Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 5FWV


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 278 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  GLU*     3.8    34.1    -      -       +      +
    270A  LEU      3.4     3.6    -      -       -      +
    271A  LEU*     4.0    10.3    -      -       +      -
    276A  HIS      4.4     5.4    -      -       -      +
    277A  ARG*     1.3    83.5    +      -       -      +
    279A  LEU*     1.3    63.6    +      -       -      +
    280A  ALA      3.8    22.9    -      -       -      +
    281A  ARG*     4.3    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  LEU*     2.6    23.8    +      -       +      +
    271A  LEU      3.7     6.5    -      -       -      +
    272A  ASP*     3.4    34.8    -      -       +      +
    277A  ARG*     3.3    43.1    -      -       -      +
    278A  VAL*     1.3    74.6    -      -       -      +
    280A  ALA*     1.3    60.2    +      -       +      +
    292A  PHE*     6.0     1.1    -      -       +      -
    294A  VAL*     3.9    33.2    -      -       +      -
    296A  LEU*     4.1     4.5    -      -       +      -
    299A  VAL*     4.4     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  VAL      4.5     0.2    -      -       -      -
    269A  GLU*     3.2     8.8    -      -       -      +
    270A  LEU*     2.8    31.7    +      -       +      -
    278A  VAL*     3.5     5.7    -      -       -      +
    279A  LEU*     1.3    82.8    -      -       +      +
    281A  ARG*     1.3    60.0    +      -       -      +
    282A  PHE*     3.8    28.7    -      -       +      -
    292A  PHE*     4.2    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  MET*     4.0    24.9    -      -       +      -
    268A  VAL      3.4     5.4    -      -       -      +
    269A  GLU*     2.3    43.8    +      -       +      +
    278A  VAL*     4.3    16.2    -      -       +      +
    280A  ALA*     1.3    75.7    -      -       -      +
    282A  PHE*     1.3    72.3    +      -       -      +
    283A  HIS*     4.1    21.3    +      -       -      +
    286A  SER*     3.9    10.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  PHE*     4.0    24.7    -      +       -      -
    259A  PHE*     3.6    24.0    -      -       +      -
    261A  ILE*     5.6     0.2    -      -       -      +
    267A  MET*     3.5     2.0    -      -       -      +
    268A  VAL*     2.7    50.0    +      -       +      +
    269A  GLU*     5.9     0.2    -      -       -      -
    270A  LEU*     5.3     4.0    -      -       +      -
    280A  ALA*     3.8    20.9    -      -       +      -
    281A  ARG*     1.3    82.3    -      -       -      +
    283A  HIS*     1.3    60.5    +      -       -      +
    286A  SER*     3.2     7.6    -      -       -      +
    287A  ARG      4.4     5.2    -      -       -      -
    288A  PRO*     3.7    15.9    -      -       +      -
    289A  PRO*     3.5    27.4    -      -       +      -
    292A  PHE*     3.4    34.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with HIS 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  PHE*     3.7     7.8    -      -       -      -
    261A  ILE*     4.2     7.4    -      -       -      -
    264A  SER*     3.1    24.6    +      -       -      +
    266A  ASP      3.1    21.3    -      -       -      +
    267A  MET*     4.3     4.9    -      -       +      +
    281A  ARG*     4.1    24.9    -      -       -      +
    282A  PHE*     1.3    70.8    -      -       -      +
    284A  GLY*     1.3    66.2    +      -       -      +
    285A  ARG*     3.1    17.5    -      -       +      +
    286A  SER*     2.4    83.0    +      -       -      +
----------------------------------------------------------
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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