Contacts of the strand formed by residues 162 - 167 (chain E) 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 GLU 162 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154E  GLN*     4.1    16.3    +      -       -      +
    157E  ASN*     4.7     5.5    +      -       -      +
    160E  MET      3.5    11.6    +      -       -      +
    161E  ASP*     1.3    79.8    -      -       -      +
    163E  HIS*     1.3    65.8    +      -       -      +
    164E  SER*     3.7     3.1    +      -       -      -
    228E  ASP*     5.3    12.3    -      -       +      +
    229E  LEU      3.3    10.3    -      -       -      +
    230E  SER*     5.1     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151E  CYS*     4.9     5.8    -      -       -      -
    152E  GLN      4.4     1.8    -      -       -      +
    153E  LEU*     3.4    30.3    -      -       +      +
    154E  GLN*     2.4    51.7    +      -       +      +
    155E  LEU*     3.4    22.3    -      -       +      +
    161E  ASP*     4.0    20.1    +      -       +      +
    162E  GLU*     1.3    75.0    -      -       -      +
    164E  SER*     1.3    58.2    +      -       -      +
    165E  CYS*     4.2     2.0    +      -       -      -
    201E  PHE*     3.9    28.3    -      +       +      -
    228E  ASP*     3.4     3.3    -      -       -      +
    229E  LEU*     2.7    49.2    +      -       +      +
    231E  ARG*     4.2     1.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151E  CYS*     3.4    11.0    -      -       -      -
    152E  GLN*     4.1    12.5    +      -       -      +
    154E  GLN*     6.0     0.2    -      -       -      +
    162E  GLU      3.7     2.8    +      -       -      -
    163E  HIS*     1.3    74.2    -      -       -      +
    165E  CYS*     1.3    59.2    +      -       -      +
    166E  PRO*     3.5     9.0    -      -       -      +
    207E  ARG*     5.6     0.7    -      -       -      -
    226E  TYR*     4.4    18.1    -      -       -      -
    227E  PHE      4.0     1.6    -      -       -      -
    228E  ASP*     3.1    22.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 165 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65E  VAL*     5.5     4.3    -      -       -      -
     72E  TYR*     3.5    33.6    +      -       +      -
    151E  CYS*     2.0    42.4    -      -       -      -
    153E  LEU*     5.1     2.0    -      -       -      -
    163E  HIS*     5.1     2.7    -      -       -      -
    164E  SER*     1.3    73.0    -      -       -      +
    166E  PRO*     1.3    66.0    -      -       -      +
    201E  PHE*     6.3     0.7    -      -       -      -
    226E  TYR*     3.5    16.3    -      -       -      +
    227E  PHE*     3.4    27.4    +      -       +      +
    229E  LEU*     4.2    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 166 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72E  TYR*     3.0    14.7    +      -       +      -
    115E  ASN*     3.1    31.2    -      -       -      +
    149E  ALA*     3.9     4.7    -      -       -      +
    150E  GLU      3.8    14.8    -      -       -      +
    151E  CYS*     4.2     4.0    -      -       -      -
    152E  GLN*     4.5     5.2    -      -       +      +
    164E  SER*     3.5     9.9    -      -       -      +
    165E  CYS*     1.3    87.0    -      -       +      +
    167E  LEU*     1.3    60.3    +      -       -      +
    168E  GLU*     5.3     8.7    -      -       -      +
    224E  SER*     5.4     3.4    -      -       -      +
    226E  TYR*     3.4    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 167 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57E  MET*     4.6    22.9    -      -       +      -
     72E  TYR*     4.2     6.3    -      -       -      +
     74E  ILE*     4.3    28.9    -      -       +      -
     76E  ILE*     4.7     9.9    -      -       +      -
    113E  PHE*     4.3    20.9    -      -       +      -
    115E  ASN*     4.7     4.5    -      -       +      -
    147E  ILE*     4.1    25.4    -      -       +      -
    149E  ALA*     4.5     9.9    -      -       +      -
    165E  CYS      5.2     0.4    -      -       -      +
    166E  PRO*     1.3    77.3    -      -       -      +
    168E  GLU*     1.3    62.2    +      -       -      +
    169E  PHE*     4.3     8.5    +      -       +      -
    224E  SER*     3.7     0.8    +      -       -      -
    225E  VAL*     2.9    43.3    +      -       +      +
    227E  PHE*     5.8     3.6    -      -       +      -
----------------------------------------------------------
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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