Contacts of the strand formed by residues 165 - 170 (chain E) in PDB entry 1VQN


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 165 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87E  PHE      2.7    31.6    +      -       -      +
     93E  MET*     3.1    14.6    -      -       -      +
    152E  THR*     3.4    19.5    -      -       -      -
    164E  ASP*     1.3    74.4    -      -       -      +
    166E  VAL*     1.3    64.0    +      -       -      -
    167E  TYR*     3.4    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 166 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  MET*     3.7    27.1    -      -       +      -
     85E  GLU      3.7    13.7    -      -       -      +
     86E  VAL*     4.0    15.5    -      -       +      +
     93E  MET*     4.2     3.4    -      -       -      -
     95E  VAL*     4.2     9.2    -      -       +      -
    104E  ILE*     4.0    27.4    -      -       +      -
    131E  LEU*     3.8    16.8    -      -       +      -
    148E  ILE*     4.3    17.9    -      -       +      +
    149E  GLU*     3.3    26.9    -      -       -      +
    152E  THR*     3.5     7.1    +      -       +      -
    165E  GLY*     1.3    75.5    -      -       -      -
    167E  TYR*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 167 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  MET*     3.1    25.2    -      -       -      -
     85E  GLU*     3.1    17.3    +      -       +      +
     87E  PHE*     4.8    10.3    -      +       +      -
    149E  GLU*     3.5    20.9    -      -       +      +
    152E  THR*     5.8     1.1    -      -       -      -
    159E  VAL*     5.0     8.6    -      -       +      +
    163E  GLN*     2.5    39.8    +      -       +      +
    164E  ASP      3.7     4.5    +      -       -      -
    165E  GLY*     3.4    21.3    -      -       -      -
    166E  VAL*     1.3    79.0    -      -       -      +
    168E  ILE*     1.3    70.6    +      -       -      +
    169E  THR*     3.1     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 168 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82E  TYR*     4.4     9.9    -      -       +      -
     83E  GLY      3.5     2.7    -      -       -      +
     84E  MET*     3.6    20.6    -      -       +      -
    145E  ALA*     3.3    39.3    -      -       +      +
    146E  ALA*     4.3     3.4    -      -       -      +
    149E  GLU*     2.8    26.4    +      -       +      +
    167E  TYR*     1.3    73.6    -      -       -      +
    169E  THR*     1.3    62.2    +      -       -      +
    170E  ARG      4.0    11.0    -      -       -      +
    171E  LYS*     3.9    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83E  GLY*     2.5    23.8    +      -       -      -
     85E  GLU*     3.2    51.8    +      -       +      +
    167E  TYR*     3.5     2.4    +      -       -      +
    168E  ILE*     1.3    75.2    -      -       -      +
    170E  ARG*     1.3    71.4    +      -       +      +
    171E  LYS*     4.4     1.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 170 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  GLU*     4.6    18.9    +      -       -      +
     82E  TYR*     3.4    13.3    -      -       -      +
     83E  GLY*     3.1    45.6    +      -       -      +
    130E  GLU*     5.8     2.6    +      -       -      -
    132E  THR*     4.7     9.7    +      -       -      -
    168E  ILE*     4.0     4.0    -      -       -      +
    169E  THR*     1.3    96.3    -      -       +      +
    171E  LYS*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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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