Contacts of the strand formed by residues 440 - 445 (chain F) 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 PRO 440 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432F  TYR*     3.6    28.3    -      -       +      -
    435F  HIS*     4.2    21.3    -      -       +      +
    437F  SER      4.8     1.8    -      -       -      +
    438F  THR      3.6     8.5    -      -       -      +
    439F  VAL*     1.3    88.9    -      -       -      +
    441F  LEU*     1.3    63.2    +      -       -      +
    442F  ALA      4.0     0.2    -      -       -      -
    453F  ILE*     4.2    18.8    -      -       +      -
    454F  THR      4.2     1.8    -      -       -      +
    455F  ASP*     4.1     8.1    -      -       -      +
    482F  SER*     3.9    14.1    -      -       -      +
    483F  ILE*     3.3    19.7    -      -       +      +
    486F  LYS*     4.2    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 441 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439F  VAL      4.0     0.4    +      -       -      -
    440F  PRO*     1.3    83.0    -      -       -      +
    442F  ALA*     1.3    60.0    +      -       -      +
    443F  LEU*     3.4     8.9    +      -       +      +
    453F  ILE*     3.3     4.3    -      -       -      +
    454F  THR*     2.9    49.4    +      -       -      +
    456F  LEU*     3.8    18.6    -      -       +      -
    459F  MET*     3.7    30.1    -      -       +      -
    462F  LEU*     4.1     3.6    -      -       +      -
    479F  MET*     3.5    62.4    -      -       +      +
    482F  SER*     4.1     0.2    -      -       -      -
    483F  ILE*     4.0    11.0    -      -       +      -
    627F  ILE*     4.8     1.1    -      -       +      -
    650F  ILE*     6.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 442 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423F  PHE*     4.2    12.0    -      -       +      -
    426F  VAL*     4.2     5.2    -      -       +      +
    427F  LEU*     3.7    26.0    -      -       +      -
    432F  TYR*     4.3     3.8    -      -       +      -
    440F  PRO      4.0     0.4    -      -       -      -
    441F  LEU*     1.3    70.0    -      -       -      +
    443F  LEU*     1.3    66.8    +      -       -      +
    453F  ILE*     3.7    28.3    -      -       +      -
    478F  ALA*     4.5     6.7    -      -       -      +
    479F  MET*     5.6     0.6    -      -       -      +
    482F  SER*     3.2    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 443 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426F  VAL*     3.4     9.9    -      -       -      +
    441F  LEU*     3.4    11.5    +      -       +      +
    442F  ALA*     1.3    79.9    -      -       -      +
    444F  GLY*     1.3    67.1    +      -       -      +
    451F  PRO*     4.1     1.4    -      -       -      +
    452F  ILE      3.7    23.3    +      -       -      +
    453F  ILE*     4.3     0.5    -      -       -      +
    454F  THR*     4.4    10.3    -      -       +      +
    475F  GLY*     5.4     3.1    -      -       -      +
    478F  ALA*     5.5     6.7    -      -       +      -
    479F  MET*     3.9    28.9    -      -       +      -
    650F  ILE*     4.0    15.5    -      -       +      -
    678F  MET*     3.7    37.7    -      -       +      -
    680F  TYR*     4.1    16.8    -      -       +      -
    691F  VAL*     3.8    14.4    -      -       +      -
    693F  GLY*     5.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 444 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421F  VAL*     4.6     0.7    -      -       -      -
    426F  VAL*     3.7    22.4    -      -       -      -
    442F  ALA      4.0     0.2    +      -       -      -
    443F  LEU*     1.3    81.2    -      -       -      +
    445F  HIS*     1.3    66.8    +      -       -      -
    451F  PRO*     3.9     4.9    -      -       -      -
    452F  ILE      3.1    15.1    +      -       -      -
    691F  VAL*     3.3     5.7    -      -       -      +
    692F  HIS      3.2    18.7    +      -       -      -
    693F  GLY*     4.5     0.4    -      -       -      -
    694F  ALA*     4.5     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 445 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363F  PRO*     4.9    11.4    -      -       +      -
    421F  VAL*     3.5    34.0    -      -       +      +
    422F  ARG      5.2     0.8    +      -       -      -
    425F  GLU*     3.5    32.0    +      -       +      +
    426F  VAL*     4.3     2.2    -      -       +      +
    444F  GLY*     1.3    74.6    -      -       -      -
    446F  ASP*     1.3    67.7    +      -       -      +
    449F  GLY*     4.1     6.7    -      -       -      -
    450F  ARG*     3.3    16.7    +      -       -      +
    451F  PRO*     3.2    32.6    -      -       +      -
    691F  VAL*     3.4     1.8    -      -       -      +
    692F  HIS*     2.7    41.8    +      -       +      +
----------------------------------------------------------
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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