Contacts of the strand formed by residues 210 - 219 (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 TRP 210 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ASP*     3.3    33.7    +      -       +      +
     15A  GLN*     4.7     4.3    -      -       -      -
     16A  LYS*     3.4    45.0    -      -       +      +
     17A  ASN*     4.0     3.6    -      -       -      -
      1B  GLN*     3.8    29.4    -      -       -      -
     55B  GLN*     3.8    36.6    -      -       +      +
     56B  VAL      3.4    20.2    -      -       -      -
     57B  HIS*     3.4    48.3    +      +       +      -
     95B  PRO*     3.2    19.3    -      -       +      +
    208B  PRO*     3.5    10.1    -      -       -      +
    209B  GLU*     1.3    89.3    -      -       +      +
    211B  VAL*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  GLN*     3.4     5.7    -      -       -      -
     56B  VAL*     2.8    49.7    +      -       +      +
     58B  LEU*     4.0    24.2    -      -       +      -
     92B  ILE*     3.5    24.9    -      -       +      -
     93B  ALA      3.1    17.3    -      -       -      +
     95B  PRO*     3.9     5.8    -      -       -      -
    207B  LEU*     4.1     9.2    -      -       +      -
    208B  PRO*     3.5    21.3    -      -       +      +
    210B  TRP*     1.3    80.4    -      -       -      +
    212B  ARG*     1.3    64.7    +      -       -      +
    213B  VAL*     4.7     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ILE*     3.7    25.5    -      -       -      +
     51B  LEU*     4.5    21.6    -      -       +      +
     52B  PHE      3.6    17.9    +      -       -      +
     53B  SER*     2.9    29.3    +      -       -      +
     54B  ALA      4.5     4.0    -      -       -      +
     55B  GLN*     4.1    25.3    -      -       +      +
     56B  VAL*     5.0     0.9    -      -       -      +
     91B  PHE      4.1     0.2    -      -       -      +
     92B  ILE*     3.5     3.8    -      -       -      +
     93B  ALA*     2.9    32.6    +      -       -      +
     94B  PRO      4.8     1.1    -      -       -      +
     95B  PRO*     2.9    46.5    +      -       +      +
     97B  THR*     5.3     0.7    -      -       +      -
    211B  VAL*     1.3    77.6    -      -       -      +
    213B  VAL*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  PHE*     4.3    10.5    -      -       +      -
     51B  LEU*     3.4     5.8    -      -       -      -
     52B  PHE*     3.0    31.1    +      -       +      +
     56B  VAL*     4.3    20.2    -      -       +      -
     90B  PHE*     4.2    10.1    -      -       +      -
     91B  PHE      3.4     4.9    -      -       -      +
     92B  ILE*     4.0    26.5    -      -       +      -
    211B  VAL*     4.7     2.9    -      -       +      -
    212B  ARG*     1.3    80.5    -      -       -      +
    214B  GLY*     1.3    59.8    +      -       -      +
    231B  TRP*     3.7    21.1    -      -       +      -
    233B  PHE*     4.1    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ILE      3.1    14.4    -      -       -      -
     51B  LEU*     4.0     5.1    -      -       -      +
     90B  PHE*     3.3    11.2    -      -       -      -
     91B  PHE*     2.8    34.5    +      -       -      -
    213B  VAL*     1.3    77.7    -      -       -      +
    215B  PHE*     1.3    71.4    +      -       -      -
    231B  TRP*     4.1     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     4.0    18.6    -      -       +      +
     49B  ARG*     3.0     6.8    -      -       -      +
     50B  ILE*     2.9    41.0    +      -       +      +
     73B  PHE*     3.5    55.0    -      +       +      -
     88B  ILE*     4.5     9.4    -      -       +      -
     89B  ALA      3.1    16.6    -      -       -      +
     90B  PHE*     3.8    20.0    -      +       +      -
     91B  PHE*     3.6     3.9    -      -       -      -
    214B  GLY*     1.3    78.4    -      -       -      -
    216B  SER*     1.3    62.4    +      -       -      +
    228B  LEU*     3.5    28.5    -      -       +      -
    231B  TRP*     3.4    36.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     4.3     2.9    -      -       -      -
     48B  GLY      3.5     6.7    +      -       -      -
     49B  ARG*     3.1    29.4    -      -       -      +
     88B  ILE*     3.4     2.3    -      -       -      +
     89B  ALA*     2.8    33.3    +      -       -      +
     91B  PHE*     3.9     3.1    -      -       -      -
    108B  LEU*     2.7    27.4    +      -       -      +
    109B  GLY*     3.7     3.6    -      -       -      -
    110B  LEU*     3.9    18.8    -      -       -      -
    215B  PHE*     1.3    76.2    -      -       -      +
    217B  ALA*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     3.8    17.3    -      -       +      -
     34B  THR*     3.9     2.9    -      -       +      +
     47B  VAL*     3.5     3.8    -      -       -      +
     48B  GLY      3.0    29.3    +      -       -      +
     87B  GLY      3.2    16.6    -      -       -      +
     88B  ILE*     4.0     1.8    -      -       -      -
    108B  LEU*     4.2     5.4    -      -       -      -
    216B  SER*     1.3    76.7    +      -       -      +
    218B  ALA*     1.3    65.5    +      -       -      +
    226B  HIS*     3.5    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  THR*     3.8     4.9    -      -       -      +
     46B  THR      3.3    12.6    -      -       -      +
     47B  VAL*     3.8    15.0    -      -       +      -
     86B  ASP*     2.8    33.9    +      -       +      +
     87B  GLY      3.4     4.1    +      -       -      -
    105B  GLY      3.8    24.9    -      -       -      +
    108B  LEU*     3.9    14.7    +      -       -      +
    109B  GLY      4.1     0.4    -      -       -      +
    217B  ALA*     1.3    78.7    -      -       -      +
    219B  SER*     1.3    55.7    +      -       -      +
    226B  HIS*     3.3     6.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  THR*     4.3     2.3    -      -       -      +
     43B  VAL      4.1     1.1    +      -       -      -
     45B  SER*     3.2     4.9    +      -       -      -
     46B  THR*     2.9    43.4    +      -       -      +
     47B  VAL*     5.4     0.2    -      -       -      +
     85B  ALA      2.7    17.7    +      -       -      -
     86B  ASP*     3.6     5.2    -      -       -      -
    105B  GLY*     4.2     6.1    +      -       -      -
    218B  ALA*     1.3    72.2    +      -       -      +
    220B  GLY*     1.3    60.3    +      -       -      +
    222B  GLN      3.5    13.5    -      -       -      -
    223B  TYR*     3.6    13.3    -      -       -      +
    224B  GLN      3.6     8.0    +      -       -      -
    226B  HIS*     3.4    11.6    +      -       -      -
----------------------------------------------------------
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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