Contacts of the strand formed by residues 257 - 263 (chain C) in PDB entry 6RKU


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 GLU 257 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248C  VAL*     5.9     6.6    -      -       +      +
    249C  GLU      3.3     7.2    -      -       -      +
    250C  VAL*     3.6    24.2    -      -       +      +
    256C  ARG*     1.3    77.6    -      -       -      +
    258C  THR*     1.3    67.4    +      -       -      +
    259C  ILE*     6.3     0.4    -      -       +      -
    307C  VAL*     3.3    36.0    +      -       +      +
    311C  ALA      2.8    17.7    -      -       -      +
    312C  VAL*     2.8    31.8    -      -       -      +
    313C  GLY*     4.5     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248C  VAL*     3.5     2.1    -      -       -      -
    249C  GLU*     2.7    57.4    +      -       -      +
    256C  ARG*     3.6    13.9    +      -       -      +
    257C  GLU*     1.3    79.0    +      -       -      +
    259C  ILE*     1.3    69.4    +      -       -      +
    260C  ILE*     5.3     1.6    -      -       +      -
    293C  ARG*     5.5     2.9    -      -       -      +
    304C  VAL*     3.6    26.0    -      -       +      -
    305C  ILE      3.3    17.3    -      -       -      +
    306C  GLU*     4.7     5.0    -      -       +      +
    307C  VAL*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246C  ALA*     4.4    11.7    -      -       +      -
    247C  GLU      3.5    17.0    -      -       -      +
    248C  VAL*     3.7    25.1    -      -       +      -
    257C  GLU*     6.3     0.7    -      -       +      -
    258C  THR*     1.3    83.2    -      -       -      +
    260C  ILE*     1.3    74.3    +      -       -      +
    261C  VAL*     4.6     7.9    -      -       +      -
    303C  ILE      3.7     0.5    -      -       -      +
    304C  VAL*     3.6     6.4    -      -       -      -
    305C  ILE*     3.2    43.9    +      -       +      +
    307C  VAL*     4.0    19.5    -      -       +      -
    313C  GLY*     5.2    10.3    -      -       -      +
    317C  LEU*     4.7    19.3    -      -       +      -
    320C  LEU*     6.4     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246C  ALA*     3.3    26.0    -      -       -      +
    247C  GLU*     3.3    20.8    +      -       +      +
    249C  GLU*     3.1    34.5    -      -       +      +
    258C  THR*     4.3     2.7    +      -       +      -
    259C  ILE*     1.3    79.6    -      -       -      +
    261C  VAL*     1.3    68.3    +      -       -      +
    262C  HIS*     3.5    38.4    +      -       +      +
    302C  ARG*     3.3    38.6    -      -       +      +
    303C  ILE      3.6     6.3    -      -       -      +
    304C  VAL*     4.9     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 261 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244C  ALA*     5.1     2.2    -      -       +      -
    245C  ARG      3.8     9.2    -      -       -      +
    246C  ALA*     4.1    13.0    -      -       +      -
    259C  ILE*     4.6     8.7    -      -       +      -
    260C  ILE*     1.3    79.0    -      -       -      +
    262C  HIS*     1.3    63.9    +      -       -      +
    263C  GLU      4.0    17.5    -      -       -      +
    264C  ILE*     4.6    12.3    -      -       +      -
    301C  MET*     5.1     1.9    -      -       +      +
    302C  ARG*     3.7     8.0    +      -       -      -
    303C  ILE*     3.1    50.2    +      -       +      +
    305C  ILE*     5.1     9.4    -      -       +      -
    326C  LEU*     5.1    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245C  ARG*     3.4    29.4    +      -       +      +
    246C  ALA*     5.4     1.6    -      -       -      -
    247C  GLU*     4.5    16.8    +      -       +      -
    260C  ILE*     3.5    34.5    -      -       +      +
    261C  VAL*     1.3    75.1    +      -       -      +
    263C  GLU*     1.3    70.5    +      -       +      +
    301C  MET*     3.4    34.1    +      -       -      +
    302C  ARG*     4.4    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219C  THR*     5.1     5.1    -      -       -      -
    220C  ALA*     3.0    56.9    +      -       -      +
    221C  ALA*     3.5     6.0    +      -       -      -
    244C  ALA*     3.4    20.3    -      -       -      +
    245C  ARG*     3.6    40.4    +      -       +      +
    261C  VAL*     3.8     4.3    -      -       -      +
    262C  HIS*     1.3    83.4    -      -       +      +
    264C  ILE*     1.3    63.8    +      -       -      +
    301C  MET*     3.6     7.2    -      -       -      +
----------------------------------------------------------
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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