Contacts of the strand formed by residues 56 - 61 (chain G) in PDB entry 6PSS


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 56 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55G  ALA*     1.3    76.0    -      -       -      +
     57G  THR*     1.3    60.5    +      -       -      +
     59G  VAL*     4.4    13.7    -      -       +      -
     85G  LEU      3.4    28.5    -      -       -      +
     86G  LYS*     4.4     3.0    +      -       -      +
     88G  LEU*     4.2    18.1    +      -       +      +
     90G  VAL*     4.9     1.6    -      -       +      -
    144G  ILE*     3.8    24.0    -      -       +      -
    145G  LYS      3.6    10.3    -      -       -      +
    146G  VAL*     4.0    16.2    -      -       +      +
    173G  VAL*     3.8    27.2    -      -       +      +
    175G  ALA*     3.3    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 57 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55G  ALA      3.7     3.4    -      -       -      +
     56G  VAL*     1.3    80.1    -      -       -      +
     58G  GLU*     1.3    65.4    +      -       -      +
    145G  LYS*     2.8    30.3    +      -       -      +
    147G  GLN*     3.6    33.3    +      -       +      +
    158G  ARG*     3.6    18.7    +      -       -      +
    172G  LEU*     3.5     2.3    -      -       -      -
    173G  VAL*     2.8    32.2    +      -       -      +
    175G  ALA*     3.7     9.6    -      -       +      -
    177G  TYR*     3.6    24.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 58 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56G  VAL*     5.1     0.2    -      -       -      +
     57G  THR*     1.3    85.9    +      -       -      +
     59G  VAL*     1.3    65.6    +      -       -      +
     60G  GLU*     6.4     0.2    -      -       +      -
    143G  ARG      3.5     1.5    -      -       -      +
    144G  ILE*     4.7     0.2    -      -       -      +
    145G  LYS*     2.7    72.1    +      -       +      +
    158G  ARG*     5.4     2.8    -      -       -      -
    166G  ARG*     4.6     0.9    -      -       -      -
    170G  ARG*     2.6    54.7    +      -       +      +
    171G  LEU      3.3     7.5    -      -       -      +
    172G  LEU*     4.3    21.0    -      -       +      +
    173G  VAL      4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56G  VAL*     4.4     7.6    -      -       +      -
     58G  GLU*     1.3    79.8    -      -       -      +
     60G  GLU*     1.3    64.4    +      -       -      +
     61G  ILE*     4.2    21.3    -      -       +      -
     82G  LEU*     3.8    26.0    -      -       +      -
     85G  LEU*     3.7    33.2    -      -       +      -
    142G  MET*     4.6     4.9    -      -       -      -
    143G  ARG      3.6     4.3    -      -       -      +
    144G  ILE*     4.2    14.4    -      -       +      -
    171G  LEU*     2.7    41.0    +      -       +      +
    173G  VAL*     4.1    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59G  VAL*     1.3    73.9    -      -       -      +
     61G  ILE*     1.3    67.6    +      -       -      +
    142G  MET*     3.2     4.9    -      -       -      +
    143G  ARG*     2.7    66.7    +      -       +      +
    167G  PRO*     4.7     9.4    -      -       -      +
    169G  GLY*     3.3    25.4    -      -       -      +
    170G  ARG*     3.3    30.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 61 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59G  VAL*     4.2    13.2    -      -       +      -
     60G  GLU*     1.3    85.3    -      -       -      +
     62G  ASP*     1.3    74.5    +      -       -      +
     63G  GLY      3.3     0.3    +      -       -      -
     64G  VAL*     3.3    41.2    +      -       +      +
     71G  LYS*     4.0    18.2    -      -       +      -
     78G  ILE*     4.1    26.5    -      -       +      -
     81G  ILE*     4.5     9.9    -      -       +      -
     82G  LEU*     5.9     0.7    -      -       +      -
    140G  ILE*     5.4     2.0    -      -       +      -
    141G  SER      3.3    11.9    -      -       -      +
    142G  MET*     3.9    33.0    -      -       +      -
    169G  GLY*     4.2     4.5    +      -       -      +
    171G  LEU*     4.7     4.6    -      -       +      +
----------------------------------------------------------
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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