Contacts of the strand formed by residues 124 - 130 (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 LEU 124 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU*     5.6    13.7    -      -       +      -
    175A  GLY      5.2     8.3    -      -       -      +
    177A  GLY      5.8     0.7    -      -       -      +
     97B  ALA      3.1     7.4    +      -       -      +
     98B  ASN*     3.7    20.7    -      -       -      +
     99B  VAL*     2.8    30.3    +      -       -      +
    121B  GLN*     5.7    11.0    -      -       +      +
    122B  LYS*     3.7    19.1    -      -       +      +
    123B  ILE*     1.3    75.5    -      -       -      +
    125B  TYR*     1.3    60.1    +      -       -      +
    175B  GLY*     3.7    24.0    -      -       -      +
    177B  GLY*     4.0    17.7    -      -       -      +
    178B  GLN*     3.9    20.2    -      -       -      -
    179B  ASN*     4.1     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  LEU*     3.8    19.8    -      -       +      +
     87B  ILE*     3.6    20.3    -      -       +      +
     99B  VAL*     3.3    33.7    -      -       +      -
    101B  THR*     5.6     1.8    -      -       +      -
    113B  ALA*     3.6    18.4    -      -       +      -
    114B  LEU*     2.6    45.2    +      -       -      +
    123B  ILE*     3.5    24.9    -      -       +      +
    124B  LEU*     1.3    74.4    -      -       -      +
    126B  THR*     1.3    63.1    +      -       -      +
    127B  SER*     6.0     0.2    -      -       -      -
    143B  LEU*     4.0    14.6    -      -       +      -
    146B  ALA*     3.4    19.1    -      -       +      -
    147B  ARG      3.1    14.9    +      -       -      -
    177B  GLY*     3.4     2.2    -      -       -      -
    178B  GLN      3.0    26.6    +      -       -      +
    179B  ASN*     3.5     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  VAL*     2.9     6.7    +      -       -      +
    100B  VAL*     3.2    17.1    -      -       +      +
    101B  THR*     3.0    25.5    +      -       -      +
    125B  TYR*     1.3    71.4    -      -       -      +
    127B  SER*     1.3    60.1    +      -       -      +
    128B  ILE*     4.0    22.9    -      -       +      -
    147B  ARG*     3.4    26.0    +      -       -      +
    149B  VAL*     4.5     6.5    -      -       +      -
    168B  LEU*     4.5    12.8    -      -       +      +
    172B  GLY*     3.7    11.4    -      -       -      -
    176B  GLY      4.3     0.9    -      -       -      -
    177B  GLY*     3.2    24.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  THR*     3.3    17.1    +      -       -      -
    106B  ASN*     3.7     2.4    +      -       -      -
    125B  TYR*     4.1     1.2    -      -       -      -
    126B  THR*     1.3    71.9    -      -       -      +
    128B  ILE*     1.3    57.1    +      -       -      +
    129B  TYR*     3.5     8.3    -      -       -      -
    141B  SER*     2.7    31.0    +      -       -      -
    143B  LEU*     4.9     4.7    -      -       -      -
    146B  ALA*     4.9     5.6    -      -       -      -
    147B  ARG      2.9     9.1    +      -       -      +
    148B  ASN*     3.5    20.4    -      -       -      -
    149B  VAL      2.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  VAL*     3.9    13.7    -      -       +      -
    101B  THR      3.0    10.0    +      -       -      +
    102B  LEU*     3.5    24.1    -      -       +      -
    103B  GLY      2.7    32.2    +      -       -      -
    126B  THR*     4.0    13.7    -      -       +      +
    127B  SER*     1.3    75.1    +      -       -      +
    129B  TYR*     1.3    58.8    +      -       -      +
    141B  SER*     5.0     0.2    -      -       -      -
    149B  VAL*     3.4     8.7    -      -       +      +
    151B  ILE*     4.1    21.5    -      -       +      -
    159B  LEU*     5.0     3.7    -      -       +      +
    165B  VAL*     4.2    15.0    -      -       +      +
    168B  LEU*     3.4    49.6    -      -       +      -
    169B  ILE      4.3     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  GLY*     4.4     7.6    -      -       -      +
    127B  SER*     3.5    25.1    -      -       -      -
    128B  ILE*     1.3    76.0    -      -       -      +
    130B  SER*     1.3    58.9    +      -       -      +
    136B  VAL      6.0     0.2    -      -       -      +
    138B  ASN*     3.6    26.5    -      -       +      +
    141B  SER*     3.6    33.2    -      -       -      +
    142B  ARG*     3.4    41.0    +      -       +      -
    148B  ASN*     3.3    32.1    +      -       +      +
    149B  VAL      3.0     9.9    +      -       -      -
    150B  GLN*     3.3    25.3    +      -       +      +
    151B  ILE*     2.9    28.0    +      -       -      -
    159B  LEU*     5.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  TYR*     1.3    75.9    -      -       -      +
    131B  SER*     1.3    58.5    +      -       -      +
    132B  ALA*     2.9     9.3    +      -       -      +
    133B  ASP*     2.9    29.7    +      -       -      +
    138B  ASN*     3.0    16.1    +      -       -      +
    151B  ILE*     3.3    22.1    +      -       -      -
    153B  GLY      3.9     1.2    +      -       -      -
    154B  VAL*     2.7    44.1    +      -       -      -
    159B  LEU*     4.4     7.9    -      -       -      +
----------------------------------------------------------
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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