Contacts of the strand formed by residues 314 - 318 (chain A) 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 TYR 314 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLY*     4.0    15.7    -      -       -      -
    168A  ASN      4.1     0.7    -      -       -      -
    169A  ASN*     3.1    48.6    +      -       +      -
    170A  PRO      3.8    17.3    -      -       -      +
    171A  THR      4.8     0.3    -      -       -      +
    172A  GLY*     4.3     6.8    -      -       -      +
    200A  TYR*     3.9    15.9    +      +       -      -
    205A  TYR*     4.6     1.0    +      -       -      -
    311A  ALA      4.0     5.7    -      -       -      +
    312A  THR*     2.8    37.7    +      -       -      +
    313A  MET*     1.3   106.5    -      -       +      +
    315A  LEU*     1.3    70.5    +      -       -      +
    316A  TRP      4.4     0.2    +      -       -      -
    354A  ARG*     3.6    37.5    -      -       +      -
    355A  ILE      3.3     3.6    -      -       -      -
    356A  ALA*     4.5     2.5    -      -       -      -
    357A  LEU*     4.6     0.9    -      -       -      -
    501A  EPE      3.5    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  PRO      4.7     0.7    -      -       -      -
    205A  TYR*     5.1     0.2    -      -       -      +
    293A  ALA*     3.9    37.2    -      -       +      +
    296A  MET*     4.2    21.8    -      -       +      -
    297A  ALA*     4.3     6.1    -      -       -      +
    300A  LEU*     4.5     8.7    -      -       +      -
    306A  LEU*     4.1    16.2    -      -       +      -
    307A  LEU      5.7     1.1    -      -       -      +
    309A  PRO*     4.2    19.5    -      -       +      -
    314A  TYR*     1.3    83.3    -      -       -      +
    316A  TRP*     1.3    60.6    +      -       -      +
    317A  GLY      3.9     0.7    -      -       -      -
    353A  VAL      3.6     1.4    -      -       -      +
    354A  ARG*     3.3     5.7    -      -       -      +
    355A  ILE*     2.8    47.5    +      -       +      +
    357A  LEU*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  VAL*     3.9    19.5    -      -       +      -
    140A  LEU*     5.3     3.8    -      -       -      +
    170A  PRO*     3.3    40.4    -      -       +      +
    171A  THR*     3.5    42.2    +      -       +      +
    305A  SER      4.2     1.9    -      -       -      +
    306A  LEU*     3.7     8.8    -      -       -      +
    307A  LEU*     4.0    31.4    +      -       +      +
    315A  LEU*     1.3    71.9    -      -       -      +
    317A  GLY*     1.3    59.5    +      -       -      +
    318A  ARG      4.1     0.7    +      -       -      -
    342A  GLY*     3.6    32.3    -      -       -      -
    345A  PHE*     3.8     9.4    -      +       -      -
    348A  GLY      4.7     0.2    -      -       -      -
    349A  GLY*     4.1     8.1    -      -       -      -
    352A  PHE*     3.2    42.4    -      +       +      -
    353A  VAL      3.7     8.3    -      -       -      -
    354A  ARG*     3.7    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  LEU*     4.2    14.3    -      -       -      +
    305A  SER      3.7     3.8    -      -       -      -
    306A  LEU*     3.5    20.6    -      -       -      +
    315A  LEU      3.9     0.8    -      -       -      -
    316A  TRP*     1.3    74.4    -      -       -      +
    318A  ARG*     1.3    61.8    +      -       -      -
    319A  LEU      3.7     0.7    +      -       -      -
    352A  PHE*     3.4     7.5    -      -       -      -
    353A  VAL*     3.1    38.8    +      -       -      +
    355A  ILE*     5.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLU*     5.6     7.7    +      -       -      +
    303A  VAL      4.6     0.2    -      -       -      +
    304A  LEU*     3.7     6.4    -      -       -      -
    305A  SER*     3.1    45.9    +      -       -      +
    307A  LEU*     6.1     2.2    -      -       -      +
    316A  TRP      4.1     0.4    +      -       -      -
    317A  GLY*     1.3    71.5    -      -       -      -
    319A  LEU*     1.3    73.3    +      -       -      +
    351A  GLY      3.7     7.9    -      -       -      +
    352A  PHE*     3.5    45.4    -      -       +      -
----------------------------------------------------------
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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