Contacts of the strand formed by residues 258 - 263 (chain C) in PDB entry 3V56


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 258 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  LYS*     5.5     5.1    -      -       +      +
    184C  LYS*     3.4    32.9    -      -       +      +
    185C  ILE      3.2     8.5    -      -       -      +
    186C  LEU*     3.8    26.8    -      -       +      +
    213C  GLN      3.8     0.2    -      -       -      +
    214C  ARG*     3.4     4.3    -      -       -      +
    215C  LYS*     2.7    50.2    +      -       +      +
    256C  GLY      3.8     5.4    +      -       -      +
    257C  ASP*     1.3    79.2    -      -       -      +
    259C  LEU*     1.3    63.5    +      -       -      +
    260C  GLN*     5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178C  LEU*     5.4     0.2    -      -       +      -
    184C  LYS*     3.4     9.7    -      -       -      +
    185C  ILE*     2.7    48.8    +      -       +      +
    187C  VAL*     4.8     6.7    -      -       +      -
    195C  ILE*     3.8    24.5    -      -       +      -
    212C  ILE*     5.0     3.4    -      -       +      -
    213C  GLN      3.3    12.1    -      -       -      +
    214C  ARG*     4.2     3.4    -      -       +      -
    229C  LEU*     3.9    24.7    -      -       +      -
    253C  LEU*     3.8    34.5    -      -       +      -
    257C  ASP*     6.0     0.2    -      -       +      -
    258C  GLU*     1.3    79.1    -      -       -      +
    260C  GLN*     1.3    61.0    +      -       -      +
    279C  PHE*     3.8    15.0    -      -       +      -
    281C  ALA*     4.3    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 260 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  PHE*     3.9    30.5    -      -       +      -
    183C  ASN      5.2     2.9    -      -       -      +
    184C  LYS*     4.2    24.2    -      -       +      +
    211C  LEU      3.3     1.6    -      -       -      +
    212C  ILE*     3.5     2.6    -      -       -      -
    213C  GLN*     2.7    74.5    +      -       +      +
    215C  LYS*     5.8     2.7    -      -       +      +
    226C  LEU*     3.9    21.9    -      -       +      +
    258C  GLU      5.7     0.9    -      -       -      +
    259C  LEU*     1.3    76.2    -      -       -      +
    261C  LEU*     1.3    60.3    +      -       -      +
    279C  PHE*     3.8    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  PHE*     3.4    21.8    -      -       -      -
    166C  VAL*     4.4    18.3    +      -       +      -
    168C  TRP*     4.1    28.3    +      -       +      +
    183C  ASN      5.9     0.2    +      -       -      -
    197C  GLY*     4.3    10.1    -      -       -      -
    199C  VAL*     3.6    28.7    -      -       +      -
    210C  HIS*     3.7    39.0    -      -       +      +
    211C  LEU      3.3     4.5    -      -       -      +
    212C  ILE*     4.6     3.4    -      -       +      +
    260C  GLN*     1.3    71.6    -      -       -      +
    262C  ALA*     1.3    59.0    +      -       -      +
    263C  ILE*     4.4     5.8    +      -       +      -
    278C  PHE      4.3     2.2    -      -       -      +
    279C  PHE*     3.8    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  TYR*     3.9    15.5    -      -       +      -
    164C  THR      4.1     0.2    -      -       -      -
    165C  PHE*     3.5    28.9    -      -       +      -
    210C  HIS*     3.3     3.1    -      -       -      -
    211C  LEU*     2.8    36.7    +      -       +      +
    213C  GLN*     3.6    26.2    -      -       -      +
    260C  GLN*     4.0     0.4    -      -       -      +
    261C  LEU*     1.3    73.8    -      -       -      +
    263C  ILE*     1.3    63.0    +      -       -      +
    264C  PRO*     3.5     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  TYR*     3.3     3.4    -      -       -      -
    164C  THR*     2.9    49.1    +      -       +      +
    166C  VAL*     4.1    24.2    -      -       +      -
    199C  VAL*     4.2     7.6    -      -       +      -
    201C  TYR*     4.0    14.4    -      -       +      +
    208C  MET*     4.1     7.6    -      -       +      -
    209C  GLY      3.5    13.7    -      -       -      +
    210C  HIS*     4.0     6.3    -      -       +      -
    261C  LEU*     4.4     4.3    -      -       +      -
    262C  ALA*     1.3    74.8    -      -       -      +
    264C  PRO*     1.4    54.5    -      -       -      +
    265C  ARG*     2.7    28.2    +      -       +      -
    268C  ALA*     3.7    24.0    -      -       +      -
    270C  ILE*     4.0    28.0    -      -       +      -
----------------------------------------------------------
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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