Contacts of the strand formed by residues 833 - 841 (chain C) in PDB entry 4OQB


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 833 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    806C  ARG*     4.5    13.7    +      -       -      -
    815C  ARG*     4.4    23.6    -      -       +      -
    818C  VAL*     3.7    41.7    -      -       +      -
    832C  GLU*     1.3    72.0    -      -       -      +
    834C  ILE*     1.3    62.1    +      -       -      +
    835C  ASP      3.5    25.6    -      -       -      +
    836C  ILE*     3.5    21.5    -      -       +      -
   1003C  LEU*     4.5     7.0    -      -       +      -
   1004C  LYS      3.9     4.9    -      -       -      +
   1005C  LEU*     4.8     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 834 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    806C  ARG*     5.8     1.0    +      -       -      -
    832C  GLU*     3.8    13.2    -      -       +      +
    833C  VAL*     1.3    74.9    -      -       -      +
    835C  ASP*     1.3    80.3    +      -       -      +
    916C  ILE*     3.6    31.6    -      -       +      -
   1004C  LYS*     2.9    27.2    +      -       +      +
   1006C  LYS*     3.9    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 835 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    668C  PRO*     3.3    31.0    -      -       -      +
    803C  VAL*     4.3    10.4    -      -       -      +
    833C  VAL*     3.5     4.9    -      -       -      +
    834C  ILE*     1.3   105.2    -      -       -      +
    836C  ILE*     1.3    73.9    +      -       -      +
    837C  PHE*     3.4    26.1    -      -       +      -
   1003C  LEU*     3.7     1.0    -      -       -      -
   1004C  LYS*     3.3    34.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 836 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    803C  VAL*     3.9     7.0    -      -       -      +
    804C  VAL*     3.1    56.3    +      -       +      +
    811C  ALA*     5.0     6.3    -      -       +      +
    814C  ILE*     3.4    53.8    -      -       +      -
    815C  ARG*     4.9    15.9    -      -       +      +
    833C  VAL*     3.5    19.7    -      -       +      -
    835C  ASP*     1.3    82.5    +      -       -      +
    837C  PHE*     1.3    68.1    +      -       -      +
   1001C  TYR*     4.7     3.8    -      -       +      -
   1002C  LEU      4.0     2.0    -      -       -      +
   1003C  LEU*     3.7     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 837 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    668C  PRO*     3.4    43.1    -      -       +      -
    669C  VAL*     3.9    19.7    -      -       +      -
    672C  LEU*     4.3    18.6    -      -       +      -
    801C  ILE*     3.6    26.9    -      -       +      -
    802C  LYS      3.3    10.3    -      -       -      +
    803C  VAL*     4.0     9.0    -      -       +      -
    804C  VAL*     4.5     1.3    -      -       -      -
    835C  ASP*     3.4    25.8    -      -       +      -
    836C  ILE*     1.3    78.1    -      -       -      +
    838C  LYS*     1.3    60.7    +      -       -      +
    839C  ILE*     4.5     0.4    -      -       +      -
   1001C  TYR*     3.3     4.9    -      -       -      +
   1002C  LEU*     2.7    62.1    +      -       +      +
   1003C  LEU      5.2     0.4    -      -       -      -
   1004C  LYS*     4.3    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 838 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800C  ASP      3.7     2.4    -      -       -      +
    801C  ILE*     3.6     3.1    -      -       -      +
    802C  LYS*     2.8    46.4    +      -       +      +
    804C  VAL*     3.8    19.7    -      -       +      +
    810C  GLU*     4.9    10.5    -      -       -      +
    837C  PHE*     1.3    69.5    -      -       -      +
    839C  ILE*     1.3    65.6    +      -       -      +
    840C  GLU*     5.9     3.9    +      -       +      -
    965C  ASP*     5.3     3.8    +      -       -      -
   1000C  LYS*     3.6    35.1    +      -       -      +
   1001C  TYR*     4.1    20.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 839 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799C  THR*     6.1     0.2    -      -       -      -
    800C  ASP      4.0     2.2    -      -       -      -
    801C  ILE*     4.2    24.0    -      -       +      -
    837C  PHE      4.2     0.9    -      -       -      +
    838C  LYS*     1.3    81.0    +      -       -      +
    840C  GLU*     1.3    63.7    +      -       -      +
    841C  ARG*     4.2     2.9    -      -       +      +
    873C  LEU*     4.6    13.2    -      -       +      -
    920C  LEU*     3.5    31.6    -      -       +      -
    999C  LEU*     3.1    46.3    -      -       +      +
   1000C  LYS*     2.8    32.2    +      -       -      +
   1001C  TYR      3.7    11.9    -      -       -      +
   1002C  LEU*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 840 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799C  THR*     3.5     3.2    -      -       -      -
    800C  ASP*     2.8    57.8    +      -       +      +
    838C  LYS*     5.9     3.9    +      -       +      -
    839C  ILE*     1.3    78.7    -      -       -      +
    841C  ARG*     1.3    68.4    +      -       -      +
    844C  GLU*     5.7     0.5    -      -       -      +
    845C  CYS*     3.2    32.5    -      -       -      -
    998C  ASN*     5.0     5.2    +      -       -      +
    999C  LEU      4.9     2.5    -      -       -      +
   1000C  LYS*     5.9     1.2    +      -       -      -
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Residues in contact with ARG 841 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    798C  LYS*     4.9     2.0    +      -       -      +
    799C  THR*     3.6    21.7    -      -       +      +
    839C  ILE*     4.2     2.6    -      -       +      -
    840C  GLU*     1.3    86.2    +      -       -      +
    842C  GLU*     1.3    76.7    +      -       -      +
    843C  GLY      3.2     7.8    +      -       -      -
    844C  GLU*     3.3    55.0    +      -       +      +
    845C  CYS*     5.0     1.4    +      -       -      -
    847C  ARG*     4.2    16.8    -      -       -      +
    872C  ILE      4.1     3.8    -      -       -      -
    873C  LEU*     2.8    33.7    +      -       +      +
    874C  SER      3.1    18.6    +      -       -      -
    875C  GLN*     3.7    12.9    +      -       -      +
    876C  GLY*     3.2    25.9    -      -       -      +
    999C  LEU*     4.2    12.7    +      -       +      +
----------------------------------------------------------
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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