Contacts of the strand formed by residues 169 - 173 (chain A) in PDB entry 2EYZ


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 TRP 169 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ARG*     3.1    17.7    -      -       -      -
    104A  TYR*     5.3     0.4    -      -       -      -
    114A  LEU*     5.0     9.0    -      -       +      -
    115A  ILE      4.1     7.3    +      -       -      -
    116A  GLU*     2.8    48.8    -      -       +      +
    117A  PRO*     4.6     0.2    -      -       +      -
    150A  ASP*     5.7     0.2    -      -       +      -
    151A  LEU      5.9     0.2    -      -       -      -
    153A  PHE*     4.6     7.4    -      +       -      -
    165A  PRO*     3.2    19.2    -      -       -      +
    166A  GLU*     3.0    42.0    +      -       -      +
    167A  GLU      3.7     0.8    -      -       -      -
    168A  GLN*     1.3   117.0    +      -       +      +
    170A  TRP*     1.3    66.4    +      -       -      +
    181A  MET*     4.0    13.5    -      -       +      -
    182A  ILE*     3.0    13.9    -      -       -      +
    183A  PRO*     3.1    50.0    -      -       +      -
    184A  VAL*     3.7     1.2    -      -       -      +
    185A  PRO*     5.8     0.9    -      -       +      +
    186A  TYR*     5.6     4.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLU*     6.0     1.8    -      -       -      -
    137A  VAL*     5.1     9.6    -      -       +      -
    161A  ILE*     3.6    30.5    -      -       +      -
    163A  ASP      3.7     5.4    -      -       -      +
    164A  LYS*     3.1    49.6    -      -       +      -
    165A  PRO*     3.8     0.7    -      -       -      -
    166A  GLU      4.3     1.1    -      -       -      -
    169A  TRP*     1.3    84.1    -      -       -      +
    171A  ASN*     1.3    59.5    +      -       -      +
    181A  MET*     3.0     4.1    -      -       -      -
    182A  ILE*     2.6    47.2    +      -       +      +
    183A  PRO      6.0     0.4    -      -       -      -
    184A  VAL*     2.8    25.8    -      -       +      +
    187A  VAL*     6.0     4.5    -      -       +      -
    189A  LYS*     4.6    14.8    -      -       +      -
    191A  ARG*     6.2     0.4    -      -       -      -
    223A  GLN*     3.9    12.3    -      -       +      -
    224A  PRO*     3.1    24.7    -      -       +      +
    226A  VAL*     3.3    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ILE*     5.4    13.9    -      -       -      +
    149A  GLU*     4.9     6.8    +      -       -      +
    161A  ILE*     3.4     5.2    -      -       -      -
    162A  ARG*     2.7    38.4    +      -       +      -
    163A  ASP*     2.7    32.1    +      -       +      +
    165A  PRO*     3.3    28.4    -      -       -      +
    170A  TRP*     1.3    70.0    -      -       -      +
    172A  ALA*     1.3    59.1    +      -       -      +
    180A  GLY*     2.7    28.3    -      -       -      +
    181A  MET*     3.3    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  LEU*     4.0     7.6    -      -       -      +
    159A  LEU*     3.5    26.4    -      -       +      +
    160A  ARG      3.0    23.3    -      -       -      +
    161A  ILE*     4.3     1.6    -      -       +      +
    162A  ARG*     4.8     2.2    -      -       -      +
    170A  TRP      3.7     1.8    +      -       -      -
    171A  ASN*     1.3    73.9    -      -       -      +
    173A  GLU*     1.3    60.5    +      -       -      +
    179A  ARG*     4.7     4.0    -      -       -      -
    180A  GLY      2.7    32.2    +      -       -      +
    181A  MET*     4.4     0.4    -      -       -      +
    182A  ILE*     3.9    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  ILE      4.2     1.2    -      -       -      +
    159A  LEU*     3.0    27.4    -      -       -      +
    160A  ARG*     3.5    11.2    +      -       +      +
    172A  ALA*     1.3    74.9    -      -       -      +
    174A  ASP*     1.3    73.3    +      -       -      +
    177A  GLY*     3.4    24.1    -      -       -      +
    178A  LYS      3.1    20.9    -      -       -      +
    179A  ARG*     2.6    55.7    +      -       -      +
----------------------------------------------------------
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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