Contacts of the strand formed by residues 329 - 332 (chain M) in PDB entry 6D6Q


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 HIS 329 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319M  TYR*     3.5     2.7    -      -       -      -
    320M  ILE*     3.1    31.3    +      -       +      +
    322M  PRO*     4.4     9.6    -      -       +      +
    325M  GLY*     5.7     2.7    -      -       -      -
    327M  GLY*     3.1    29.9    +      -       -      -
    328M  LEU*     1.3    73.7    -      -       -      +
    330M  LEU*     1.3    63.8    +      -       -      +
    331M  VAL*     3.8     4.3    +      -       +      +
    342M  ASN*     3.6    37.0    -      -       +      +
    343M  PHE*     5.4     0.2    -      -       -      -
    345M  THR*     3.8    24.7    -      -       +      +
    346M  ALA*     3.9    18.6    -      -       +      +
    349M  VAL*     4.2    20.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 330 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317M  GLN*     5.0     4.0    -      -       +      -
    318M  HIS      3.3    14.4    -      -       -      +
    319M  TYR*     3.4    34.4    -      -       +      +
    328M  LEU      4.1     0.8    +      -       -      -
    329M  HIS*     1.3    74.9    -      -       -      +
    331M  VAL*     1.3    64.1    +      -       -      +
    332M  VAL      3.1    29.4    -      -       -      +
    333M  ASP*     4.5     9.9    -      -       +      +
    339M  ARG*     3.2    35.8    -      -       +      +
    342M  ASN*     2.9    42.9    -      -       -      +
    343M  PHE      3.8     1.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 331 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318M  HIS*     3.5    21.8    +      -       +      +
    319M  TYR*     4.7     0.7    -      -       -      +
    320M  ILE*     3.4    35.7    -      -       +      -
    329M  HIS*     4.1     2.7    -      -       +      +
    330M  LEU*     1.3    84.4    -      -       -      +
    332M  VAL*     1.3    71.3    +      -       +      +
    337M  ASP      3.8     0.2    -      -       -      +
    338M  PHE*     3.2    17.9    -      -       +      -
    339M  ARG*     2.5    41.7    +      -       -      +
    343M  PHE*     3.9    17.0    -      -       +      -
    552M  LEU*     3.3    28.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 332 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316M  LEU      5.7     0.4    -      -       -      +
    317M  GLN*     4.3     0.7    -      -       -      -
    318M  HIS*     3.2    47.9    +      -       +      +
    330M  LEU*     3.1    19.7    -      -       -      +
    331M  VAL*     1.3    84.8    -      -       +      +
    333M  ASP*     1.3    70.5    +      -       -      +
    336M  GLY*     3.4    34.1    -      -       -      +
    337M  ASP      3.4     6.1    -      -       -      +
    338M  PHE*     3.9    14.1    -      -       +      +
    552M  LEU*     5.0     5.2    -      -       +      -
    553M  LYS*     6.1     4.0    -      -       +      -
----------------------------------------------------------
 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