Contacts of the strand formed by residues 6164 - 6168 (chain F) in PDB entry 2H7C


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 VAL6164 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6121F  ILE*     3.9    21.8    -      -       +      -
   6122F  TYR      3.5    11.2    -      -       -      +
   6123F  THR*     3.6    22.9    -      -       -      +
   6124F  PRO*     4.3     0.4    -      -       -      -
   6133F  LEU*     4.2     9.6    -      -       +      -
   6134F  PRO      2.9    11.1    +      -       -      +
   6135F  VAL*     3.4     8.6    -      -       +      +
   6136F  MET*     2.8    28.2    +      -       -      +
   6163F  VAL*     1.3    73.8    -      -       -      +
   6165F  VAL*     1.3    62.1    +      -       -      +
   6166F  VAL*     4.2     4.7    -      -       +      -
   6205F  ILE*     4.0    18.6    -      -       +      -
   6208F  PHE      4.2     1.8    -      -       -      +
   6209F  GLY      4.1     4.5    -      -       -      +
   6210F  GLY*     3.8    27.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL6165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6121F  ILE*     3.5     1.0    -      -       -      -
   6122F  TYR*     2.8    47.8    +      -       +      +
   6136F  MET*     3.5     9.4    -      -       +      +
   6138F  TRP*     5.3     0.4    -      -       +      -
   6154F  GLY*     3.9    25.6    -      -       -      +
   6157F  LEU*     3.9    21.8    -      -       +      -
   6158F  ALA*     3.8    27.6    -      -       -      +
   6163F  VAL*     3.9     8.3    -      -       +      -
   6164F  VAL*     1.3    74.6    -      -       -      +
   6166F  VAL*     1.3    66.5    +      -       -      +
   6167F  THR*     4.5    14.1    -      -       +      -
   6218F  PHE*     5.0     4.5    -      -       +      -
   6476F  PHE*     4.6    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL6166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6119F  LEU*     4.2    21.5    -      -       +      -
   6120F  ASN      3.3     9.0    -      -       -      +
   6121F  ILE*     4.2     8.1    -      -       +      -
   6135F  VAL*     4.0    14.8    -      -       +      -
   6136F  MET      3.0     8.7    +      -       -      +
   6137F  VAL*     3.3    10.0    -      -       +      +
   6138F  TRP*     2.7    33.1    +      -       -      +
   6164F  VAL*     4.2     4.5    -      -       +      -
   6165F  VAL*     1.3    78.0    -      -       -      +
   6167F  THR*     1.3    58.5    +      -       -      +
   6168F  ILE*     3.9    20.2    -      -       +      -
   6201F  VAL*     4.5     9.9    -      -       +      -
   6205F  ILE*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR6167 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6119F  LEU*     3.2     3.6    -      -       -      +
   6120F  ASN*     2.9    52.3    +      -       -      +
   6122F  TYR*     4.4     7.0    -      -       +      -
   6138F  TRP*     3.8    26.5    -      -       +      -
   6149F  ALA*     3.7    21.2    +      -       -      +
   6152F  TYR*     3.8    22.3    +      -       +      +
   6154F  GLY      5.3     0.2    -      -       -      +
   6165F  VAL*     4.5    12.1    -      -       +      -
   6166F  VAL*     1.3    75.0    -      -       -      +
   6168F  ILE*     1.3    62.3    +      -       -      +
   6476F  PHE*     4.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE6168 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6055F  PHE*     4.9     0.2    -      -       +      -
   6118F  TYR      4.0     4.0    -      -       -      +
   6119F  LEU*     4.1     7.9    -      -       +      -
   6137F  VAL*     3.6    26.0    -      -       +      -
   6138F  TRP*     3.2    16.7    +      -       -      +
   6139F  ILE*     4.0    24.5    -      -       +      -
   6140F  HIS*     3.6    14.9    +      -       -      -
   6149F  ALA*     3.4    10.7    -      -       -      +
   6166F  VAL*     3.9    11.7    -      -       +      -
   6167F  THR*     1.3    78.9    -      -       -      +
   6169F  GLN*     1.3    69.6    +      -       -      +
   6170F  TYR*     4.6     2.7    -      -       +      -
   6194F  GLN*     4.1    26.7    -      -       +      +
   6197F  ALA*     3.9    33.4    -      -       +      -
   6198F  LEU*     5.7     1.6    -      -       +      -
   6201F  VAL*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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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