Contacts of the strand formed by residues 252 - 257 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133F  MET*     3.7    28.5    -      -       -      -
    134F  GLU      3.3    11.2    -      -       -      -
    135F  GLN*     3.8    23.3    -      -       -      -
    218F  LEU*     4.3     6.3    -      -       -      -
    222F  ARG*     4.5     0.4    -      -       -      -
    251F  GLY*     1.3    74.3    -      -       -      +
    253F  HIS*     1.3    70.2    +      -       -      +
    254F  THR*     3.1    14.2    +      -       -      -
    342F  PRO*     2.8    16.8    +      -       -      +
    343F  SER      2.9    22.9    -      -       -      +
    344F  ALA*     3.8     2.7    -      -       -      -
    346F  CYS*     3.9    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 253 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132F  GLY      3.6     1.7    -      -       -      +
    133F  MET*     3.3     3.8    -      -       -      -
    134F  GLU*     2.9    44.1    +      -       +      +
    136F  GLU*     4.4     3.4    +      -       -      -
    251F  GLY*     4.7     1.6    -      -       -      -
    252F  CYS*     1.3    78.8    -      -       -      +
    254F  THR*     1.3    60.1    +      -       -      +
    255F  ASN*     3.8     0.7    -      -       -      -
    338F  GLU*     2.7    22.4    +      -       +      +
    339F  ASP      3.4     7.0    -      -       -      +
    340F  ARG*     3.3    37.5    +      -       -      -
    342F  PRO*     4.9     0.7    -      -       -      -
    401F   MN      4.2     2.7    -      -       -      -
    402F   MN      2.3    31.4    +      -       -      -
    601F  P3S      2.8    53.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 254 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131F  PHE*     3.9    12.3    -      -       +      -
    132F  GLY      3.6     2.0    -      -       -      -
    133F  MET*     3.4    23.1    -      -       +      +
    252F  CYS      3.1    12.7    +      -       -      -
    253F  HIS*     1.3    70.9    -      -       -      +
    255F  ASN*     1.3    69.2    -      -       -      +
    256F  PHE*     4.0     2.9    +      -       -      +
    337F  PHE      4.1     0.3    -      -       -      +
    339F  ASP*     2.9    36.6    +      -       -      +
    342F  PRO*     3.5     7.4    -      -       -      +
    351F  VAL*     3.3    26.0    -      -       +      +
    352F  THR*     5.0     0.2    -      -       +      -
    355F  LEU*     3.6    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 255 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131F  PHE*     3.3     7.6    -      -       -      +
    132F  GLY      2.7    41.5    +      -       -      +
    134F  GLU*     3.1    28.2    +      -       -      +
    253F  HIS      4.1     1.6    +      -       -      -
    254F  THR*     1.3    75.5    -      -       -      +
    256F  PHE*     1.3    60.5    +      -       -      +
    326F  PRO*     5.1     0.3    -      -       -      +
    336F  TYR*     3.1    25.9    -      -       +      -
    337F  PHE      3.4     4.5    -      -       -      -
    338F  GLU*     3.2    23.6    -      -       -      +
    501F  ADP      3.4    41.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 256 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  PRO*     3.8    24.9    -      -       +      -
    130F  TRP      3.4    12.1    -      -       -      -
    131F  PHE*     3.5    22.7    -      +       +      -
    254F  THR      4.6     2.0    -      -       -      +
    255F  ASN*     1.3    75.1    -      -       -      +
    257F  SER*     1.3    71.5    +      -       -      +
    258F  THR*     3.9    17.7    -      -       +      -
    261F  MET*     4.2    16.8    -      -       +      +
    336F  TYR*     3.3     3.6    -      -       -      +
    337F  PHE*     3.0    64.6    +      +       +      +
    355F  LEU*     4.3    25.1    -      -       +      -
    356F  ILE*     4.1    13.7    -      -       +      -
    359F  CYS*     4.2    19.3    -      -       +      -
    360F  LEU*     4.6     5.2    -      -       +      -
    501F  ADP      3.8     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  PRO*     3.5     3.5    -      -       -      +
    130F  TRP*     3.0    31.4    +      -       -      +
    256F  PHE*     1.3    78.6    -      -       -      +
    258F  THR*     1.3    63.2    +      -       -      +
    261F  MET*     3.8     7.4    -      -       -      -
    262F  ARG*     2.9    21.7    +      -       -      -
    335F  GLY      3.1    26.2    -      -       -      -
    336F  TYR*     3.7     0.9    -      -       -      -
    501F  ADP      2.7    32.0    +      -       -      -
----------------------------------------------------------
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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