Contacts of the strand formed by residues 365 - 372 (chain E) 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 ILE 365 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362E  GLY*     3.3    24.1    +      -       -      -
    364E  VAL*     1.3    89.3    -      -       +      +
    366E  THR*     1.3    73.9    +      -       -      +
    367E  ARG*     4.5     2.2    -      -       +      +
    412E  GLU*     3.8    27.1    -      -       +      -
    413E  ILE      3.3    11.2    -      -       -      +
    414E  PRO*     3.8    22.4    -      -       +      -
    447E  ILE*     3.7    34.5    +      -       +      +
    673E  LEU*     4.5     0.7    -      -       +      -
    690E  ARG*     3.4    33.0    -      -       -      +
    692E  HIS*     4.0    14.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 366 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336E  LEU*     4.5    10.6    -      -       +      +
    359E  VAL*     4.3     4.3    -      -       +      -
    360E  HIS      3.3    18.6    -      -       -      +
    361E  PRO*     3.8    11.2    -      -       +      +
    362E  GLY      4.1     4.2    +      -       -      -
    365E  ILE*     1.3    79.8    +      -       -      +
    367E  ARG*     1.3    61.6    +      -       -      +
    368E  PHE*     3.6    31.7    +      -       +      -
    411E  ILE      3.7     0.9    -      -       -      +
    412E  GLU*     3.4     1.2    -      -       -      -
    413E  ILE*     2.7    38.8    +      -       -      +
    415E  ASN*     3.0    28.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 367 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359E  VAL*     3.7     1.0    -      -       -      -
    360E  HIS*     2.9    48.0    +      -       +      +
    365E  ILE*     4.3     3.2    -      -       +      +
    366E  THR*     1.3    72.5    -      -       -      +
    368E  PHE*     1.3    68.4    +      -       -      +
    369E  GLU*     3.7    27.3    +      -       +      +
    400E  VAL*     4.9     8.6    -      -       -      +
    403E  ILE*     3.3    47.3    -      -       -      +
    404E  PRO*     5.0     4.8    -      -       -      +
    410E  GLY*     4.8     7.6    -      -       -      -
    411E  ILE      3.5     5.4    -      -       -      +
    412E  GLU*     4.2    25.5    +      -       +      -
    447E  ILE*     3.4    38.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 368 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336E  LEU*     4.7     7.2    -      -       +      -
    339E  MET*     3.6    33.0    -      -       +      -
    340E  SER*     4.5    12.6    -      -       -      -
    343E  LEU*     3.7    25.4    -      -       +      -
    356E  VAL*     5.2     3.1    -      -       +      -
    358E  SER      3.9     2.7    -      -       -      -
    359E  VAL*     3.7    24.0    -      -       +      -
    366E  THR*     3.6    28.3    -      -       +      -
    367E  ARG*     1.3    77.9    -      -       -      +
    369E  GLU*     1.3    61.7    +      -       -      +
    370E  ILE*     3.0    25.9    +      -       +      +
    411E  ILE*     2.6    36.1    +      -       +      +
    413E  ILE*     3.6    28.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 369 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357E  ASP*     3.1     9.2    +      -       -      +
    358E  SER*     2.5    55.7    +      -       -      +
    360E  HIS*     2.9    34.6    +      -       +      -
    367E  ARG*     3.7    24.8    +      -       +      +
    368E  PHE*     1.3    70.8    -      -       -      +
    370E  ILE*     1.3    58.8    +      -       -      +
    403E  ILE*     5.1     9.2    -      -       +      +
    406E  LYS*     4.8    16.8    +      -       -      +
    408E  THR*     3.8    25.2    +      -       +      +
    409E  VAL      4.4     3.6    -      -       -      -
    410E  GLY*     5.1     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 370 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343E  LEU*     4.6     8.5    -      -       +      -
    347E  LEU*     5.4     1.8    -      -       +      -
    354E  VAL*     3.7    26.0    -      -       +      -
    355E  SER      4.0     3.6    -      -       -      +
    356E  VAL*     3.7    33.7    -      -       +      +
    357E  ASP      4.0     0.2    -      -       -      +
    368E  PHE*     3.0    20.4    +      -       +      +
    369E  GLU*     1.3    77.2    -      -       -      +
    371E  GLN*     1.3    63.6    +      -       -      +
    372E  PRO*     3.8     3.4    -      -       +      +
    381E  ILE*     5.6     7.0    -      -       +      -
    408E  THR*     3.3     3.6    -      -       -      -
    409E  VAL*     2.8    55.0    +      -       +      +
    411E  ILE*     3.7    24.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 371 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354E  VAL*     3.3     7.2    -      -       -      +
    355E  SER*     3.3    29.0    +      -       -      +
    357E  ASP*     4.3    14.1    -      -       +      +
    370E  ILE*     1.3    75.7    -      -       -      +
    372E  PRO*     1.3    82.5    +      -       +      +
    407E  THR*     3.5    29.6    +      -       -      +
    408E  THR*     4.3    12.6    -      -       +      +
    346F  LYS*     5.4     8.1    -      -       -      +
    390F  ARG*     5.3     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 372 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353E  GLU      3.8     2.9    -      -       -      +
    354E  VAL*     3.8    15.4    -      -       +      -
    370E  ILE*     3.8     8.7    -      -       +      +
    371E  GLN*     1.3   104.9    +      -       +      +
    373E  ALA*     1.3    70.4    +      -       -      +
    376E  VAL*     3.7    18.6    -      -       +      +
    377E  LYS      5.7     1.8    -      -       -      +
    378E  VAL*     6.0     0.4    -      -       +      -
    381E  ILE*     5.9     8.7    -      -       +      -
    407E  THR      4.5     1.1    -      -       -      +
    409E  VAL*     4.1    13.0    -      -       +      -
    390F  ARG*     3.4    38.6    -      -       -      +
----------------------------------------------------------
 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