Contacts of the strand formed by residues 830 - 839 (chain A) in PDB entry 6EJ9


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 830 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    826A  LEU*     3.3     2.5    -      -       -      -
    827A  HIS*     2.8    46.9    +      -       +      +
    828A  HIS*     4.0     7.2    -      -       +      +
    829A  TRP*     1.3    77.8    -      -       -      +
    831A  PRO*     1.3    82.4    -      -       +      +
    832A  VAL*     3.7     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 831 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    826A  LEU*     3.8    16.1    -      -       +      -
    829A  TRP      3.3     9.6    -      -       -      +
    830A  VAL*     1.3    98.5    -      -       +      +
    832A  VAL*     1.3    62.9    +      -       -      +
    833A  ALA      5.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 832 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727A  ILE*     3.2    30.6    -      -       +      +
    737A  LEU*     3.7    32.1    -      -       +      -
    772A  TRP*     6.1     0.7    -      -       +      -
    780A  VAL*     5.5     3.4    -      -       +      -
    825A  ILE*     2.9    23.1    +      -       +      +
    826A  LEU      4.0     1.6    -      -       -      -
    827A  HIS*     3.7    27.1    -      -       +      +
    830A  VAL*     3.7    10.3    -      -       +      +
    831A  PRO*     1.3    80.4    -      -       -      +
    833A  ALA*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 833 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725A  PHE*     3.8    16.4    -      -       +      -
    726A  LYS      3.3    14.4    -      -       -      +
    727A  ILE*     3.9     8.5    -      -       +      -
    737A  LEU*     3.5    27.6    -      -       +      -
    740A  SER*     5.8     0.2    -      -       -      -
    824A  LYS*     3.8     1.4    -      -       -      +
    825A  ILE*     3.0    30.9    +      -       +      +
    832A  VAL*     1.3    80.8    -      -       -      +
    834A  GLU*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 834 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724A  VAL      3.6     2.8    -      -       -      +
    725A  PHE*     3.5     6.5    -      -       -      -
    726A  LYS*     3.0    50.2    +      -       +      +
    740A  SER*     5.6     1.3    -      -       -      -
    822A  THR*     3.9    11.2    -      -       +      +
    823A  VAL      3.2    13.7    -      -       -      +
    824A  LYS*     3.4    32.5    -      -       +      -
    825A  ILE*     5.9     0.9    -      -       -      -
    833A  ALA*     1.3    77.3    -      -       -      +
    835A  THR*     1.3    63.6    +      -       -      +
    836A  LYS*     4.2    20.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 835 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724A  VAL*     3.6    21.1    +      -       -      +
    725A  PHE*     4.3     6.1    +      -       -      +
    740A  SER*     3.7    41.1    +      -       -      +
    741A  GLU*     4.4     5.3    -      -       -      +
    742A  VAL*     4.5    13.5    +      -       +      -
    822A  THR*     3.5     5.6    -      -       -      +
    823A  VAL*     2.8    48.8    +      -       +      +
    834A  GLU*     1.3    75.1    -      -       -      +
    836A  LYS*     1.3    77.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 836 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724A  VAL*     3.5    44.2    -      -       +      +
    742A  VAL*     5.5     1.2    +      -       -      +
    820A  VAL*     4.0    20.9    -      -       +      +
    821A  TRP      3.3    14.4    -      -       -      +
    822A  THR*     3.4    21.2    +      -       +      +
    834A  GLU*     4.2    19.3    +      -       -      +
    835A  THR*     1.3    86.1    +      -       -      +
    837A  PHE*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 837 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    742A  VAL*     3.6    42.0    -      -       +      +
    758A  GLY      6.0     1.3    -      -       -      +
    760A  LEU*     3.9    24.7    -      -       +      -
    766A  PRO*     4.4     8.5    -      -       +      -
    784A  TRP*     3.9    24.9    -      +       -      -
    816A  LEU*     5.9     0.2    -      -       +      -
    820A  VAL*     3.6     5.1    -      -       -      -
    821A  TRP*     2.9    63.8    +      +       +      +
    823A  VAL*     3.9    13.9    -      -       +      -
    835A  THR      5.5     0.2    -      -       -      -
    836A  LYS*     1.3    79.1    -      -       -      +
    838A  LEU*     1.3    61.1    +      -       -      +
    839A  VAL*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 838 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    651A  LEU*     4.9    10.8    -      -       +      -
    758A  GLY      4.5     6.7    +      -       -      +
    760A  LEU*     3.6    23.9    +      -       -      +
    819A  GLY*     3.6    25.4    -      -       -      +
    820A  VAL*     4.3    13.5    -      -       +      +
    837A  PHE*     1.3    75.1    -      -       -      +
    839A  VAL*     1.3    74.0    +      -       -      +
    840A  ALA*     3.8    17.8    +      -       +      +
    841A  PRO*     5.5     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 839 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    760A  LEU*     3.9     8.7    -      -       +      -
    761A  GLY      3.7    26.9    -      -       -      +
    762A  PRO*     3.8    11.4    -      -       +      -
    816A  LEU*     4.2    20.2    -      -       +      +
    817A  ARG      4.1     4.3    -      -       -      +
    818A  PRO*     3.3    14.7    -      -       +      +
    819A  GLY      2.8    38.6    +      -       -      +
    821A  TRP*     3.7    18.2    -      -       -      +
    837A  PHE*     3.6    27.3    +      -       +      -
    838A  LEU*     1.3    72.5    -      -       -      +
    840A  ALA*     1.3    63.8    +      -       -      +
    841A  PRO*     4.0     0.2    -      -       -      +
----------------------------------------------------------
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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