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


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ALA*     1.3    80.7    -      -       +      +
     57A  THR*     1.3    66.2    +      -       -      +
     58A  GLU      4.5     6.7    -      -       -      +
     59A  VAL*     4.8     7.9    -      -       +      -
     85A  LEU*     3.9    32.5    -      -       +      +
     86A  LYS*     4.5    10.3    -      -       -      +
     88A  LEU*     5.3    11.4    +      -       +      +
    144A  ILE*     3.5    32.5    -      -       +      -
    145A  LYS      3.6     5.6    -      -       -      +
    146A  VAL*     3.7    11.4    -      -       +      -
    173A  VAL*     3.6    15.9    -      -       +      +
    174A  ASP      4.4     7.3    -      -       -      +
    175A  ALA*     4.5     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ALA      4.8     1.0    +      -       -      -
     56A  VAL*     1.3    76.3    +      -       -      +
     58A  GLU*     1.3    79.6    +      -       +      +
    145A  LYS*     3.1    13.9    +      -       +      -
    147A  GLN*     3.3    38.2    +      -       -      +
    158A  ARG*     3.3    30.4    +      -       -      +
    171A  LEU      4.0     0.3    -      -       -      +
    172A  LEU*     4.0     1.4    -      -       +      -
    173A  VAL*     3.1    36.2    +      -       -      +
    175A  ALA*     5.0     4.5    -      -       -      +
    177A  TYR*     4.0     8.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  VAL*     4.5     0.9    -      -       -      +
     57A  THR*     1.3    95.5    -      -       +      +
     59A  VAL*     1.3    68.7    +      -       -      +
    143A  ARG      4.0     0.9    -      -       -      +
    144A  ILE*     3.7     1.6    -      -       -      -
    145A  LYS*     2.9    60.6    +      -       +      +
    158A  ARG*     5.9     0.9    +      -       -      -
    162A  GLU*     5.3     5.4    -      -       -      +
    166A  ARG*     5.2     6.3    -      -       -      -
    170A  ARG*     2.2    44.4    +      -       +      +
    171A  LEU      3.5     7.9    -      -       -      +
    172A  LEU*     5.2    11.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  VAL*     4.8     9.2    -      -       +      -
     58A  GLU*     1.3    80.3    -      -       -      +
     60A  GLU*     1.3    64.7    +      -       -      +
     61A  ILE*     3.6    27.4    -      -       +      -
     81A  ILE*     6.0     0.2    -      -       +      -
     82A  LEU*     3.9    23.1    -      -       +      -
     85A  LEU*     3.7    29.8    -      -       +      -
    142A  MET*     5.1     4.0    -      -       +      -
    143A  ARG      3.6     5.6    -      -       -      +
    144A  ILE*     4.7     7.4    -      -       +      -
    170A  ARG*     3.8     1.7    -      -       -      -
    171A  LEU*     2.9    40.0    +      -       +      +
    173A  VAL*     4.4    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  VAL*     1.3    75.2    -      -       -      +
     61A  ILE*     1.3    66.7    +      -       -      +
     62A  ASP*     3.9     1.7    +      -       -      +
    142A  MET*     3.3     3.4    -      -       -      -
    143A  ARG*     2.5    87.2    +      -       +      +
    169A  GLY*     3.5    21.9    -      -       -      +
    170A  ARG*     4.9    14.1    +      -       +      +
    171A  LEU*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  VAL*     3.6    24.7    +      -       +      -
     60A  GLU*     1.3    79.2    -      -       -      +
     62A  ASP*     1.3    70.5    +      -       -      +
     63A  GLY      4.2     3.1    -      -       -      +
     64A  VAL*     3.6    41.1    +      -       +      +
     71A  LYS*     4.6    15.5    -      -       +      -
     78A  ILE*     4.7    20.2    -      -       +      -
     81A  ILE*     5.3     7.0    -      -       +      -
     82A  LEU*     5.0     3.1    -      -       +      -
    140A  ILE*     5.6     3.4    -      -       +      -
    141A  SER      4.1     9.4    -      -       -      +
    142A  MET*     4.1    23.8    -      -       +      -
    169A  GLY      4.6     4.3    +      -       -      +
    171A  LEU*     4.6    21.4    -      -       +      +
----------------------------------------------------------
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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