  ILE*     3.7     4.3    -      -       -      +
    168B  ASN*     5.1     0.7    -      -       -      -
    193B  MET*     3.2     4.9    -      -       -      +
    194B  SER      2.8    33.2    +      -       -      -
    196B  ILE*     3.2    21.2    -      -       -      +
      2D  ASN*     3.6    16.8    +      -       -      -
      4D  TRP*     3.9    18.9    -      -       -      -
      5D  ILE*     3.7     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     3.9    26.1    -      -       +      -
    101B  SER*     1.3    76.4    -      -       -      +
    103B  ARG*     1.3    74.5    +      -       -      +
    104B  ASP*     3.7     4.0    +      -       +      +
    116B  LYS      5.2     0.2    -      -       -      +
    117B  GLU*     3.6    46.2    -      -       +      +
    118B  THR*     5.6     0.4    -      -       -      -
    119B  PHE*     5.6     1.3    -      -       +      -
    150B  ALA*     5.7     0.4    -      -       -      -
    151B  ALA*     4.5    15.3    -      -       +      +
    166B  LYS*     4.8     3.3    +      -       -      +
    168B  ASN*     5.0     3.8    +      -       -      -
    192B  CYS      3.9     7.2    -      -       -      +
    193B  MET*     4.1    14.6    -      -       +      -
      1D  SER*     4.2     5.4    +      -       -      +
      2D  ASN*     2.7    25.9    +      -       -      +
----------------------------------------------------------
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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