Contacts of the strand formed by residues 210 - 219 (chain A) 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 TRP 210 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GLN*     3.7    28.9    -      -       -      -
     55A  GLN*     3.6    37.9    -      -       +      +
     56A  VAL      3.4     7.6    -      -       -      -
     57A  HIS*     3.5    57.3    +      +       +      -
     95A  PRO*     3.4    17.9    -      -       +      +
    208A  PRO*     3.4    10.6    -      -       -      +
    209A  GLU*     1.3    86.0    -      -       +      +
    211A  VAL*     1.3    66.6    +      -       -      +
     14B  ASP*     2.7    48.9    +      -       -      -
     15B  GLN*     4.9     2.5    -      -       -      -
     16B  LYS*     3.4    40.6    -      -       +      +
     17B  ASN*     3.9     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  GLN*     3.4     6.4    -      -       -      -
     56A  VAL*     2.8    51.9    +      -       +      +
     58A  LEU*     4.1    17.9    -      -       +      -
     92A  ILE*     3.5    25.1    -      -       +      -
     93A  ALA      3.2    15.5    -      -       -      +
     95A  PRO*     4.0     5.4    -      -       -      -
    207A  LEU*     4.0    18.8    -      -       +      -
    208A  PRO*     3.6    22.2    -      -       +      +
    210A  TRP*     1.3    81.2    -      -       -      +
    212A  ARG*     1.3    65.9    +      -       -      +
    213A  VAL*     4.7     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     3.8    23.9    -      -       -      +
     51A  LEU*     4.3    22.4    -      -       +      +
     52A  PHE      3.6    16.2    +      -       -      +
     53A  SER*     2.9    30.3    +      -       -      -
     54A  ALA      4.5     2.0    -      -       -      +
     55A  GLN*     4.1    25.2    -      -       +      +
     56A  VAL*     5.0     0.9    -      -       -      +
     91A  PHE      4.1     0.2    -      -       -      +
     92A  ILE*     3.5     3.3    -      -       -      +
     93A  ALA      2.8    32.3    +      -       -      +
     94A  PRO      4.7     1.6    -      -       -      +
     95A  PRO*     2.9    47.3    +      -       +      +
     96A  ASP*     5.0     0.8    -      -       -      +
    211A  VAL*     1.3    79.4    -      -       -      +
    213A  VAL*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PHE*     4.2    12.6    -      -       +      -
     51A  LEU*     3.4     6.1    -      -       -      -
     52A  PHE*     3.0    30.3    +      -       +      +
     56A  VAL*     4.3    18.6    -      -       +      +
     90A  PHE*     4.2     8.5    -      -       +      -
     91A  PHE      3.4     6.1    -      -       -      +
     92A  ILE*     4.1    25.8    -      -       +      -
    211A  VAL*     4.7     2.5    -      -       +      -
    212A  ARG*     1.3    80.1    -      -       -      +
    214A  GLY*     1.3    59.2    +      -       -      +
    231A  TRP*     3.7    21.0    -      -       +      -
    233A  PHE*     4.1    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE      3.1    13.9    -      -       -      -
     51A  LEU*     4.1     4.3    -      -       -      +
     90A  PHE*     3.3    13.0    -      -       -      -
     91A  PHE*     2.9    34.0    +      -       -      -
    213A  VAL*     1.3    77.7    -      -       -      +
    215A  PHE*     1.3    65.4    +      -       -      -
    231A  TRP*     4.1    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     4.1    18.1    -      -       +      +
     49A  ARG*     3.1     7.6    -      -       -      +
     50A  ILE*     3.0    41.7    +      -       +      +
     73A  PHE*     3.6    55.9    -      +       +      -
     88A  ILE*     4.5     9.4    -      -       +      -
     89A  ALA      3.1    17.3    -      -       -      +
     90A  PHE*     3.8    18.4    -      +       +      -
     91A  PHE*     3.5     4.4    -      -       -      -
    214A  GLY*     1.3    77.4    -      -       -      -
    216A  SER*     1.3    60.1    +      -       -      +
    228A  LEU*     3.5    29.4    -      -       +      -
    231A  TRP*     3.4    36.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     4.4     2.5    -      -       -      -
     48A  GLY      3.5     6.3    -      -       -      -
     49A  ARG*     3.1    29.3    -      -       -      +
     87A  GLY      4.2     0.2    -      -       -      +
     88A  ILE*     3.3     2.1    -      -       -      +
     89A  ALA*     2.8    33.6    +      -       -      +
     91A  PHE*     3.9     9.2    -      -       -      -
    108A  LEU*     2.6    27.0    +      -       -      +
    109A  GLY*     3.7     4.0    -      -       -      -
    110A  LEU*     4.0    14.6    -      -       -      -
    215A  PHE*     1.3    75.8    -      -       -      +
    217A  ALA*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     3.8    17.3    -      -       +      -
     34A  THR*     3.8     3.4    -      -       +      +
     47A  VAL*     3.5     3.5    -      -       -      +
     48A  GLY      3.0    30.8    +      -       -      +
     87A  GLY      3.4    15.3    -      -       -      +
     88A  ILE*     4.1     2.0    -      -       -      -
    108A  LEU*     4.2     4.9    -      -       -      -
    216A  SER*     1.3    77.4    +      -       -      +
    218A  ALA*     1.3    65.1    +      -       -      +
    226A  HIS*     3.6    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  THR*     3.7     4.7    -      -       -      +
     46A  THR      3.2    12.6    -      -       -      +
     47A  VAL*     3.9    15.9    -      -       +      -
     86A  ASP*     2.8    32.6    +      -       -      +
     87A  GLY      3.5     3.9    +      -       -      -
    105A  GLY      3.7    24.2    -      -       -      +
    108A  LEU*     4.0    15.8    +      -       -      +
    217A  ALA*     1.3    79.7    -      -       -      +
    219A  SER*     1.3    56.3    +      -       -      +
    226A  HIS*     3.3     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  THR*     4.3     1.7    -      -       -      +
     43A  VAL      4.0     1.5    +      -       -      -
     45A  SER*     3.2     4.7    +      -       -      -
     46A  THR*     2.9    46.5    +      -       -      +
     47A  VAL*     5.5     0.3    -      -       -      +
     85A  ALA      2.7    18.0    +      -       -      -
     86A  ASP*     3.7     4.3    -      -       -      -
    105A  GLY*     4.3     5.0    +      -       -      -
    218A  ALA*     1.3    70.8    -      -       -      +
    220A  GLY*     1.3    59.9    +      -       -      +
    222A  GLN      3.5    13.2    -      -       -      -
    223A  TYR*     3.6    13.3    -      -       -      +
    224A  GLN      3.5     8.7    +      -       -      -
    226A  HIS*     3.4    13.9    +      -       -      -
----------------------------------------------------------
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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