Contacts of the strand formed by residues 96 - 102 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  LYS*     4.0    12.7    +      -       -      +
     71B  VAL*     3.3    13.5    -      -       +      +
     73B  ILE*     4.0    19.3    -      -       +      -
     86B  TYR*     3.8    25.6    -      -       +      -
     87B  ILE*     4.4     6.3    -      -       +      -
     92B  GLY      3.4    16.3    +      -       -      +
     93B  GLY      4.8     0.7    -      -       -      +
     94B  ASN      3.5     1.1    -      -       -      -
     95B  LYS*     1.3    87.1    +      -       -      +
     97B  ALA*     1.3    63.9    +      -       -      +
     98B  ASN      4.1     4.9    -      -       -      +
     99B  VAL*     3.5    31.9    -      -       +      -
    123B  ILE*     3.5    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ASN*     3.5    17.5    -      -       -      +
     70B  LYS*     4.1    16.1    -      -       +      +
     71B  VAL      3.0     9.9    +      -       -      -
     72B  ASP*     3.3    12.1    -      -       -      +
     96B  VAL*     1.3    73.9    -      -       -      +
     98B  ASN*     1.3    69.2    +      -       -      +
    121B  GLN*     6.3     3.4    -      -       +      -
    122B  LYS      4.4     1.8    -      -       -      +
    123B  ILE*     3.5     9.6    -      -       -      +
    124B  LEU*     3.1    24.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ASN*     5.0     1.4    -      -       -      +
     72B  ASP*     2.9    31.4    +      -       +      +
     73B  ILE      2.9    26.0    +      -       -      +
     96B  VAL*     4.1     0.7    -      -       -      +
     97B  ALA*     1.3    83.7    -      -       -      +
     99B  VAL*     1.3    63.0    +      -       -      +
    124B  LEU*     3.7    19.9    -      -       -      +
    172B  GLY      3.5    22.2    -      -       -      +
    173B  LEU*     3.3    25.5    +      -       +      +
    174B  ASN      4.5     0.4    -      -       -      -
    175B  GLY*     3.4    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  ILE*     3.5    12.1    -      -       +      +
     83B  THR*     4.5    13.2    -      -       +      -
     84B  LEU*     6.4     0.4    -      -       +      -
     87B  ILE*     4.3     7.4    -      -       +      -
     96B  VAL*     3.5    30.3    -      -       +      -
     98B  ASN*     1.3    73.5    -      -       -      +
    100B  VAL*     1.3    70.0    +      -       -      +
    101B  THR*     4.0    20.2    -      -       +      -
    123B  ILE*     3.8    14.4    -      -       +      -
    124B  LEU      2.8    10.4    +      -       -      +
    125B  TYR*     3.3    34.7    -      -       +      -
    126B  THR*     2.9    24.8    +      -       -      +
    172B  GLY*     5.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  ILE      2.9    10.9    +      -       -      +
     74B  VAL*     3.2    11.3    -      -       +      +
     75B  ALA      2.8    24.4    +      -       -      +
     99B  VAL*     1.3    80.7    -      -       -      +
    101B  THR*     1.3    63.1    +      -       -      +
    102B  LEU*     4.0    11.2    -      -       +      -
    126B  THR*     3.2    14.8    -      -       +      +
    128B  ILE*     3.9    25.4    -      -       +      -
    169B  ILE*     4.1    18.2    -      -       +      +
    172B  GLY*     3.8    33.4    -      -       -      -
    173B  LEU*     4.2    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  ALA*     3.2     9.6    -      -       +      -
     80B  GLY*     4.1    14.1    -      -       -      +
     83B  THR*     5.8     1.3    -      -       -      -
     84B  LEU*     5.9     2.2    -      -       +      -
     99B  VAL*     4.0    17.7    -      -       +      -
    100B  VAL*     1.3    77.5    -      -       -      +
    102B  LEU*     1.3    66.4    +      -       -      +
    104B  GLY*     4.3     7.2    +      -       -      -
    106B  ASN*     3.3    39.2    +      -       -      +
    125B  TYR*     5.6     0.9    -      -       +      -
    126B  THR      3.0     5.8    +      -       -      +
    127B  SER*     3.3    16.5    +      -       -      -
    128B  ILE*     3.0    27.0    +      -       -      +
    143B  LEU*     5.4     6.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  PHE*     4.7     0.7    -      -       +      -
     22B  ILE*     3.8    30.1    -      -       +      -
     74B  VAL*     4.0    14.1    -      -       +      -
     75B  ALA      2.7    14.7    +      -       -      +
     76B  HIS*     3.4    16.7    -      -       +      -
     77B  SER      2.9    18.4    +      -       -      -
    100B  VAL*     4.0     9.2    -      -       +      -
    101B  THR*     1.3    79.6    -      -       -      +
    103B  GLY*     1.3    67.5    +      -       -      +
    128B  ILE*     3.5    21.8    -      -       +      -
    159B  LEU*     3.8    22.9    -      -       +      +
    160B  LEU*     4.2    12.1    -      -       +      -
    165B  VAL*     3.7    22.2    -      -       +      -
    169B  ILE*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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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