Contacts of the strand formed by residues 492 - 497 (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 ALA 492 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438E  THR*     4.6    12.3    -      -       -      +
    439E  VAL*     4.8     8.7    -      -       +      -
    483E  ILE*     5.0     6.1    -      -       +      -
    487E  SER*     4.3    20.6    -      -       -      +
    488E  THR      2.8     8.5    +      -       -      +
    489E  PRO*     3.3     5.7    -      -       -      +
    490E  SER      3.7     0.2    -      -       -      -
    491E  GLU*     1.3    78.5    -      -       +      +
    493E  ARG*     1.3    66.9    +      -       -      +
    494E  LEU*     6.3     0.4    -      -       +      -
    512E  HIS*     3.1    22.7    -      -       -      -
    588E  PRO*     4.6     0.6    -      -       -      +
    589E  THR*     3.3    17.9    -      -       -      +
    591E  VAL*     6.2     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 493 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489E  PRO*     2.7    40.2    +      -       -      +
    490E  SER*     4.0     2.6    -      -       -      +
    492E  ALA*     1.3    75.3    -      -       -      +
    494E  LEU*     1.3    63.9    +      -       -      +
    511E  PRO      3.3    15.4    +      -       -      -
    512E  HIS*     3.3    18.8    -      -       -      +
    513E  LEU      3.0    29.2    +      -       -      +
    514E  LEU*     3.6    24.5    -      -       +      -
    588E  PRO*     4.4    14.2    -      -       +      +
    589E  THR      2.8    16.1    +      -       -      +
    590E  ILE*     3.3    28.9    -      -       +      +
    591E  VAL      3.3     3.8    +      -       -      -
    715E  ASP*     2.8    32.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 494 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480E  LEU*     3.9    19.3    -      -       +      -
    483E  ILE*     4.8    18.2    -      -       +      -
    484E  LEU*     5.0    11.0    -      -       +      -
    492E  ALA*     6.3     0.2    -      -       +      -
    493E  ARG*     1.3    75.7    -      -       -      +
    495E  ILE*     1.3    71.7    +      -       -      +
    496E  MET*     3.8    26.9    -      -       +      -
    510E  ILE*     4.4    13.2    -      -       +      -
    512E  HIS*     2.4    33.1    +      -       +      +
    513E  LEU*     3.3    29.8    -      -       +      +
    514E  LEU*     3.4     4.5    +      -       -      +
    590E  ILE*     5.2     0.7    -      -       -      -
    591E  VAL*     3.5    36.1    -      -       +      +
    593E  VAL*     4.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 495 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494E  LEU*     1.3    80.5    -      -       -      +
    496E  MET*     1.3    57.6    +      -       -      +
    497E  ILE*     4.1    22.9    -      -       +      -
    513E  LEU*     4.5     2.5    -      -       -      -
    514E  LEU*     3.9    20.2    -      -       +      -
    515E  CYS*     4.0    20.6    -      -       -      -
    518E  VAL*     5.1     0.4    -      -       +      -
    527E  ALA*     4.7     9.2    -      -       +      +
    530E  TRP*     3.7    31.4    -      -       +      -
    531E  SER*     4.9     3.1    -      -       -      +
    590E  ILE*     4.4    10.8    -      -       +      -
    591E  VAL      3.4     5.7    +      -       -      +
    592E  VAL*     3.5    16.6    -      -       +      +
    593E  VAL*     2.8    33.3    +      -       -      +
    720E  ILE*     3.8    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 496 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480E  LEU*     3.8    19.5    -      -       +      -
    494E  LEU*     3.8    26.5    -      -       +      -
    495E  ILE*     1.3    75.5    -      -       -      +
    497E  ILE*     1.3    63.8    +      -       -      +
    498E  ASP      4.1     0.7    -      -       -      -
    504E  LEU*     4.3    19.5    -      -       +      +
    507E  TYR*     3.6    51.6    -      -       +      -
    510E  ILE*     4.3     5.6    -      -       +      -
    513E  LEU*     4.6    15.0    -      -       +      +
    515E  CYS*     5.3     1.6    -      -       -      -
    516E  PRO      4.4     1.4    +      -       -      +
    517E  VAL*     3.9    19.4    -      -       +      -
    518E  VAL*     3.2    24.8    +      -       -      +
    593E  VAL*     3.4    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 497 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495E  ILE*     4.1    11.7    -      -       +      +
    496E  MET*     1.3    78.3    -      -       -      +
    498E  ASP*     1.3    63.4    +      -       -      +
    499E  PRO*     4.1     1.0    -      -       -      +
    504E  LEU*     5.1     0.7    -      -       -      +
    518E  VAL*     3.8    16.4    -      -       +      -
    524E  ALA*     4.2    12.6    -      -       +      +
    527E  ALA*     3.9    22.0    -      -       +      -
    528E  LEU*     4.7    11.9    -      -       +      -
    592E  VAL*     3.9    16.2    -      -       +      -
    593E  VAL*     2.6    14.1    +      -       -      +
    594E  VAL*     3.3    24.7    -      -       +      +
    595E  ASP*     3.2    23.9    +      -       -      +
    600E  MET*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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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