Contacts of the strand formed by residues 78 - 83 (chain K) in PDB entry 5O6I


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 TYR 78 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40K  ILE      4.1     0.2    -      -       -      +
     41K  THR*     3.2     5.5    -      -       -      -
     42K  GLN      2.8    37.8    +      -       -      +
     43K  LYS*     3.4    28.0    -      -       -      -
     45K  GLU*     3.1    52.3    +      -       +      -
     48K  ILE*     4.2    19.3    -      -       +      +
     49K  LYS*     4.8     4.5    -      -       -      -
     71K  ILE*     4.1    20.2    -      -       +      -
     72K  VAL      3.5     2.0    -      -       -      -
     73K  LYS*     3.4    56.3    +      -       +      +
     77K  ARG*     1.3    77.2    -      -       -      +
     79K  GLU*     1.3    61.3    +      -       -      +
     80K  LEU      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 79 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37K  ARG*     4.5     2.3    +      -       -      -
     39K  VAL*     3.7    32.0    -      -       +      +
     40K  ILE      3.7     2.2    -      -       -      -
     41K  THR*     4.1     3.1    -      -       +      -
     48K  ILE*     5.1     0.4    -      -       -      -
     70K  GLN      3.4     1.6    -      -       -      +
     71K  ILE*     3.3     7.6    -      -       -      -
     72K  VAL*     2.8    47.8    +      -       +      +
     77K  ARG*     3.6    21.4    +      -       -      +
     78K  TYR*     1.3    74.9    -      -       -      +
     80K  LEU*     1.3    63.9    +      -       -      +
     81K  ARG*     2.8    49.2    +      -       +      +
     16L    T      5.1     2.6    -      -       -      +
     17L    T      4.7     2.1    -      -       -      +
      9N    A      3.3    16.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38K  VAL      4.9     2.0    -      -       -      +
     39K  VAL*     3.2     7.3    -      -       -      +
     40K  ILE*     2.7    51.2    +      -       +      +
     48K  ILE*     4.0    20.4    -      -       +      +
     52K  PHE*     3.9    17.5    -      -       +      +
     53K  ALA*     3.7    38.6    -      -       +      +
     56K  MET*     4.2    33.0    -      -       +      -
     69K  ILE*     4.1    13.7    -      -       +      -
     70K  GLN      3.4     3.8    -      -       -      -
     71K  ILE*     4.7     3.1    -      -       +      +
     78K  TYR      4.2     0.4    -      -       -      -
     79K  GLU*     1.3    70.1    -      -       -      +
     81K  ARG*     1.3    62.7    +      -       -      +
     82K  VAL*     4.3    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 81 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35K  GLU*     4.5     1.6    -      -       -      -
     37K  ARG*     3.4    45.5    -      -       +      +
     38K  VAL      3.4     3.1    -      -       -      -
     39K  VAL*     4.4     4.3    -      -       +      -
     68K  LYS      3.8     0.5    -      -       -      +
     69K  ILE*     3.9     0.2    -      -       -      -
     70K  GLN*     2.8    67.5    +      -       +      +
     72K  VAL*     4.1    11.8    -      -       +      +
     79K  GLU*     2.8    47.0    +      -       +      +
     80K  LEU*     1.3    75.5    -      -       -      +
     82K  VAL*     1.3    70.7    +      -       -      +
     83K  SER      4.4     0.7    -      -       -      +
      7N    G      3.2    33.7    +      -       -      -
      8N    G      3.2    23.4    +      -       -      -
      9N    A      3.2    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37K  ARG*     3.5     0.3    -      -       -      -
     38K  VAL*     2.9    37.9    +      -       +      +
     56K  MET*     4.0    28.5    -      -       +      -
     60K  ILE*     4.1    10.5    -      -       +      -
     67K  SER*     3.9    12.8    -      -       -      -
     68K  LYS      4.0     6.1    -      -       -      +
     69K  ILE*     4.0    16.4    -      -       +      -
     80K  LEU*     4.3     6.1    -      -       +      -
     81K  ARG*     1.3    79.9    -      -       -      +
     83K  SER*     1.3    60.2    +      -       -      +
     84K  SER*     3.3    22.4    +      -       -      -
     87K  LEU*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35K  GLU*     3.0    40.4    +      -       -      +
     36K  TYR      3.2     6.5    +      -       -      -
     37K  ARG*     4.6     2.2    -      -       -      +
     67K  SER*     2.4    27.9    +      -       -      -
     68K  LYS      4.5     1.6    +      -       -      -
     70K  GLN*     4.0    16.5    -      -       -      +
     81K  ARG*     4.1     3.0    +      -       -      +
     82K  VAL*     1.3    68.6    -      -       -      +
     84K  SER*     1.3    53.4    +      -       -      +
      5N    C      3.4    36.5    +      -       -      +
      6N    C      4.5     1.1    +      -       -      -
----------------------------------------------------------
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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