Contacts of the strand formed by residues 35 - 39 (chain E) 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 VAL 35 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  ARG      3.0     7.7    +      -       -      +
     34E  CYS*     1.3    72.6    -      -       -      +
     36E  GLU*     1.3    62.5    +      -       -      +
     37E  VAL*     3.3    11.8    +      -       +      +
     51E  VAL*     3.4    33.2    -      -       +      -
     52E  LYS      3.6     2.7    -      -       -      -
     53E  LEU*     4.0    25.1    -      -       +      +
    154E  ILE*     5.2     6.1    -      -       +      -
      3H  MET*     4.3     9.4    -      -       +      -
      4H  GLU      3.9     6.0    +      -       -      +
      5H  MET*     3.5    36.6    -      -       +      -
      6H  ARG      3.6    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 36 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  CYS*     3.0    16.4    -      -       -      +
     35E  VAL*     1.3    70.0    -      -       -      +
     37E  VAL*     1.3    62.0    +      -       -      +
     50E  ARG*     3.9     6.2    +      -       -      +
     51E  VAL*     3.4     4.2    -      -       -      -
     52E  LYS*     2.9    56.9    +      -       +      +
      6H  ARG*     3.0    30.0    -      -       -      +
      7H  LEU      2.6    30.5    -      -       -      +
      8H  PRO*     3.3    17.2    -      -       +      +
      9H  VAL      4.8     0.2    +      -       -      -
    274H  PRO*     5.6     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 37 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  VAL*     3.3    21.3    +      -       +      +
     36E  GLU*     1.3    75.9    -      -       -      +
     38E  GLU*     1.3    71.8    +      -       -      +
     39E  THR*     5.7     1.6    -      -       -      -
     50E  ARG      3.7     5.8    -      -       -      +
     51E  VAL*     4.6     5.4    -      -       +      -
    154E  ILE*     4.6    13.5    -      -       +      -
    158E  ALA*     4.6    18.2    -      -       +      -
    270E  LEU*     4.6     8.5    -      -       +      -
    273E  VAL*     4.9    12.5    -      -       +      +
    274E  VAL*     5.0     8.1    -      -       +      -
    277E  GLU*     4.9     3.1    -      -       -      +
      5H  MET*     4.3    24.5    -      -       +      -
      6H  ARG      3.4     5.1    +      -       -      +
      7H  LEU*     3.6    12.1    -      -       -      +
      8H  PRO*     3.2    19.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  VAL*     1.3    81.7    -      -       -      +
     39E  THR*     1.3    69.8    +      -       -      +
     41E  VAL*     3.8    23.3    -      -       +      +
     49E  ALA*     3.4     4.3    -      -       -      +
     50E  ARG*     2.9    64.1    +      -       -      +
    158E  ALA*     5.1     0.2    -      -       -      +
    277E  GLU*     4.6     9.2    -      -       -      +
    286E  LYS*     3.7    17.0    -      -       -      +
    287E  VAL*     2.6    37.0    +      -       -      +
    288E  GLY*     3.8     4.0    +      -       -      -
      7H  LEU*     6.2     0.4    -      -       +      -
      8H  PRO*     3.7    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 39 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  VAL*     5.7     1.8    -      -       +      -
     38E  GLU*     1.3    83.2    -      -       -      +
     40E  ASP*     1.3    71.5    +      -       +      +
     41E  VAL      3.4     2.2    +      -       -      +
     48E  SER      3.2     8.0    +      -       -      -
     49E  ALA*     4.2     3.1    -      -       -      +
    158E  ALA*     4.0    10.1    +      -       -      -
    162E  ASN*     2.0    46.7    +      -       -      +
    274E  VAL*     5.1    14.6    -      -       +      -
    277E  GLU*     3.2    42.0    +      -       +      +
    286E  LYS*     4.7     5.4    -      -       -      +
----------------------------------------------------------
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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