Contacts of the strand formed by residues 409 - 414 (chain C) in PDB entry 6T8G


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 409 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  ILE*     2.9    40.3    +      -       +      +
    372C  PRO*     4.3    15.0    -      -       +      -
    377C  LYS      6.1     0.2    -      -       -      +
    378C  VAL*     4.2    24.5    -      -       +      -
    381C  ILE*     4.8    16.8    -      -       +      -
    399C  VAL*     4.7     6.7    -      -       +      -
    400C  VAL      3.4    16.6    -      -       -      +
    401C  GLU*     4.5     6.5    -      -       -      +
    402C  VAL      5.7     0.2    -      -       -      +
    408C  THR*     1.3    81.7    -      -       -      +
    410C  GLY*     1.3    66.2    +      -       -      +
    411C  ILE*     3.8     1.1    +      -       +      +
    390D  ARG*     3.8    27.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 410 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367C  ARG*     4.6     9.2    -      -       -      -
    368C  PHE      3.8    11.0    -      -       -      -
    369C  GLU*     5.3     0.2    -      -       -      -
    399C  VAL*     3.5     3.1    -      -       -      +
    400C  VAL*     2.6    59.0    +      -       -      +
    402C  VAL      5.4     0.2    -      -       -      +
    403C  ILE*     5.5     4.2    -      -       -      +
    408C  THR*     4.2     1.7    +      -       -      -
    409C  VAL*     1.3    73.7    -      -       -      +
    411C  ILE*     1.3    65.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 411 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  LEU*     4.4    11.7    -      -       +      -
    347C  LEU*     4.9     2.5    -      -       +      -
    366C  THR      3.6     1.4    -      -       -      +
    367C  ARG*     3.9     0.4    -      -       -      +
    368C  PHE*     3.0    40.7    +      -       +      +
    370C  ILE*     3.6    29.2    -      -       +      -
    381C  ILE*     4.2    20.0    -      -       +      -
    388C  LEU*     4.5    19.3    -      -       +      -
    397C  VAL*     3.7    22.7    -      -       +      -
    398C  ARG      3.4     7.9    -      -       -      +
    399C  VAL*     4.4    11.4    -      -       +      -
    409C  VAL*     3.8     2.1    +      -       +      +
    410C  GLY*     1.3    78.6    -      -       -      +
    412C  GLU*     1.3    63.5    +      -       -      +
    413C  ILE*     3.9    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 412 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  ILE*     3.8    19.7    -      -       +      +
    366C  THR      3.5     5.4    -      -       -      -
    367C  ARG*     4.1    13.8    +      -       -      -
    397C  VAL*     3.3    13.6    -      -       -      +
    398C  ARG*     3.0    54.8    +      -       +      +
    400C  VAL*     4.0    11.9    -      -       +      +
    411C  ILE*     1.3    74.7    -      -       -      +
    413C  ILE*     1.3    63.8    -      -       -      +
    414C  PRO*     3.6     3.6    -      -       -      +
    447C  ILE*     3.7    22.2    -      -       -      +
    690C  ARG*     2.4    44.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 413 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  MET*     4.3    23.1    -      -       +      -
    343C  LEU*     3.7    25.1    -      -       +      -
    365C  ILE*     3.3     4.4    -      -       -      +
    366C  THR*     3.0    32.0    +      -       -      +
    368C  PHE*     3.5    31.2    -      -       +      -
    392C  LEU*     4.3    15.3    -      -       +      -
    394C  VAL*     4.1     9.9    -      -       +      -
    397C  VAL*     3.7     7.6    -      -       +      -
    411C  ILE*     3.9    17.2    -      -       +      -
    412C  GLU*     1.3    70.6    -      -       -      +
    414C  PRO*     1.3    84.0    -      -       +      +
    415C  ASN*     3.4     1.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 414 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  MET*     6.1     0.3    -      -       -      +
    365C  ILE*     4.0    10.3    -      -       +      -
    394C  VAL*     3.4    34.6    -      -       +      +
    395C  ILE*     4.7     2.5    -      -       +      +
    396C  SER      3.3    27.4    -      -       -      +
    397C  VAL*     3.9     7.9    -      -       +      -
    412C  GLU      3.6     7.4    -      -       -      +
    413C  ILE*     1.3    98.3    -      -       +      +
    415C  ASN*     1.3    61.3    +      -       -      +
    416C  GLU*     4.0    10.5    +      -       -      +
    673C  LEU*     3.7    26.5    -      -       +      -
----------------------------------------------------------
 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