Contacts of the strand formed by residues 208 - 213 (chain P) in PDB entry 3QUM


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 VAL 208 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  A2G      3.5    35.7    -      -       -      +
      2F  GAL      3.7    19.5    -      -       -      +
     28H  ALA*     3.7    15.9    -      -       +      +
    121P  MET*     4.9     1.1    -      -       -      -
    122P  ASP      4.6     2.0    -      -       -      +
    124P  PRO*     3.4    24.0    -      -       +      -
    200P  VAL*     3.4     3.9    -      -       -      -
    201P  CYS      2.8    36.5    +      -       -      +
    202P  ASN*     4.5     3.1    -      -       +      +
    203P  GLY*     1.3    77.4    -      -       -      +
    209P  LEU*     1.3    80.6    +      -       -      +
    210P  GLN*     4.0     7.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 209 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29P  TRP*     6.4     0.2    -      -       +      -
     45P  VAL*     4.6    14.1    -      -       +      -
     47P  VAL*     5.5     1.1    -      -       +      -
     53P  LEU*     4.7    14.8    -      -       +      -
    121P  MET*     3.5    35.9    -      -       +      -
    122P  ASP      4.4     5.3    +      -       -      +
    123P  LEU*     5.0    12.8    -      -       +      -
    124P  PRO*     2.9    23.7    -      -       +      +
    198P  PRO*     3.9    25.4    -      -       +      -
    199P  LEU      3.8    10.3    -      -       -      +
    200P  VAL*     3.7     9.6    -      -       +      -
    203P  GLY      3.6     1.4    +      -       -      -
    208P  VAL*     1.3    83.5    -      -       -      +
    210P  GLN*     1.3    68.5    +      -       -      +
    211P  GLY      3.9    13.0    -      -       -      +
    212P  ILE*     5.1     2.9    -      -       +      -
    231P  VAL*     4.6    16.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 210 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  A2G      4.5     6.1    +      -       -      -
    124P  PRO*     3.7    15.7    -      -       -      +
    128P  GLN      3.1    23.0    -      -       -      +
    129P  GLU*     3.7     1.2    -      -       -      -
    130P  PRO*     3.0    45.2    -      -       +      +
    181P  LEU*     3.3    15.1    -      -       +      +
    199P  LEU*     3.1    12.4    +      -       +      +
    201P  CYS*     3.7    29.7    +      -       +      +
    208P  VAL*     4.0    16.2    -      -       -      +
    209P  LEU*     1.3    75.7    -      -       -      +
    211P  GLY*     1.3    60.1    +      -       -      +
    230P  LYS*     4.1     0.7    -      -       +      +
    231P  VAL*     3.3    24.5    +      -       -      +
    232P  VAL*     4.6     4.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 211 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181P  LEU*     4.6     0.4    -      -       -      -
    198P  PRO*     3.5     4.0    -      -       -      +
    199P  LEU*     2.8    46.2    +      -       -      +
    209P  LEU*     3.9     4.3    -      -       -      +
    210P  GLN*     1.3    79.2    -      -       -      +
    212P  ILE*     1.3    64.5    +      -       -      -
    228P  TYR*     4.5     3.1    -      -       -      -
    229P  THR      3.4    13.5    -      -       -      -
    231P  VAL*     3.6     8.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 212 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45P  VAL*     5.4     5.2    -      -       +      -
     53P  LEU*     3.5    43.3    -      -       +      +
     54P  THR*     4.0     9.0    -      -       -      +
     55P  ALA*     3.9    18.4    -      -       +      +
    102P  ASP      4.5     7.4    -      -       -      +
    103P  LEU*     4.1    15.3    -      -       +      -
    196P  GLY*     3.9    25.1    -      -       -      +
    197P  GLY      3.9     2.2    -      -       -      +
    198P  PRO*     5.2     2.9    -      -       +      -
    209P  LEU*     5.1     6.1    -      -       +      -
    211P  GLY*     1.3    76.8    -      -       -      +
    213P  THR*     1.3    74.4    +      -       -      +
    214P  SER      3.4     0.2    +      -       -      -
    228P  TYR*     3.3     3.8    -      -       -      -
    229P  THR*     2.7    38.9    +      -       -      -
    231P  VAL*     4.1     8.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 213 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55P  ALA*     3.8     6.9    -      -       -      +
     57P  HIS*     3.9     1.7    -      -       -      -
    194P  ASP      4.8     3.4    +      -       -      +
    195P  SER*     4.4    11.0    -      -       -      +
    196P  GLY*     3.5    27.0    +      -       -      +
    197P  GLY*     2.9    21.6    +      -       -      -
    212P  ILE*     1.3    79.9    -      -       -      +
    214P  SER*     1.3    74.3    +      -       -      +
    217P  SER*     3.5    18.6    -      -       -      +
    218P  GLU*     5.3     3.1    -      -       -      -
    219P  PRO*     5.4     7.1    -      -       +      +
    226P  SER*     6.1     0.4    -      -       -      -
    228P  TYR*     3.2    28.5    -      -       +      -
----------------------------------------------------------
 Back to top of page


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