Contacts of the strand formed by residues 255 - 260 (chain G) in PDB entry 5TWV


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 LEU 255 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233E  LEU      4.1    17.3    -      -       -      +
    234E  HIS*     5.6     0.4    -      -       -      -
    235E  GLN*     3.5    39.3    -      -       +      +
    201G  ARG*     3.4     3.5    -      -       -      -
    202G  VAL*     3.2    28.7    +      -       -      +
    249G  ILE*     4.0    17.7    -      -       +      -
    250G  PHE      3.6    16.8    -      -       -      +
    251G  LEU*     3.7    18.6    -      -       +      +
    253G  ALA*     3.2    12.9    +      -       +      +
    254G  PRO*     1.3    76.8    -      -       -      +
    256G  ILE*     1.3    67.1    +      -       -      +
    257G  ILE*     3.5    10.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 256 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231E  VAL*     5.0    17.5    -      -       +      -
    199G  MET*     3.5    32.3    -      -       +      -
    200G  LEU      3.2     8.7    -      -       -      +
    201G  ARG*     3.8    22.7    -      -       -      +
    249G  ILE*     6.2     0.5    -      -       -      +
    254G  PRO      5.3     0.9    -      -       -      +
    255G  LEU*     1.3    79.9    -      -       -      +
    257G  ILE*     1.3    67.9    +      -       -      +
    258G  TYR*     4.0    13.1    +      -       +      -
    315G  PHE*     3.9    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 257 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198G  PHE*     3.1    12.5    -      -       +      +
    199G  MET*     3.2     3.6    -      -       -      -
    200G  LEU*     2.6    38.3    +      -       +      +
    202G  VAL*     4.2    17.0    -      -       +      -
    215G  ILE*     5.3    11.7    -      -       +      -
    217G  MET*     3.6    37.5    -      -       +      -
    240G  MET*     4.4    27.6    -      -       +      +
    249G  ILE*     6.2     4.5    -      -       +      -
    255G  LEU*     3.5    14.4    -      -       +      +
    256G  ILE*     1.3    78.8    -      -       -      +
    258G  TYR*     1.3    71.3    +      -       -      +
    259G  HIS*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 258 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234E  HIS*     5.1    14.2    -      +       -      -
    192G  ARG*     3.4    33.4    -      -       -      +
    197G  CYS*     4.3    15.9    -      -       +      -
    198G  PHE      3.2     4.7    -      -       -      +
    199G  MET*     5.4     3.1    -      -       +      -
    239G  PRO      4.1     1.6    -      -       -      +
    240G  MET      3.8    13.3    +      -       -      +
    241G  GLU*     3.2    55.5    +      -       +      +
    242G  ASN*     4.6     8.0    +      -       -      -
    249G  ILE*     6.4     2.5    -      -       +      -
    256G  ILE*     4.2    12.8    -      -       +      -
    257G  ILE*     1.3    82.2    -      -       -      +
    259G  HIS*     1.3    61.1    +      -       -      +
    260G  VAL*     4.3    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 259 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197G  CYS*     3.2     5.3    -      -       -      -
    198G  PHE*     2.8    54.2    +      -       +      +
    217G  MET*     6.1     1.1    -      -       -      -
    238G  ILE*     4.2    22.9    -      -       +      -
    239G  PRO*     4.5     9.9    -      -       +      +
    257G  ILE*     6.2     0.7    -      -       +      -
    258G  TYR*     1.3    72.7    -      -       -      +
    260G  VAL*     1.3    65.2    +      -       -      +
    261G  ILE*     3.3    13.9    +      -       +      +
    267G  LEU*     5.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 260 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195G  ARG*     4.3    35.9    -      -       +      +
    196G  LEU      3.6     5.8    -      -       -      -
    197G  CYS*     3.7    16.8    -      -       -      -
    239G  PRO*     4.8    13.4    +      -       +      +
    241G  GLU*     4.1    23.4    -      -       +      +
    258G  TYR*     3.9     7.3    +      -       +      -
    259G  HIS*     1.3    69.5    -      -       -      +
    261G  ILE*     1.3    68.8    +      -       -      +
    262G  ASP*     3.3    20.7    +      -       +      +
    265G  SER*     4.4     2.4    -      -       -      -
----------------------------------------------------------
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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