Contacts of the strand formed by residues 461 - 465 (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 HIS 461 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468A  THR*     6.1     0.2    -      -       -      -
    456F  LEU*     6.1     0.2    -      -       -      -
    459F  MET*     3.7     7.4    -      -       -      +
    460F  PRO*     1.3   105.6    +      -       +      +
    462F  LEU*     1.3    66.0    +      -       -      +
    615F  ILE*     5.1     1.8    -      -       +      -
    616F  ALA*     4.3    28.8    +      -       +      -
    619F  ALA*     4.1    24.2    +      -       +      -
    620F  ARG*     4.7     1.2    +      -       -      +
    624F  ILE      3.8     8.5    -      -       -      -
    625F  HIS*     3.7    17.5    -      +       -      -
    626F  LEU*     3.1    34.4    +      -       +      +
    645F  ASN      4.5     8.7    -      -       -      -
    646F  ILE*     3.6    26.1    -      -       +      +
    648F  THR*     3.3    22.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 462 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441F  LEU*     4.1     2.7    -      -       +      -
    459F  MET*     3.7    20.4    -      -       +      -
    461F  HIS*     1.3    80.3    -      -       -      +
    463F  LEU*     1.3    69.6    +      -       -      +
    464F  VAL*     4.3     4.5    -      -       +      -
    479F  MET*     3.6    38.4    -      -       +      -
    626F  LEU      3.0     3.9    +      -       -      +
    627F  ILE*     3.7    26.2    -      -       +      -
    628F  LEU*     2.9    32.4    +      -       -      +
    646F  ILE*     3.5     4.4    -      -       -      +
    648F  THR*     3.5    32.3    -      -       +      +
    650F  ILE*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 463 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462F  LEU*     1.3    75.3    -      -       -      +
    464F  VAL*     1.3    63.7    +      -       -      +
    465F  ALA*     6.3     0.9    -      -       +      -
    597F  PHE*     5.9     1.8    -      -       +      -
    628F  LEU*     3.4    37.0    -      -       +      +
    630F  THR*     5.1    10.3    -      -       +      -
    638F  ILE*     4.3    29.4    -      -       +      -
    642F  ILE*     4.4    21.3    -      -       +      +
    646F  ILE*     4.3    10.5    -      -       +      -
    648F  THR      3.3     6.7    +      -       -      -
    649F  ARG*     3.6    39.4    -      -       +      +
    650F  ILE*     2.6    32.9    +      -       -      +
    663F  ILE*     5.3     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 464 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462F  LEU*     4.3     8.7    -      -       +      -
    463F  LEU*     1.3    81.1    -      -       -      +
    465F  ALA*     1.3    65.8    +      -       -      +
    472F  LYS*     4.6    15.0    -      -       +      +
    475F  GLY      6.4     0.2    -      -       -      -
    476F  VAL*     5.4     4.3    -      -       +      +
    479F  MET*     4.1    24.2    -      -       +      -
    627F  ILE*     5.3     4.3    -      -       +      -
    628F  LEU      3.4     6.1    +      -       -      -
    629F  ALA*     3.4    13.9    -      -       +      -
    630F  THR*     2.8    30.1    +      -       -      +
    650F  ILE*     3.2    19.5    -      -       +      +
    652F  PHE*     3.7    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 465 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463F  LEU*     6.3     0.7    -      -       +      -
    464F  VAL*     1.3    79.1    -      -       -      +
    466F  GLY*     1.3    57.2    +      -       -      +
    472F  LYS*     5.4     1.6    -      -       -      +
    630F  THR*     3.3    26.2    -      -       +      +
    633F  PRO*     4.1    10.3    -      -       +      -
    638F  ILE*     4.9     1.1    -      -       +      -
    650F  ILE      3.3     5.9    +      -       -      -
    651F  ALA*     3.7     2.1    -      -       -      -
    652F  PHE*     2.7    36.9    +      -       -      +
    654F  VAL*     4.6     2.5    -      -       -      +
    663F  ILE*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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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