Contacts of the strand formed by residues 354 - 361 (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 VAL 354 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343E  LEU*     5.1     2.7    -      -       +      -
    344E  GLU*     3.9    29.6    -      -       +      +
    347E  LEU*     3.7    36.6    -      -       +      -
    348E  LYS*     5.5     1.0    -      -       -      +
    352E  VAL*     5.7     1.6    -      -       +      -
    353E  GLU*     1.3    84.7    -      -       -      +
    355E  SER*     1.3    65.4    +      -       -      +
    370E  ILE*     3.7    36.6    -      -       +      -
    371E  GLN      3.3    17.7    -      -       -      +
    372E  PRO*     3.8     8.1    -      -       +      -
    373E  ALA*     4.3     2.2    -      -       -      +
    381E  ILE*     6.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 355 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344E  GLU*     3.3    11.4    -      -       -      -
    354E  VAL*     1.3    79.8    -      -       -      +
    356E  VAL*     1.3    67.5    +      -       -      +
    357E  ASP*     3.3     3.8    +      -       -      -
    370E  ILE*     4.0     0.7    -      -       -      -
    371E  GLN*     3.3    29.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 356 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340E  SER*     3.5    49.8    -      -       -      +
    341E  ARG*     3.7    15.7    +      -       -      +
    343E  LEU*     4.5     9.0    -      -       +      -
    344E  GLU*     2.9    18.1    +      -       +      -
    354E  VAL*     6.0     0.9    -      -       +      -
    355E  SER*     1.3    72.6    +      -       -      +
    357E  ASP*     1.3    64.8    +      -       -      +
    358E  SER      4.4     9.0    -      -       -      +
    359E  VAL*     4.5    11.2    -      -       +      -
    368E  PHE*     5.2     6.3    -      -       +      -
    369E  GLU      4.6     0.7    -      -       -      +
    370E  ILE*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 357 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355E  SER*     3.3     4.3    +      -       -      +
    356E  VAL*     1.3    76.9    -      -       -      +
    358E  SER*     1.3    74.3    +      -       -      +
    359E  VAL*     5.6     0.2    -      -       -      +
    369E  GLU*     3.1    18.2    +      -       -      +
    371E  GLN*     4.3    20.6    -      -       +      +
    406E  LYS*     5.7     5.7    +      -       -      +
    408E  THR*     4.4    14.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 358 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356E  VAL*     3.9     1.9    -      -       -      +
    357E  ASP*     1.3    88.9    +      -       -      +
    359E  VAL*     1.3    68.7    +      -       -      +
    360E  HIS*     4.0     4.4    +      -       -      -
    368E  PHE*     3.8     1.9    -      -       -      -
    369E  GLU*     2.5    64.5    +      -       -      +
    406E  LYS*     5.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 359 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336E  LEU*     3.9    33.7    -      -       +      +
    337E  GLU*     5.8     1.3    -      -       -      +
    340E  SER*     4.0    19.5    -      -       -      +
    356E  VAL*     4.5     7.4    -      -       +      -
    358E  SER*     1.3    79.4    -      -       -      +
    360E  HIS*     1.3    81.8    +      -       -      +
    361E  PRO*     4.1     6.5    -      -       +      +
    366E  THR*     4.3     3.8    -      -       +      -
    367E  ARG      3.7     3.1    -      -       -      -
    368E  PHE*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 360 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358E  SER*     4.0     4.7    +      -       -      -
    359E  VAL*     1.3    85.1    +      -       -      +
    361E  PRO*     1.3    70.3    -      -       -      +
    362E  GLY*     3.6     0.5    +      -       -      -
    366E  THR*     3.3     4.1    -      -       -      +
    367E  ARG*     2.9    51.1    +      -       +      +
    369E  GLU*     2.9    46.8    +      -       +      -
    447E  ILE*     5.2     8.0    -      -       +      +
    448E  GLY*     6.0     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 361 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331E  TYR*     5.7     4.0    -      -       +      +
    336E  LEU*     4.2    22.0    -      -       +      -
    359E  VAL*     4.1    12.3    -      -       +      +
    360E  HIS*     1.3    88.6    -      -       -      +
    362E  GLY*     1.3    60.6    +      -       -      +
    366E  THR*     3.8    11.6    -      -       +      +
    447E  ILE      4.9     0.2    -      -       -      -
    448E  GLY*     4.8     8.1    -      -       -      -
----------------------------------------------------------
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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