Contacts of the strand formed by residues 164 - 168 (chain A) in PDB entry 6D6U


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 ILE 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  PRO*     3.8     0.6    -      -       -      +
     36A  VAL*     3.7    15.9    -      -       +      +
     38A  VAL*     3.7    25.8    -      -       +      -
     92A  TRP*     4.4     9.9    -      -       +      -
     94A  PRO*     3.9    21.3    -      -       +      -
     95A  ASP*     5.7     0.7    -      -       -      +
    156A  SER*     3.9    20.0    -      -       -      +
    159A  TYR*     3.8    36.1    -      -       +      +
    160A  THR      3.3     2.7    +      -       -      +
    161A  THR*     3.9     5.4    -      -       -      +
    163A  ASP*     1.3    78.5    -      -       -      +
    165A  GLU*     1.3    76.0    +      -       -      +
    166A  PHE*     4.0    15.7    -      -       +      -
    206A  PRO*     3.9    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  PRO*     4.2    21.7    -      -       +      +
     36A  VAL      3.1    10.9    +      -       -      +
     37A  ALA*     3.9     9.1    -      -       +      -
     38A  VAL*     2.8    31.5    +      -       -      +
    161A  THR*     3.0    30.9    +      -       -      +
    164A  ILE*     1.3    77.5    -      -       -      +
    166A  PHE*     1.3    69.6    +      -       -      +
    167A  TYR*     4.3     3.6    -      -       +      -
    197A  LYS*     4.7    14.3    +      -       -      -
    206A  PRO*     5.2     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     3.4    27.6    -      -       +      -
     40A  MET*     4.1    20.9    -      -       -      -
     65A  GLN*     5.5     0.2    -      -       -      -
     94A  PRO*     5.4     1.3    -      -       +      -
     95A  ASP      4.7     0.9    -      -       -      -
     96A  THR*     3.9    23.1    -      -       +      -
    154A  ILE      4.9     0.9    -      -       -      -
    155A  GLU*     3.7    13.0    -      -       -      -
    156A  SER*     3.4    40.4    -      -       -      -
    164A  ILE*     4.0    20.4    +      -       +      -
    165A  GLU*     1.3    85.7    +      -       -      +
    167A  TYR*     1.3    64.1    +      -       -      +
    195A  THR*     4.4    14.6    -      -       -      +
    206A  PRO*     4.6    21.6    -      -       +      +
    207A  ARG      5.4     1.1    -      -       -      +
    208A  LEU*     3.6    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ALA*     3.8    26.6    +      -       +      +
     38A  VAL      3.4    10.3    +      -       -      -
     39A  GLY*     3.2    40.2    +      -       -      -
     40A  MET      3.3     3.8    +      -       -      -
     66A  ALA      5.0     2.6    +      -       -      -
    165A  GLU*     4.3     6.1    -      -       +      -
    166A  PHE*     1.3    78.0    -      -       -      +
    168A  TRP*     1.3    76.1    +      -       -      +
    169A  ARG*     4.5    16.2    -      -       +      -
    195A  THR*     5.4     2.2    -      -       +      -
    208A  LEU*     4.2     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     4.1    19.7    -      -       +      +
     42A  ILE*     3.6    43.3    -      -       +      -
    154A  ILE*     4.8     5.2    -      -       +      -
    167A  TYR*     1.3    83.2    -      -       -      +
    169A  ARG*     1.3    59.2    +      -       -      +
    170A  GLY      3.8     1.2    +      -       -      -
    171A  ASP*     3.3    27.3    +      -       -      +
    174A  ALA*     3.6    27.4    -      -       +      -
    175A  VAL*     4.3    13.0    -      -       +      -
    193A  LEU*     4.0    27.0    -      -       +      +
    194A  ILE      3.4    18.5    +      -       -      -
    195A  THR*     3.9     9.8    +      -       -      -
    208A  LEU*     3.5    34.6    -      -       +      +
    209A  SER      3.7    21.6    +      -       -      -
    210A  LEU*     4.8     4.0    -      -       +      -
----------------------------------------------------------
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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