Contacts of the strand formed by residues 304 - 308 (chain l) in PDB entry 6QX2


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 304 (chain l).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259l  ILE      3.7     1.7    -      -       -      +
    260l  VAL*     3.5     3.1    -      -       -      -
    261l  VAL*     2.9    49.9    +      -       +      +
    264l  ILE*     5.5     0.7    -      -       +      -
    270l  LYS*     4.2    15.3    -      -       +      -
    273l  MET*     4.8    12.1    -      -       +      -
    274l  ILE*     3.9    31.9    -      -       +      -
    277l  ILE*     5.5     1.3    -      -       +      -
    292l  LEU*     4.3    15.5    -      -       +      -
    293l  ARG      3.6    10.8    -      -       -      +
    294l  ASP*     3.9    13.5    -      -       -      +
    302l  VAL*     4.5     5.8    -      -       +      -
    303l  ARG*     1.3    75.1    -      -       -      +
    305l  VAL*     1.3    61.8    +      -       -      +
    306l  ILE*     4.8     7.3    -      -       +      +
    327l  LEU*     6.3     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 305 (chain l). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258l  ARG*     3.6    20.9    -      -       +      +
    259l  ILE      3.6     3.6    -      -       -      +
    260l  VAL*     4.8     3.1    -      -       +      -
    291l  ASP      4.2     0.3    -      -       -      +
    292l  LEU*     3.4     4.7    -      -       -      +
    293l  ARG*     2.8    66.7    +      -       +      +
    295l  GLU*     3.4    33.9    -      -       +      +
    303l  ARG*     3.9    23.1    -      -       +      +
    304l  VAL*     1.3    75.0    -      -       -      +
    306l  ILE*     1.3    64.1    -      -       -      +
    307l  ASP*     3.4    14.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 306 (chain l). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258l  ARG*     3.3     1.7    -      -       -      -
    259l  ILE*     2.8    56.8    +      -       +      +
    261l  VAL*     4.7    12.3    -      -       +      -
    277l  ILE*     4.4    13.5    -      -       +      -
    289l  ILE*     3.6    43.5    -      -       +      -
    291l  ASP      3.5     4.0    -      -       -      +
    292l  LEU*     3.7    21.8    -      -       +      -
    304l  VAL*     4.8     6.3    -      -       +      +
    305l  VAL*     1.3    76.6    -      -       -      +
    307l  ASP*     1.3    62.7    +      -       -      +
    308l  VAL*     3.8     2.6    +      -       +      +
    321l  LEU*     3.6    26.9    -      -       +      -
    327l  LEU*     5.4     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 307 (chain l). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252l  ARG*     3.7    29.9    +      -       -      +
    258l  ARG*     3.6    11.9    -      -       -      +
    289l  ILE*     3.5     6.9    -      -       -      +
    290l  THR*     2.9    43.1    +      -       -      +
    291l  ASP*     3.0    20.2    +      -       +      +
    293l  ARG*     3.0    28.2    +      -       -      -
    305l  VAL*     3.4    21.0    -      -       -      +
    306l  ILE*     1.3    71.2    -      -       -      +
    308l  VAL*     1.3    57.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 308 (chain l). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252l  ARG*     2.7    25.3    +      -       -      -
    256l  ARG*     4.4     0.3    -      -       -      +
    257l  GLN*     3.5    23.7    +      -       +      +
    258l  ARG*     4.5     3.4    -      -       -      -
    259l  ILE*     4.2    21.3    -      -       +      -
    288l  GLY      3.4     3.8    -      -       -      +
    289l  ILE*     5.5     0.2    -      -       +      -
    290l  THR*     3.9     0.9    -      -       -      -
    306l  ILE*     4.0    12.3    -      -       +      +
    307l  ASP*     1.3    76.3    -      -       -      +
    309l  ARG*     1.3    74.6    +      -       -      +
    310l  LYS      3.7     0.2    +      -       -      -
    312l  ALA*     3.7    16.2    -      -       +      +
    314l  ALA*     4.2    16.4    -      -       +      -
    317l  ILE*     3.5    33.4    -      -       +      -
----------------------------------------------------------
 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