Contacts of the strand formed by residues 440 - 445 (chain C) in PDB entry 6T8O


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 PRO 440 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432C  TYR*     3.6    35.0    -      -       +      -
    435C  HIS*     3.9    23.1    -      -       +      +
    437C  SER      3.6     6.9    -      -       -      +
    438C  THR      3.5     8.3    -      -       -      +
    439C  VAL*     1.3    92.1    -      -       -      +
    441C  LEU*     1.3    72.9    +      -       -      +
    442C  ALA      4.2     0.2    -      -       -      -
    453C  ILE*     4.4     3.1    -      -       +      -
    454C  THR      4.0     3.8    -      -       -      +
    482C  SER*     3.7    17.7    -      -       -      +
    483C  ILE*     3.3    12.6    -      -       +      +
    486C  LYS*     3.7    19.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 441 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440C  PRO*     1.3    84.2    -      -       -      +
    442C  ALA*     1.3    60.3    +      -       -      +
    443C  LEU*     3.2    15.6    +      -       +      -
    453C  ILE*     3.4     5.7    -      -       -      -
    454C  THR*     2.9    42.0    +      -       -      +
    456C  LEU*     3.7    34.5    -      -       +      -
    459C  MET*     3.7    23.3    -      -       +      -
    462C  LEU*     4.7     3.6    -      -       +      -
    479C  MET*     3.7    46.9    -      -       +      +
    482C  SER*     3.8     1.8    -      -       -      -
    483C  ILE*     4.2    10.5    -      -       +      -
    627C  ILE*     5.1     2.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 442 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423C  PHE*     4.1    12.0    -      -       +      -
    426C  VAL*     3.7    22.2    -      -       +      +
    427C  LEU*     3.8    22.0    -      -       +      -
    432C  TYR*     4.7     5.3    -      -       +      -
    440C  PRO      4.2     0.4    -      -       -      -
    441C  LEU*     1.3    69.0    -      -       -      +
    443C  LEU*     1.3    65.5    +      -       -      +
    444C  GLY      3.6     0.7    -      -       -      -
    453C  ILE*     4.2    15.2    -      -       +      +
    478C  ALA*     4.3     9.7    -      -       -      +
    479C  MET*     5.3     1.1    -      -       -      +
    482C  SER*     3.0    26.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 443 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426C  VAL*     4.7     0.2    -      -       -      -
    441C  LEU*     3.2    12.3    +      -       +      +
    442C  ALA*     1.3    76.9    -      -       -      +
    444C  GLY*     1.3    58.7    +      -       -      +
    452C  ILE*     3.4    15.3    +      -       +      +
    454C  THR*     3.8    27.1    -      -       +      +
    459C  MET*     5.9     0.4    -      -       +      -
    478C  ALA*     5.2     3.8    -      -       -      +
    479C  MET*     3.7    36.3    -      -       +      -
    650C  ILE*     4.9     1.6    -      -       +      -
    678C  MET*     4.3    18.0    -      -       +      +
    680C  TYR*     3.7    37.5    -      -       +      -
    691C  VAL*     4.0    14.4    -      -       +      -
    693C  GLY*     3.5     6.5    -      -       -      -
    694C  ALA*     3.1    21.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 444 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421C  VAL*     4.8     0.2    -      -       -      -
    426C  VAL*     3.9    22.5    -      -       -      +
    442C  ALA      3.6     1.4    -      -       -      -
    443C  LEU*     1.3    79.4    -      -       -      +
    445C  HIS*     1.3    65.0    +      -       -      -
    451C  PRO*     4.1     2.9    -      -       -      -
    452C  ILE      2.8    25.8    +      -       -      -
    691C  VAL*     3.5     7.6    -      -       -      +
    692C  HIS      3.4    10.1    -      -       -      -
    694C  ALA*     4.2     3.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 445 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363C  PRO*     5.0     5.4    -      -       +      -
    421C  VAL*     3.5    35.3    -      -       +      +
    422C  ARG      4.7     0.7    -      -       -      -
    425C  GLU*     3.7    37.4    +      -       +      +
    426C  VAL*     3.6    12.9    -      -       +      +
    444C  GLY*     1.3    72.9    -      -       -      -
    446C  ASP*     1.3    65.2    +      -       -      +
    449C  GLY*     2.4    34.4    +      -       -      +
    450C  ARG      3.4     2.9    -      -       -      -
    451C  PRO*     3.2    32.0    -      -       +      -
    691C  VAL*     4.2     0.4    -      -       -      -
    692C  HIS*     2.8    32.5    +      -       +      +
----------------------------------------------------------
 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