Contacts of the strand formed by residues 182 - 188 (chain B) in PDB entry 2ARE


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 ASN 182 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  THR      3.7     1.0    -      -       -      +
    176B  PHE*     3.4     5.4    -      -       -      -
    177B  ASN*     3.1    26.0    +      -       +      +
    180B  THR*     3.1    32.5    +      -       -      +
    181B  ARG*     1.3    79.7    -      -       -      +
    183B  LEU*     1.3    59.5    +      -       -      +
    184B  ASP*     3.8    25.0    +      -       -      +
    198B  SER*     5.0     6.0    -      -       -      -
    199B  TYR      3.6     6.7    -      -       -      +
    200B  GLU*     3.9    15.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  PHE*     4.2    10.8    -      -       +      -
     92B  ILE*     6.0     0.4    -      -       +      -
    125B  ILE*     4.0    22.9    -      -       +      -
    127B  VAL*     4.6    11.7    -      -       +      -
    149B  ILE*     4.0    32.9    -      -       +      +
    151B  VAL*     6.1     0.2    -      -       +      -
    174B  VAL*     3.7    22.9    -      -       +      -
    175B  THR      3.3    14.1    -      -       -      +
    176B  PHE*     4.1    20.4    -      -       +      -
    181B  ARG      3.7     0.8    +      -       -      -
    182B  ASN*     1.3    71.7    -      -       -      +
    184B  ASP*     1.3    59.1    +      -       -      +
    185B  VAL*     5.1     1.3    -      -       +      -
    197B  VAL      4.0     0.3    -      -       -      +
    198B  SER*     3.2     4.2    -      -       -      -
    199B  TYR*     2.8    38.9    +      -       +      +
    201B  VAL*     4.3    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173B  LEU      3.7     1.4    -      -       -      +
    174B  VAL*     3.3     5.9    -      -       -      +
    175B  THR*     2.8    48.4    +      -       -      +
    177B  ASN*     5.9     2.1    -      -       -      +
    182B  ASN*     4.0    21.3    +      -       -      +
    183B  LEU*     1.3    74.7    -      -       -      +
    185B  VAL*     1.3    63.7    +      -       -      +
    186B  VAL*     5.4     7.2    -      -       +      -
    197B  VAL      3.8     2.2    -      -       -      -
    198B  SER*     2.6    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     3.9    44.0    -      -       +      -
    129B  PHE*     4.7     2.5    -      -       +      -
    147B  ILE*     4.5     8.7    -      -       +      -
    149B  ILE*     4.4    10.1    -      -       +      -
    172B  VAL*     4.2    18.2    -      -       +      -
    173B  LEU      3.5     2.7    -      -       -      +
    174B  VAL*     4.4     5.6    -      -       +      -
    183B  LEU*     5.1     1.6    -      -       +      -
    184B  ASP*     1.3    80.0    -      -       -      +
    186B  VAL*     1.3    71.4    +      -       -      +
    187B  ALA*     4.9     3.6    -      -       +      +
    195B  TYR      5.6     0.7    -      -       -      +
    196B  GLU*     3.3     5.7    -      -       -      +
    197B  VAL*     2.9    53.1    +      -       +      +
    198B  SER*     5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ASN      3.9     0.5    -      -       -      +
    172B  VAL*     3.4     2.3    -      -       -      +
    173B  LEU*     2.9    45.7    +      -       +      +
    184B  ASP*     5.4     6.7    -      -       +      -
    185B  VAL*     1.3    84.0    -      -       -      +
    187B  ALA*     1.3    63.5    +      -       -      +
    188B  THR*     4.6     4.9    -      -       +      -
    194B  ARG*     3.6    41.3    -      -       +      +
    195B  TYR      3.4     7.0    -      -       -      +
    196B  GLU*     4.2    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  PHE*     4.4     2.0    -      -       +      -
    147B  ILE*     4.2    20.6    -      -       +      -
    170B  LEU*     3.9    26.0    -      -       +      -
    171B  ASN      3.2     9.0    -      -       -      +
    172B  VAL*     4.1     9.0    -      -       +      -
    185B  VAL*     4.3     2.4    -      -       +      +
    186B  VAL*     1.3    74.6    -      -       -      +
    188B  THR*     1.3    67.1    +      -       -      +
    194B  ARG*     3.4     0.5    -      -       -      +
    195B  TYR*     2.9    38.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  SER      4.1     0.3    -      -       -      +
    170B  LEU*     3.4    10.2    -      -       -      +
    171B  ASN*     2.8    45.9    +      -       -      +
    186B  VAL*     4.6     4.7    -      -       +      -
    187B  ALA*     1.3    81.4    -      -       -      +
    189B  TYR*     1.3    66.6    +      -       -      +
    192B  GLY*     4.9     5.4    -      -       -      +
    193B  THR      3.2     9.9    -      -       -      +
    194B  ARG*     3.8    36.8    -      -       +      +
    195B  TYR*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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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