Contacts of the strand formed by residues 252 - 257 (chain G) in PDB entry 2QC8


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 CYS 252 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133G  MET*     3.4    34.5    -      -       -      -
    134G  GLU      3.2    12.6    -      -       -      +
    135G  GLN*     3.8    22.7    -      -       -      +
    218G  LEU*     4.1     5.6    -      -       -      -
    251G  GLY*     1.3    72.6    -      -       -      +
    253G  HIS*     1.3    68.7    +      -       -      +
    254G  THR*     3.2    10.4    +      -       -      -
    342G  PRO*     2.7    19.6    +      -       -      +
    343G  SER      3.3    20.2    -      -       -      +
    344G  ALA*     3.8     5.6    -      -       -      +
    346G  CYS*     4.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 253 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132G  GLY      3.6     2.3    -      -       -      +
    133G  MET*     3.4     3.3    -      -       -      -
    134G  GLU*     2.9    49.5    +      -       +      +
    136G  GLU*     4.5     2.0    -      -       -      -
    251G  GLY*     4.6     2.7    -      -       -      -
    252G  CYS*     1.3    80.0    -      -       -      +
    254G  THR*     1.3    60.0    +      -       -      +
    255G  ASN*     4.0     0.4    +      -       -      -
    338G  GLU*     2.9    12.9    +      -       +      +
    339G  ASP      3.5    10.3    -      -       -      +
    340G  ARG*     3.5    38.2    +      -       -      +
    342G  PRO*     4.7     1.1    -      -       -      -
    401G   MN      4.1     2.9    -      -       -      -
    402G   MN      2.5    19.8    +      -       -      -
    601G  P3S      2.8    59.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 254 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131G  PHE*     4.0     9.0    -      -       +      -
    132G  GLY      3.7     2.2    -      -       -      -
    133G  MET*     3.5    24.8    -      -       +      +
    252G  CYS      3.2    11.9    +      -       -      -
    253G  HIS*     1.3    70.6    -      -       -      +
    255G  ASN*     1.3    69.1    -      -       -      +
    256G  PHE*     4.2     1.6    +      -       -      +
    337G  PHE      3.9     0.3    -      -       -      +
    338G  GLU*     4.6     0.2    -      -       -      -
    339G  ASP*     2.6    47.6    +      -       -      +
    342G  PRO*     3.9     5.2    -      -       -      +
    351G  VAL*     3.4    23.7    -      -       +      +
    352G  THR*     5.1     0.2    -      -       +      -
    355G  LEU*     3.7    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 255 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131G  PHE*     3.2     7.6    -      -       -      -
    132G  GLY      2.7    48.6    +      -       -      +
    134G  GLU*     3.2    24.8    +      -       -      +
    253G  HIS      4.0     3.2    +      -       -      -
    254G  THR*     1.3    77.5    -      -       -      +
    256G  PHE*     1.3    61.8    +      -       -      +
    326G  PRO*     5.2     0.2    -      -       -      +
    336G  TYR*     3.3    23.3    -      -       +      -
    337G  PHE      3.3     5.2    -      -       -      +
    338G  GLU*     3.5    20.7    -      -       -      +
    501G  ADP      3.4    40.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 256 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129G  PRO*     3.9    15.9    -      -       +      -
    130G  TRP      3.3     6.5    -      -       -      -
    131G  PHE*     3.2    39.0    -      +       +      -
    254G  THR      5.0     1.8    -      -       -      +
    255G  ASN*     1.3    75.2    -      -       -      +
    257G  SER*     1.3    73.1    +      -       -      +
    258G  THR*     4.1    16.4    -      -       +      -
    261G  MET*     4.3    11.8    -      -       +      +
    336G  TYR*     3.3     5.1    -      -       -      +
    337G  PHE*     2.9    67.2    +      +       +      +
    355G  LEU*     4.5    20.4    -      -       +      -
    356G  ILE*     4.1    14.8    -      -       +      -
    359G  CYS*     4.2    24.0    -      -       +      -
    360G  LEU*     4.3     5.4    -      -       +      -
    501G  ADP      4.2     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129G  PRO*     3.5     2.4    -      -       -      +
    130G  TRP*     2.8    35.5    +      -       -      +
    256G  PHE*     1.3    78.5    -      -       -      +
    258G  THR*     1.3    61.8    +      -       -      +
    261G  MET*     3.7     8.1    -      -       -      -
    262G  ARG*     3.0    21.4    +      -       -      -
    335G  GLY      3.2    26.9    -      -       -      -
    336G  TYR*     3.6     0.7    -      -       -      -
    501G  ADP      2.6    32.1    +      -       -      -
----------------------------------------------------------
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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