Contacts of the strand formed by residues 352 - 356 (chain B) in PDB entry 2DOU


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 PHE 352 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305B  SER      5.3     0.9    -      -       -      -
    316B  TRP*     3.3    50.7    -      +       +      -
    317B  GLY      3.2     8.7    -      -       -      +
    318B  ARG*     3.3    68.4    -      -       +      -
    319B  LEU      4.6     0.7    -      -       -      +
    325B  ASP*     3.3    10.2    -      -       -      +
    342B  GLY*     2.6    26.9    +      -       -      -
    348B  GLY      3.9    17.5    -      -       -      -
    349B  GLY      2.9    12.6    +      -       -      +
    350B  LYS      4.5     5.2    -      -       -      -
    351B  GLY*     1.3    84.4    -      -       -      +
    353B  VAL*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304B  LEU*     4.0    24.9    -      -       +      -
    315B  LEU      3.8     0.3    -      -       -      +
    316B  TRP*     3.6     8.6    -      -       -      -
    317B  GLY      3.1    30.2    +      -       -      +
    319B  LEU*     3.9    25.8    -      -       +      -
    325B  ASP*     4.3     9.6    -      -       +      +
    328B  PHE*     4.7     7.2    -      -       +      -
    329B  GLY*     5.7     2.0    -      -       -      +
    339B  LEU*     3.8    33.2    -      -       +      -
    340B  ALA      3.5     9.6    -      -       -      +
    341B  PRO*     5.0     2.0    -      -       +      -
    342B  GLY      5.0     0.2    -      -       -      +
    352B  PHE*     1.3    80.3    -      -       -      +
    354B  ARG*     1.3    59.8    +      -       -      +
    355B  ILE*     4.6     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  LEU      3.8     5.0    -      -       -      +
     31B  SER      3.2    23.6    +      -       -      -
     33B  GLY      3.6     8.9    -      -       -      +
    169B  ASN*     3.1    16.7    +      -       -      +
    170B  PRO*     3.3    34.1    -      -       +      +
    314B  TYR*     3.5    28.6    -      -       +      -
    315B  LEU      3.5     5.4    -      -       -      +
    316B  TRP*     4.0     6.0    -      -       +      -
    339B  LEU*     4.1     1.8    -      -       -      +
    340B  ALA*     2.8    33.4    +      -       +      +
    345B  PHE*     3.4    34.9    -      -       +      -
    353B  VAL*     1.3    74.8    -      -       -      +
    355B  ILE*     1.3    65.3    +      -       -      +
    356B  ALA*     4.1     3.5    +      -       -      +
    505B  SO4      2.7    44.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  LEU*     3.8    26.0    -      -       +      -
    296B  MET*     3.2    41.1    -      -       +      -
    300B  LEU*     3.9    14.6    -      -       +      -
    304B  LEU*     4.1    16.2    -      -       +      -
    306B  LEU*     5.8     0.7    -      -       +      -
    313B  MET      3.5     0.9    -      -       -      +
    314B  TYR*     3.2     5.9    -      -       -      -
    315B  LEU*     2.9    48.2    +      -       +      +
    317B  GLY      6.2     0.4    -      -       -      +
    339B  LEU*     3.9    16.6    -      -       +      -
    353B  VAL*     4.6     4.7    -      -       +      -
    354B  ARG*     1.3    77.7    -      -       -      +
    356B  ALA*     1.3    66.4    +      -       -      +
    357B  LEU*     3.6     4.5    +      -       +      +
    371B  ILE*     4.1    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  LEU*     3.1    34.3    +      -       -      +
     32B  ILE      3.8    31.6    -      -       -      +
     33B  GLY*     4.0    10.1    -      -       -      +
    313B  MET      3.3     7.2    -      -       -      +
    314B  TYR*     4.3     7.2    -      -       +      -
    354B  ARG*     4.1     4.6    +      -       -      +
    355B  ILE*     1.3    72.5    -      -       -      +
    357B  LEU*     1.3    51.8    +      -       -      +
    358B  VAL*     2.6    27.8    +      -       +      +
----------------------------------------------------------
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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