Contacts of the strand formed by residues 462 - 466 (chain C) in PDB entry 6T8B


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 LEU 462 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441C  LEU*     4.2     2.2    -      -       +      -
    443C  LEU*     5.3     0.2    -      -       +      -
    459C  MET*     4.0    20.2    -      -       +      -
    461C  HIS*     1.3    78.0    -      -       -      +
    463C  LEU*     1.3    61.8    +      -       -      +
    464C  VAL*     3.9    10.1    -      -       +      -
    479C  MET*     3.5    40.8    -      -       +      -
    626C  LEU      3.2     7.0    +      -       -      +
    627C  ILE*     3.7    21.5    -      -       +      -
    628C  LEU*     3.1    26.5    +      -       -      +
    646C  ILE*     3.8     4.9    -      -       -      +
    648C  THR*     3.3    31.4    -      -       +      +
    649C  ARG*     4.4     0.4    -      -       -      +
    650C  ILE*     3.6    28.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 463 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462C  LEU*     1.3    73.5    -      -       -      +
    464C  VAL*     1.3    64.3    +      -       -      +
    465C  ALA      3.7     0.2    +      -       -      -
    628C  LEU*     3.3    33.7    -      -       +      +
    630C  THR*     4.3    18.2    -      -       +      +
    633C  PRO*     4.0    27.6    -      -       +      -
    638C  ILE*     4.9     9.0    -      -       +      -
    643C  LYS*     4.1    13.0    -      -       +      -
    646C  ILE*     3.7    19.3    -      -       +      -
    648C  THR      3.2     7.5    +      -       -      -
    649C  ARG*     3.4    38.2    -      -       +      +
    650C  ILE      3.2    21.0    +      -       -      +
    663C  ILE*     4.5     3.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 464 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462C  LEU*     3.9    14.1    -      -       +      -
    463C  LEU*     1.3    74.0    -      -       -      +
    465C  ALA*     1.3    64.8    +      -       -      +
    472C  LYS*     3.8    21.1    -      -       +      +
    475C  GLY      6.0     0.2    -      -       -      +
    476C  VAL*     4.6    11.9    -      -       +      -
    479C  MET*     4.1    26.5    -      -       +      -
    627C  ILE*     4.7     6.7    -      -       +      -
    628C  LEU      3.0     7.5    +      -       -      +
    629C  ALA*     3.2    14.5    -      -       +      -
    630C  THR*     2.8    26.6    +      -       -      -
    650C  ILE*     3.6    11.9    -      -       +      -
    652C  PHE*     3.4    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 465 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463C  LEU      4.5     1.1    -      -       -      +
    464C  VAL*     1.3    80.6    -      -       -      +
    466C  GLY*     1.3    58.8    +      -       -      +
    472C  LYS*     3.6     5.8    -      -       -      -
    630C  THR*     3.4    26.2    -      -       -      +
    631C  GLN      4.5     0.4    -      -       -      -
    633C  PRO*     3.6    17.7    -      -       +      -
    650C  ILE      3.1     9.9    +      -       -      +
    651C  ALA*     3.4     3.5    -      -       -      -
    652C  PHE*     2.9    23.7    +      -       -      +
    663C  ILE*     3.4    24.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 466 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465C  ALA*     1.3    78.1    -      -       -      +
    467C  THR*     1.3    61.7    +      -       -      -
    470C  SER*     3.7     3.4    -      -       -      -
    472C  LYS*     2.5    28.6    +      -       -      +
    630C  THR      3.8     0.2    +      -       -      -
    631C  GLN*     3.4    22.7    +      -       -      +
    652C  PHE      3.2    17.0    -      -       -      -
    654C  VAL*     4.4     8.7    -      -       -      -
    663C  ILE*     4.0     0.2    -      -       -      +
----------------------------------------------------------
 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