Contacts of the strand formed by residues 836 - 844 (chain C) in PDB entry 6VVT


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 GLY 836 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    786C  GLU*     3.8     5.8    -      -       -      +
    787C  VAL*     3.1    35.3    +      -       -      +
    835C  SER*     1.3    77.5    -      -       -      +
    837C  LYS*     1.3    66.6    +      -       -      -
    864C  VAL*     3.8     6.3    -      -       -      -
    865C  ALA      3.3    13.2    -      -       -      -
    866C  GLN*     4.4     2.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 837 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  HIS*     5.1    11.9    -      -       +      -
     62A  GLU*     6.2     0.7    -      -       +      +
     63A  PHE*     4.8    17.7    -      -       +      -
    151A  GLN*     4.0    12.3    +      -       -      -
    152A  ASN*     3.0    41.8    +      -       -      +
    159A  ILE      5.6     0.2    +      -       -      -
    161A  ARG      4.7     2.2    +      -       -      -
    162A  ILE*     5.7     3.8    -      -       -      +
    163A  PRO*     4.7     7.7    -      -       -      +
    784C  GLY      3.8    23.3    +      -       -      +
    785C  ALA      3.5     1.6    -      -       -      -
    786C  GLU*     3.5    25.3    +      -       +      +
    836C  GLY*     1.3    75.0    -      -       -      -
    838C  VAL*     1.3    67.0    +      -       -      +
    839C  ILE*     5.2     0.4    -      -       +      -
    864C  VAL*     3.2     4.4    -      -       -      +
    865C  ALA*     2.9    33.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 838 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  HIS*     3.7     5.4    -      -       -      -
    781C  VAL*     3.7    30.1    -      -       +      -
    782C  ARG      4.0    11.4    -      -       -      +
    783C  ILE*     4.5     0.4    -      -       -      -
    784C  GLY*     3.0    27.3    +      -       -      +
    785C  ALA      3.1    18.8    +      -       -      +
    787C  VAL*     3.9    12.1    -      -       +      -
    793C  LEU*     4.6     0.2    -      -       +      -
    837C  LYS*     1.3    72.8    -      -       -      +
    839C  ILE*     1.3    62.6    +      -       -      +
    841C  ILE*     3.5    32.3    -      -       +      -
    862C  VAL*     3.5    22.2    -      -       +      -
    863C  TYR      3.6     4.3    -      -       -      +
    864C  VAL*     4.4     7.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 839 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  HIS*     3.4    19.1    +      -       +      +
     63A  PHE*     3.9    31.6    -      -       +      +
    666C  PHE*     4.6    12.1    -      -       +      +
    743C  ILE*     4.2    22.9    -      -       +      -
    783C  ILE*     3.1    24.0    -      -       -      +
    837C  LYS*     4.5     1.1    -      -       +      +
    838C  VAL*     1.3    73.3    -      -       -      +
    840C  GLY*     1.3    61.1    +      -       -      +
    863C  TYR*     2.8    20.2    +      -       +      +
    865C  ALA*     3.2    37.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 840 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    783C  ILE*     5.0     1.6    -      -       -      -
    838C  VAL      3.9     0.2    -      -       -      -
    839C  ILE*     1.3    85.4    -      -       -      +
    841C  ILE*     1.3    72.3    +      -       -      +
    862C  VAL*     3.7     0.7    -      -       -      +
    863C  TYR*     3.0    39.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 841 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778C  ARG*     4.4     9.4    -      -       -      +
    780C  ILE*     4.0    17.0    -      -       +      -
    781C  VAL      3.8    17.5    -      -       -      +
    783C  ILE*     3.6    30.8    -      -       +      +
    838C  VAL*     3.5    20.4    -      -       +      -
    840C  GLY*     1.3    82.6    -      -       -      +
    842C  ARG*     1.3    67.8    +      -       -      +
    843C  VAL*     4.2     3.8    +      -       +      +
    860C  VAL*     3.4    27.4    -      -       +      -
    861C  ARG      3.5     4.3    -      -       -      +
    862C  VAL*     4.2    16.4    -      -       +      -
    863C  TYR*     5.6     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 842 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  ASP*     3.5    26.1    +      -       -      +
    841C  ILE*     1.3    76.6    +      -       -      +
    843C  VAL*     1.3    90.5    +      -       -      +
    844C  PHE*     3.2    49.2    -      -       +      -
    859C  LEU*     3.6     2.3    -      -       +      +
    860C  VAL*     2.9     6.4    -      -       -      +
    861C  ARG*     2.8    46.1    +      -       +      +
    863C  TYR*     4.9    11.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 843 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778C  ARG*     3.6    31.4    -      -       -      +
    841C  ILE*     4.1     4.0    -      -       +      +
    842C  ARG*     1.3    94.4    +      -       -      +
    844C  PHE*     1.3    67.3    +      -       -      +
    845C  SER*     4.2     6.5    +      -       -      +
    850C  ASP*     4.5     1.2    -      -       -      +
    858C  GLU*     3.5    28.9    -      -       +      +
    859C  LEU      3.5     2.0    -      -       -      +
    860C  VAL*     4.1     8.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 844 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  ASP*     3.9    24.2    -      -       -      -
    116C  LYS*     4.6    13.0    -      -       +      -
    117C  ASP*     5.8     3.6    -      -       -      -
    842C  ARG*     3.2    57.4    -      -       +      -
    843C  VAL*     1.3    74.4    -      -       -      +
    845C  SER*     1.3    59.8    +      -       -      +
    850C  ASP*     3.3    20.0    -      -       +      +
    852C  LEU*     3.6    11.5    -      -       +      +
    858C  GLU*     3.1     4.1    -      -       -      -
    859C  LEU*     2.4    87.2    +      -       +      +
----------------------------------------------------------
 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