Contacts of the strand formed by residues 839 - 845 (chain A) in PDB entry 3K72


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 THR 839 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    803A  SER*     5.8     4.5    -      -       -      -
    804A  HIS      3.5    17.0    -      -       -      +
    805A  PRO*     4.3    11.0    -      -       +      -
    833A  PRO*     4.9     0.3    -      -       -      +
    834A  VAL      3.7     1.0    +      -       -      -
    835A  GLY*     3.3    32.7    +      -       -      +
    837A  GLN      3.8     1.5    +      -       -      -
    838A  GLY*     1.3    82.4    +      -       -      +
    840A  TRP*     1.3    66.0    +      -       -      +
    876A  LEU*     6.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 840 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    803A  SER*     4.8     2.4    -      -       -      -
    804A  HIS*     2.9    54.4    +      +       -      +
    806A  ALA*     3.2    39.6    -      -       +      +
    808A  LEU      3.7     0.4    -      -       -      -
    809A  SER*     3.5    25.8    -      -       -      -
    831A  SER*     5.0     8.3    -      -       -      -
    832A  ALA*     3.2    21.1    -      -       -      +
    833A  PRO*     3.3    43.5    -      -       +      -
    834A  VAL*     3.6    10.1    -      -       -      +
    838A  GLY      4.3     1.1    -      -       -      -
    839A  THR*     1.3    82.3    -      -       -      +
    841A  SER*     1.3    59.8    +      -       -      +
    842A  THR*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 841 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    801A  THR*     3.8    19.6    +      -       -      +
    802A  PHE      3.1    15.4    +      -       -      -
    803A  SER*     4.7     2.7    -      -       -      +
    830A  ASP      4.0     1.9    -      -       -      +
    831A  SER      3.7     0.5    -      -       -      -
    832A  ALA*     3.0    34.9    +      -       -      +
    834A  VAL*     3.4    19.5    -      -       -      +
    840A  TRP*     1.3    73.2    -      -       -      +
    842A  THR*     1.3    64.0    +      -       -      +
    843A  SER*     3.9     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 842 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    801A  THR*     3.7     1.2    -      -       -      -
    802A  PHE*     3.1    27.5    +      -       -      +
    804A  HIS*     3.1    38.5    +      -       +      +
    809A  SER*     4.8     0.7    -      -       -      -
    810A  TYR*     4.5    22.0    -      -       +      +
    829A  CYS*     5.9     0.7    -      -       -      -
    830A  ASP      3.8     4.3    -      -       -      -
    831A  SER*     3.2    34.1    -      -       -      +
    832A  ALA      4.7     0.2    -      -       -      +
    840A  TRP*     5.9     0.2    -      -       +      -
    841A  SER*     1.3    75.6    +      -       -      +
    843A  SER*     1.3    64.2    +      -       -      +
    844A  CYS*     4.1     3.9    -      -       -      -
    863A  PHE*     3.4    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 843 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799A  THR*     5.9     2.2    -      -       -      -
    801A  THR*     3.3    29.8    -      -       -      -
    828A  THR      4.6     0.2    -      -       -      -
    829A  CYS*     3.4     0.2    -      -       -      +
    830A  ASP*     3.0    45.9    +      -       -      +
    841A  SER*     3.9     5.2    +      -       -      -
    842A  THR*     1.3    74.4    -      -       -      +
    844A  CYS*     1.3    66.0    +      -       -      +
    845A  ARG      4.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 844 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799A  THR*     4.5     0.6    -      -       -      -
    800A  ILE*     2.9    49.1    +      -       +      +
    802A  PHE*     5.1    10.3    -      -       +      -
    810A  TYR*     4.6    10.1    -      -       -      -
    827A  LEU*     4.6     6.6    -      -       +      +
    828A  THR      3.3     7.6    -      -       -      -
    829A  CYS*     2.0    52.5    -      -       -      -
    842A  THR*     4.1     8.7    -      -       -      -
    843A  SER*     1.3    79.3    -      -       -      +
    845A  ARG*     1.3    62.8    +      -       -      +
    846A  ILE*     3.5     1.6    +      -       -      +
    859A  PHE*     5.9     2.5    -      -       +      -
    863A  PHE*     6.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 845 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710A  PRO*     5.3    10.5    -      -       -      +
    797A  GLY*     4.1    23.8    +      -       -      +
    798A  THR      3.7     6.3    -      -       -      +
    799A  THR*     3.4    27.0    -      -       +      +
    827A  LEU*     4.7     0.4    -      -       -      -
    828A  THR*     3.0    36.8    +      -       +      +
    843A  SER*     4.3     0.6    -      -       -      -
    844A  CYS*     1.3    71.4    -      -       -      +
    846A  ILE*     1.3    53.5    +      -       -      +
    847A  ASN*     2.7    62.4    +      -       -      -
    884A  GLU*     4.9     4.9    +      -       -      +
----------------------------------------------------------
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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