Contacts of the strand formed by residues 342 - 346 (chain A) in PDB entry 2HHQ


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 GLY 342 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  VAL*     3.4     3.0    -      -       -      +
    339A  ASN*     3.0    33.5    +      -       -      +
    340A  GLU      3.4     1.0    +      -       -      -
    341A  HIS*     1.3    80.6    -      -       -      +
    343A  ARG*     1.3    66.6    +      -       -      +
    344A  PHE*     3.6    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  MET*     3.7    25.9    -      -       -      +
    300A  ALA*     2.7    34.9    +      -       -      +
    301A  PHE*     3.5    17.1    -      -       +      +
    302A  THR*     2.9    23.6    +      -       -      -
    337A  VAL      3.4     3.8    -      -       -      -
    338A  VAL*     4.0    20.5    -      -       +      +
    342A  GLY*     1.3    78.4    -      -       -      +
    344A  PHE*     1.3    68.9    +      -       -      +
    448A  VAL*     3.7    21.5    -      -       +      -
    452A  ALA*     4.3     6.4    -      -       -      +
    904A  SO4      3.4    33.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  THR*     3.5    26.0    -      -       +      +
    310A  GLU*     3.3    37.9    -      -       +      -
    311A  MET*     3.8    44.9    -      -       +      -
    336A  ALA*     3.1     7.3    -      -       -      +
    337A  VAL*     2.7    54.6    +      -       +      +
    339A  ASN*     3.7    18.6    -      -       -      -
    341A  HIS*     4.1    14.1    -      -       +      -
    342A  GLY*     3.6    19.7    -      -       -      -
    343A  ARG*     1.3    80.7    -      -       -      +
    345A  PHE*     1.3    63.0    +      -       -      +
    346A  LEU*     5.2     2.7    -      -       +      -
    448A  VAL*     4.1     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  PHE*     4.1    21.3    -      -       +      -
    302A  THR      3.0     7.7    +      -       -      +
    303A  LEU*     3.7    20.9    -      -       +      -
    304A  ALA*     3.0    29.6    +      -       -      +
    333A  VAL      4.7     1.1    -      -       -      -
    334A  GLY*     4.1     8.5    -      -       -      -
    335A  ILE      3.3    17.0    -      -       -      -
    336A  ALA*     4.4     1.1    -      -       +      +
    344A  PHE*     1.3    75.1    -      -       -      +
    346A  LEU*     1.3    76.5    +      -       -      +
    347A  ARG*     4.2     6.7    -      -       +      -
    348A  PRO*     5.4     0.2    -      -       +      -
    440A  GLU*     4.0    28.3    -      -       +      -
    443A  LEU*     4.4    12.6    -      -       +      -
    444A  ALA*     3.6    32.3    -      -       +      -
    447A  LEU*     3.8    25.4    -      -       +      -
    448A  VAL*     4.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  ALA*     3.5    31.4    -      -       +      +
    306A  ARG      4.0    14.8    -      -       -      +
    307A  VAL*     4.1    11.2    -      -       +      -
    311A  MET*     3.9    24.9    -      -       +      -
    335A  ILE*     2.8    39.1    +      -       +      +
    337A  VAL*     5.1     7.0    -      -       +      -
    344A  PHE*     4.3     2.4    -      -       +      -
    345A  PHE*     1.3    83.6    -      -       -      +
    347A  ARG*     1.3    63.3    +      -       -      +
    348A  PRO*     3.5     0.7    -      -       -      +
    350A  THR*     4.6     7.2    -      -       -      +
    351A  ALA*     3.9    18.8    -      -       +      -
    357A  PHE*     3.9    28.0    -      -       +      -
----------------------------------------------------------
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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