Contacts of the strand formed by residues 252 - 257 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  MET*     3.5    36.1    -      -       -      -
    134H  GLU      3.3    13.0    -      -       -      -
    135H  GLN*     3.9    20.0    -      -       -      +
    218H  LEU*     4.3     2.7    -      -       -      -
    251H  GLY*     1.3    75.2    -      -       -      +
    253H  HIS*     1.3    67.9    +      -       -      +
    254H  THR*     3.1    12.0    +      -       -      -
    342H  PRO*     2.6    18.6    +      -       -      +
    343H  SER      3.2    22.7    -      -       -      +
    344H  ALA*     3.9     5.4    -      -       -      +
    346H  CYS*     4.0     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 253 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132H  GLY      3.5     2.6    -      -       -      +
    133H  MET*     3.3     3.5    -      -       -      -
    134H  GLU*     2.9    44.6    +      -       +      +
    136H  GLU*     4.3     3.4    +      -       -      -
    251H  GLY*     4.6     1.6    -      -       -      -
    252H  CYS*     1.3    77.4    -      -       -      +
    254H  THR*     1.3    60.5    +      -       -      +
    255H  ASN      3.8     0.4    +      -       -      -
    338H  GLU*     2.7    22.3    +      -       +      +
    339H  ASP      3.5     7.6    -      -       -      +
    340H  ARG*     3.3    37.5    -      -       +      +
    342H  PRO*     4.7     0.7    -      -       -      -
    401H   MN      4.3     2.7    -      -       -      -
    402H   MN      2.2    26.8    +      -       -      -
    601H  P3S      2.7    59.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 254 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  PHE*     4.1    11.4    -      -       +      -
    132H  GLY      3.6     2.5    -      -       -      -
    133H  MET*     3.4    29.9    -      -       +      +
    252H  CYS      3.1    12.2    +      -       -      -
    253H  HIS*     1.3    70.5    -      -       -      +
    255H  ASN*     1.3    68.7    +      -       -      +
    256H  PHE*     4.1     2.3    +      -       -      +
    337H  PHE      4.0     0.5    -      -       -      +
    339H  ASP*     2.9    35.1    +      -       -      +
    342H  PRO*     3.5     7.7    -      -       -      +
    351H  VAL*     3.4    18.7    -      -       +      +
    352H  THR*     4.9     0.7    -      -       +      -
    355H  LEU*     3.7    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 255 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  PHE*     3.3     7.8    -      -       -      +
    132H  GLY      2.7    45.5    +      -       -      +
    134H  GLU*     3.3    25.8    +      -       -      +
    253H  HIS      3.9     1.6    +      -       -      -
    254H  THR*     1.3    73.3    -      -       -      +
    256H  PHE*     1.3    64.2    +      -       -      +
    326H  PRO*     5.1     0.7    -      -       -      +
    336H  TYR*     3.4    24.9    -      -       +      -
    337H  PHE      3.2     5.4    -      -       -      -
    338H  GLU*     3.1    28.2    -      -       -      +
    501H  ADP      3.3    37.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 256 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  PRO*     4.0     6.5    -      -       +      -
    130H  TRP      3.4    12.3    -      -       -      -
    131H  PHE*     3.4    31.0    -      +       +      -
    254H  THR      4.7     1.6    -      -       -      +
    255H  ASN*     1.3    77.3    -      -       -      +
    257H  SER*     1.3    76.7    +      -       -      +
    258H  THR*     3.8    18.4    -      -       +      -
    261H  MET*     4.2    17.0    -      -       +      +
    336H  TYR*     3.2     4.7    -      -       -      +
    337H  PHE*     2.9    71.1    +      +       +      +
    355H  LEU*     4.5    17.9    -      -       +      -
    356H  ILE*     3.8    23.1    -      -       +      -
    359H  CYS*     4.2    17.9    -      -       +      -
    360H  LEU*     4.3     4.9    -      -       +      -
    501H  ADP      4.2     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  PRO*     3.5     3.3    -      -       -      +
    130H  TRP*     3.0    29.6    +      -       -      +
    256H  PHE*     1.3    81.0    -      -       -      +
    258H  THR*     1.3    64.2    +      -       -      +
    261H  MET*     3.7     9.0    -      -       -      -
    262H  ARG*     3.1    19.7    +      -       -      +
    335H  GLY      3.1    27.6    -      -       -      -
    336H  TYR*     3.6     5.4    -      -       -      -
    501H  ADP      2.9    22.9    +      -       -      -
----------------------------------------------------------
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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