Contacts of the strand formed by residues 440 - 445 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432A  TYR*     3.6    26.0    -      -       +      -
    435A  HIS*     5.2    13.0    -      -       +      +
    437A  SER*     4.9     1.3    -      -       -      +
    438A  THR      3.5     7.9    -      -       -      +
    439A  VAL*     1.3    91.7    -      -       -      +
    441A  LEU*     1.3    69.9    +      -       -      +
    442A  ALA      3.8     0.7    -      -       -      -
    453A  ILE*     4.0    10.5    -      -       +      -
    454A  THR      4.0     5.6    -      -       -      +
    455A  ASP*     5.0     1.6    -      -       -      -
    482A  SER*     3.4    30.6    -      -       -      +
    483A  ILE*     3.5     7.6    -      -       +      +
    486A  LYS*     3.6    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440A  PRO*     1.3    81.3    -      -       -      +
    442A  ALA*     1.3    63.8    +      -       -      +
    443A  LEU*     3.3    19.2    +      -       +      +
    453A  ILE*     3.5    10.9    -      -       -      +
    454A  THR*     3.0    26.9    +      -       -      +
    456A  LEU*     3.7    42.6    -      -       +      -
    459A  MET*     3.8    12.1    -      -       +      -
    462A  LEU*     3.8    24.5    -      -       +      -
    479A  MET*     3.7    37.5    -      -       +      +
    482A  SER*     4.1     1.3    -      -       -      -
    483A  ILE*     4.3    10.3    -      -       +      -
    627A  ILE*     5.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423A  PHE*     4.0    18.5    -      -       +      -
    426A  VAL*     3.7    20.6    -      -       +      -
    427A  LEU*     4.4     9.2    -      -       +      -
    432A  TYR*     4.5     2.9    -      -       +      -
    440A  PRO      3.8     0.4    -      -       -      -
    441A  LEU*     1.3    72.2    -      -       -      +
    443A  LEU*     1.3    63.8    +      -       -      +
    453A  ILE*     3.7    23.0    -      -       +      +
    478A  ALA*     4.1    10.6    -      -       -      +
    479A  MET*     4.8     0.3    +      -       -      -
    482A  SER*     3.1    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  VAL*     4.3     2.2    -      -       -      +
    441A  LEU*     3.3    18.2    +      -       +      +
    442A  ALA*     1.3    80.1    -      -       -      +
    444A  GLY*     1.3    60.9    +      -       -      +
    452A  ILE*     3.8    16.4    +      -       +      +
    454A  THR*     4.6     6.5    -      -       -      +
    462A  LEU*     5.9     0.9    -      -       +      -
    475A  GLY*     5.6     0.7    -      -       -      +
    478A  ALA*     5.6     4.3    -      -       +      +
    479A  MET*     3.8    35.0    -      -       +      -
    650A  ILE*     4.3     4.5    -      -       +      -
    678A  MET*     3.8    32.1    -      -       +      -
    680A  TYR*     4.2    26.7    -      -       +      -
    691A  VAL*     4.5     3.8    -      -       +      -
    692A  HIS      3.1    12.2    -      -       -      +
    693A  GLY*     3.3    18.4    -      -       -      -
    694A  ALA*     3.6     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 444 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  VAL*     5.2     0.2    -      -       -      -
    426A  VAL*     3.7    27.7    -      -       -      +
    443A  LEU*     1.3    79.9    -      -       -      +
    445A  HIS*     1.3    67.7    +      -       -      -
    451A  PRO*     4.4     2.9    -      -       -      -
    452A  ILE      3.2    22.9    +      -       -      +
    691A  VAL*     3.4     8.7    -      -       -      +
    692A  HIS      3.4     6.1    -      -       -      -
    693A  GLY      4.4     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  PRO*     4.8     8.1    -      -       +      -
    421A  VAL*     3.6    35.6    -      -       +      +
    425A  GLU*     3.3    38.4    +      -       +      +
    426A  VAL*     4.3     1.8    +      -       +      -
    428A  SER*     5.4     0.9    -      -       -      -
    444A  GLY*     1.3    74.2    -      -       -      -
    446A  ASP*     1.3    64.5    +      -       -      +
    449A  GLY*     2.4    36.5    +      -       -      +
    450A  ARG*     3.3     4.3    -      -       -      -
    451A  PRO*     3.3    29.1    -      -       +      +
    691A  VAL*     3.4     0.6    -      -       -      +
    692A  HIS*     3.3    29.5    +      -       -      +
----------------------------------------------------------
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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