Contacts of the strand formed by residues 96 - 102 (chain E) in PDB entry 2QXU


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 VAL 96 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70E  LYS*     4.0    12.3    +      -       -      +
     71E  VAL*     3.3    16.4    -      -       +      +
     73E  ILE*     4.4    11.7    -      -       +      -
     83E  THR*     5.8     0.2    -      -       +      -
     86E  TYR*     3.8    23.8    -      -       +      -
     87E  ILE*     4.3     9.9    -      -       +      -
     92E  GLY      3.5    15.6    +      -       -      +
     93E  GLY      5.1     0.5    -      -       -      +
     94E  ASN      3.6     1.1    -      -       -      -
     95E  LYS*     1.3    85.5    -      -       -      +
     97E  ALA*     1.3    62.6    +      -       -      +
     98E  ASN      4.2     5.2    -      -       -      +
     99E  VAL*     3.3    34.1    -      -       +      -
    123E  ILE*     3.5    29.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  ASN*     3.5    16.8    -      -       -      +
     70E  LYS*     4.2    15.8    -      -       +      +
     71E  VAL      3.0     9.6    +      -       -      +
     72E  ASP*     3.3    13.0    -      -       -      +
     96E  VAL*     1.3    74.5    -      -       -      +
     98E  ASN*     1.3    69.2    +      -       -      +
    121E  GLN*     6.1     5.6    -      -       +      +
    122E  LYS      4.5     1.3    -      -       -      +
    123E  ILE*     3.6     8.1    -      -       -      +
    124E  LEU*     3.0    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 98 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  ASN*     4.9     2.0    -      -       -      +
     72E  ASP*     3.0    32.9    +      -       +      +
     73E  ILE      2.7    32.2    +      -       -      +
     96E  VAL*     4.2     0.7    -      -       -      +
     97E  ALA*     1.3    89.8    -      -       -      +
     99E  VAL*     1.3    56.5    +      -       -      +
    100E  VAL      4.3     0.2    -      -       -      -
    124E  LEU*     3.6    28.8    -      -       -      +
    172E  GLY      3.4    22.2    -      -       -      +
    173E  LEU*     3.4    20.1    +      -       +      +
    174E  ASN      5.1     0.2    -      -       -      -
    175E  GLY*     4.3     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73E  ILE*     3.3    13.2    -      -       +      +
     83E  THR*     4.2    15.9    -      -       +      -
     84E  LEU*     6.3     0.4    -      -       +      -
     87E  ILE*     4.3     7.0    -      -       +      -
     96E  VAL*     3.3    30.7    -      -       +      -
     98E  ASN*     1.3    72.3    -      -       -      +
    100E  VAL*     1.3    67.8    +      -       -      +
    101E  THR*     4.1    20.9    -      -       +      -
    123E  ILE*     3.7    14.8    -      -       +      -
    124E  LEU      2.9     7.4    +      -       -      +
    125E  TYR*     3.4    31.2    -      -       +      -
    126E  THR*     3.0    23.7    +      -       -      -
    172E  GLY      5.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73E  ILE      2.7    11.1    +      -       -      +
     74E  VAL*     3.2    10.6    -      -       +      +
     75E  ALA*     2.8    23.9    +      -       -      +
     99E  VAL*     1.3    81.3    -      -       -      +
    101E  THR*     1.3    64.8    +      -       -      +
    102E  LEU*     4.2    11.2    -      -       +      -
    126E  THR*     3.3    16.2    -      -       +      +
    128E  ILE*     4.4     8.5    -      -       +      -
    169E  ILE*     4.2    30.3    -      -       +      +
    172E  GLY*     3.9    34.3    -      -       -      -
    173E  LEU*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 101 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75E  ALA*     3.1     9.6    -      -       +      +
     80E  GLY*     4.0    14.6    -      -       -      +
     83E  THR*     5.7     0.7    -      -       -      -
     84E  LEU*     5.9     2.5    -      -       +      -
     99E  VAL*     4.1    17.5    -      -       +      -
    100E  VAL*     1.3    78.8    -      -       -      +
    102E  LEU*     1.3    64.0    +      -       -      +
    103E  GLY      4.0     0.2    -      -       -      -
    104E  GLY*     4.3     7.1    +      -       -      -
    106E  ASN*     3.1    40.6    +      -       -      +
    125E  TYR*     5.7     0.7    -      -       +      -
    126E  THR      3.0     5.5    +      -       -      +
    127E  SER*     3.4    16.6    +      -       -      -
    128E  ILE*     2.9    30.7    +      -       -      +
    143E  LEU*     5.3     4.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  PHE*     4.8     2.5    -      -       +      -
     22E  ILE*     5.0     2.5    -      -       +      -
     74E  VAL*     4.2    19.3    -      -       +      -
     75E  ALA      2.7    15.7    +      -       -      +
     76E  HIS*     3.4    17.9    -      -       +      -
     77E  SER      3.1    17.3    +      -       -      -
    100E  VAL*     4.2     7.9    -      -       +      -
    101E  THR*     1.3    82.5    -      -       -      +
    103E  GLY*     1.3    66.2    +      -       -      +
    128E  ILE*     3.4    10.5    -      -       +      -
    159E  LEU*     3.8    28.5    -      -       +      +
    160E  LEU*     4.3    20.4    -      -       +      -
    165E  VAL*     3.7    22.9    -      -       +      -
    169E  ILE*     4.0    21.8    -      -       +      -
----------------------------------------------------------
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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