Contacts of the strand formed by residues 146 - 151 (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 HIS 146 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  GLU*     3.4     8.9    -      -       -      +
    129B  PHE*     3.7     1.7    -      -       -      -
    130B  ASP*     3.0    46.4    +      -       +      +
    133B  TYR*     4.5     3.1    -      -       +      -
    141B  ASP*     3.1    18.3    +      -       +      -
    142B  PRO*     3.4    16.8    -      -       +      +
    144B  TYR*     2.7    27.1    +      -       +      +
    145B  PRO*     1.3    74.1    -      -       -      +
    147B  ILE*     1.3    65.4    +      -       -      +
    159B  THR*     3.8    25.4    -      -       +      -
    160B  VAL      3.3    16.2    -      -       -      +
    162B  TRP*     3.7    11.4    -      -       -      +
    282B   MN      2.2    35.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     4.2    17.5    -      -       +      -
    128B  GLU      3.3     9.4    -      -       -      +
    129B  PHE*     3.7    31.9    -      -       +      -
    146B  HIS*     1.3    76.4    -      -       -      +
    148B  GLY*     1.3    64.0    +      -       -      +
    159B  THR*     3.2     4.2    -      -       -      -
    160B  VAL*     3.0    40.7    +      -       +      +
    162B  TRP*     3.9    24.0    -      -       +      -
    185B  VAL*     4.5     5.6    -      -       +      -
    187B  ALA*     4.2     9.4    -      -       +      -
    195B  TYR*     3.8    29.2    -      -       +      -
    197B  VAL*     4.1    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     3.4     8.1    -      -       -      +
    128B  GLU*     2.9    47.7    +      -       -      +
    146B  HIS*     4.5     0.2    -      -       -      -
    147B  ILE*     1.3    77.1    -      -       -      +
    149B  ILE*     1.3    64.3    +      -       -      -
    150B  ASP*     4.0     0.4    -      -       -      -
    156B  SER*     3.8     7.2    -      -       -      -
    158B  LYS      3.2    10.3    -      -       -      -
    159B  THR*     4.1     4.0    -      -       -      -
    197B  VAL*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  ILE*     5.3     0.4    -      -       +      -
    126B  ALA      3.6     6.1    -      -       -      +
    127B  VAL*     4.8     2.9    -      -       +      -
    148B  GLY*     1.3    74.6    -      -       -      +
    150B  ASP*     1.3    66.3    +      -       -      +
    151B  VAL*     4.3    11.4    -      -       +      -
    156B  SER*     3.4     0.3    -      -       -      -
    157B  VAL*     2.9    46.1    +      -       +      +
    158B  LYS*     3.0    10.5    +      -       +      +
    183B  LEU*     4.0    30.3    -      -       +      +
    185B  VAL*     4.4    13.0    -      -       +      -
    197B  VAL*     4.1    37.0    -      -       +      +
    198B  SER      4.1     0.9    -      -       -      -
    199B  TYR*     3.7    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  LEU*     5.0     1.2    -      -       -      +
    110B  LEU*     5.1     1.2    -      -       -      +
    111B  PHE*     4.6     8.7    -      -       +      -
    124B  VAL      3.7     1.1    -      -       -      +
    125B  ILE*     3.3     5.7    -      -       -      +
    126B  ALA*     2.7    53.4    +      -       +      +
    128B  GLU*     2.6    35.6    -      -       -      +
    149B  ILE*     1.3    74.1    -      -       -      +
    151B  VAL*     1.3    63.1    +      -       -      +
    152B  ASN      4.0     0.7    -      -       -      -
    153B  SER      3.4    21.1    -      -       -      +
    154B  ILE*     4.1    10.5    -      -       -      +
    156B  SER*     2.6    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  THR*     4.1     6.4    -      -       -      +
    124B  VAL      3.6     2.9    -      -       -      -
    125B  ILE*     4.6    10.3    -      -       +      -
    149B  ILE*     4.1     8.8    +      -       +      -
    150B  ASP*     1.3    76.2    -      -       -      +
    152B  ASN*     1.3    68.7    +      -       -      +
    153B  SER*     3.1    13.8    +      -       -      +
    155B  ARG      5.6     0.4    +      -       -      -
    157B  VAL*     4.0    24.9    -      -       +      +
    183B  LEU*     6.1     0.2    -      -       +      -
    199B  TYR*     4.1    27.4    -      -       +      +
    201B  VAL*     4.6    11.9    -      -       +      -
    206B  VAL*     4.0    34.3    -      -       +      -
----------------------------------------------------------
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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