Contacts of the strand formed by residues 124 - 130 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  ALA      2.9     8.2    +      -       -      +
     98C  ASN*     3.6    23.9    -      -       -      +
     99C  VAL*     2.8    31.5    +      -       -      +
    122C  LYS*     3.7    14.6    -      -       +      +
    123C  ILE*     1.3    74.3    -      -       -      +
    125C  TYR*     1.3    60.3    +      -       -      +
    175C  GLY*     3.9    24.7    -      -       -      +
    177C  GLY*     4.0    15.3    -      -       -      +
    178C  GLN*     3.8    23.8    -      -       -      -
    179C  ASN*     4.1     6.5    -      -       +      +
    124D  LEU*     6.5     1.1    -      -       +      -
    175D  GLY      5.2     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  LEU*     3.8    20.9    -      -       +      +
     87C  ILE*     3.6    19.9    -      -       +      +
     99C  VAL*     3.4    32.5    -      -       +      -
    101C  THR*     5.7     1.3    -      -       +      -
    113C  ALA*     3.5    18.8    -      -       +      -
    114C  LEU*     2.6    44.9    +      -       -      +
    123C  ILE*     3.5    26.8    -      -       +      +
    124C  LEU*     1.3    75.1    -      -       -      +
    126C  THR*     1.3    63.4    +      -       -      +
    127C  SER*     6.0     0.4    -      -       -      -
    143C  LEU*     4.2    14.8    -      -       +      -
    146C  ALA*     3.5    18.8    -      -       +      -
    147C  ARG*     3.0    22.7    +      -       -      +
    178C  GLN      3.0    20.7    +      -       -      +
    179C  ASN*     3.6     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  VAL      3.0    10.5    +      -       -      -
    100C  VAL*     3.3    15.3    -      -       +      +
    101C  THR*     3.0    24.2    +      -       -      -
    125C  TYR*     1.3    71.1    -      -       -      +
    127C  SER*     1.3    59.3    +      -       -      +
    128C  ILE*     4.0    22.7    -      -       +      -
    147C  ARG*     3.3    26.9    -      -       -      +
    149C  VAL*     4.5     7.0    -      -       +      -
    168C  LEU*     4.8     9.9    -      -       +      +
    172C  GLY*     3.9     9.1    -      -       -      -
    176C  GLY      4.1     2.4    +      -       -      -
    177C  GLY*     3.2    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  THR*     3.2    18.4    +      -       -      -
    106C  ASN*     3.6     2.1    +      -       -      -
    125C  TYR*     4.1     1.0    -      -       -      -
    126C  THR*     1.3    71.3    -      -       -      +
    128C  ILE*     1.3    60.4    +      -       -      +
    129C  TYR*     3.4    11.2    -      -       -      -
    141C  SER*     2.6    30.9    +      -       -      -
    143C  LEU*     4.9     5.2    -      -       -      -
    146C  ALA*     5.1     5.4    -      -       -      -
    147C  ARG      2.8     9.1    +      -       -      -
    148C  ASN*     3.5    20.6    -      -       -      -
    149C  VAL      2.9    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100C  VAL*     3.8    13.9    -      -       +      -
    101C  THR      2.9    12.1    +      -       -      +
    102C  LEU*     3.5    22.2    -      -       +      -
    103C  GLY      2.7    31.7    +      -       -      -
    104C  GLY      4.6     0.9    +      -       -      -
    126C  THR*     4.0    15.5    -      -       +      -
    127C  SER*     1.3    73.5    +      -       -      +
    129C  TYR*     1.3    59.5    +      -       -      +
    149C  VAL*     3.5     9.4    -      -       +      +
    151C  ILE*     4.2    21.5    -      -       +      -
    159C  LEU*     4.8     4.2    -      -       +      +
    165C  VAL*     4.3    15.7    -      -       +      +
    168C  LEU*     3.5    46.0    -      -       +      -
    169C  ILE      4.3     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103C  GLY*     4.3     8.3    -      -       -      +
    127C  SER*     3.4    25.6    -      -       -      -
    128C  ILE*     1.3    77.7    -      -       -      +
    130C  SER*     1.3    59.4    +      -       -      +
    133C  ASP*     5.9     0.7    -      -       -      +
    138C  ASN*     3.5    32.5    -      -       +      +
    141C  SER*     3.8    30.3    -      -       -      +
    142C  ARG*     3.1    33.7    -      -       +      -
    148C  ASN*     3.4    25.0    +      -       +      +
    149C  VAL      3.1     8.6    +      -       -      -
    150C  GLN*     3.3    39.4    -      -       +      +
    151C  ILE*     2.9    26.9    +      -       -      +
    159C  LEU*     4.9     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  TYR*     1.3    76.6    -      -       -      +
    131C  SER*     1.3    64.8    +      -       -      +
    132C  ALA      3.0     7.0    +      -       -      -
    133C  ASP*     3.0    22.6    +      -       -      +
    138C  ASN*     3.0    18.5    +      -       -      +
    151C  ILE*     3.3    23.7    +      -       -      -
    152C  HIS      3.7    12.0    -      -       -      -
    154C  VAL*     2.6    34.1    +      -       -      -
    159C  LEU*     4.5     7.5    -      -       -      +
----------------------------------------------------------
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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