Contacts of the strand formed by residues 401 - 405 (chain D) in PDB entry 3OS8


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 LYS 401 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395D  SER*     3.4    15.4    -      -       -      +
    398D  HIS*     2.9    22.0    +      -       +      +
    399D  PRO      4.0     7.9    -      -       -      +
    400D  GLY*     1.3    84.3    -      -       -      +
    402D  LEU*     1.3    59.9    +      -       -      +
    409D  LEU*     3.5    42.0    -      -       +      +
    410D  LEU      3.1    12.3    -      -       -      +
    411D  ASP*     3.7    21.7    +      -       +      +
    429D  LEU*     3.5    12.0    -      -       -      +
    432D  SER*     5.3     0.3    +      -       -      -
    436D  ARG*     5.8     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 402 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391D  LEU*     4.3    11.2    -      -       +      -
    392D  VAL*     5.5     1.1    -      -       -      -
    395D  SER*     3.4    14.8    -      -       -      +
    401D  LYS*     1.3    77.0    -      -       -      +
    403D  LEU*     1.3    61.0    +      -       -      +
    404D  PHE*     3.2    25.6    +      -       +      -
    408D  LEU      3.7     0.3    -      -       -      +
    409D  LEU*     3.4     2.4    -      -       -      -
    410D  LEU      2.7    34.5    +      -       -      -
    425D  PHE*     3.5    47.6    -      -       +      +
    428D  LEU*     3.9    42.8    -      -       +      +
    429D  LEU*     4.1    15.3    -      -       +      +
    432D  SER*     5.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 403 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326D  ILE*     5.2     2.0    -      -       +      -
    391D  LEU*     3.4     6.9    -      -       -      +
    394D  ARG*     3.1    47.0    +      -       +      +
    395D  SER*     2.8    13.3    +      -       -      +
    398D  HIS*     3.3    36.6    -      -       +      +
    402D  LEU*     1.3    68.3    -      -       -      +
    404D  PHE*     1.3    65.4    +      -       -      +
    405D  ALA*     3.1    32.8    -      -       -      +
    406D  PRO*     3.7    14.4    -      -       +      +
    408D  LEU      4.0     2.0    -      -       -      -
    409D  LEU*     3.6    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 404 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  KN0      3.9    27.1    -      +       -      -
    327D  LEU      4.7     1.4    -      -       -      +
    342D  MET*     4.9     5.2    -      -       -      -
    346D  LEU*     3.5    32.8    -      -       +      -
    349D  LEU*     3.4    17.5    -      -       +      +
    391D  LEU*     3.6    32.1    -      -       +      -
    394D  ARG*     3.1    21.0    +      -       -      +
    402D  LEU*     3.2    33.1    +      -       +      -
    403D  LEU*     1.3    73.4    -      -       -      +
    405D  ALA*     1.3    62.7    +      -       -      +
    408D  LEU*     3.0    25.4    +      -       +      +
    410D  LEU*     3.7    32.1    -      -       +      -
    425D  PHE*     4.0    11.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 405 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326D  ILE*     5.3     0.4    -      -       -      -
    327D  LEU      3.4    14.6    -      -       -      +
    329D  SER*     3.6    13.0    -      -       -      +
    349D  LEU*     4.7     3.8    -      -       +      -
    394D  ARG*     5.0     0.7    -      -       -      +
    403D  LEU*     3.1    15.4    -      -       -      +
    404D  PHE*     1.3    78.4    -      -       -      +
    406D  PRO*     1.3    73.9    -      -       +      +
    407D  ASN*     3.1    16.4    -      -       -      +
    408D  LEU*     2.8    33.9    +      -       +      +
    409D  LEU      3.8     0.3    +      -       -      -
----------------------------------------------------------
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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