Contacts of the strand formed by residues 141 - 146 (chain A) in PDB entry 4F4W


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 141 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.8    22.4    -      -       +      -
      7A  ASP      3.7     9.9    -      -       -      +
      8A  PHE*     3.6    27.1    -      -       +      -
      9A  ASP*     3.8     5.2    -      -       -      +
    130A  LYS*     2.8    57.7    +      -       +      +
    133A  ILE*     4.1    24.7    -      -       +      -
    139A  ILE*     4.0    11.6    +      -       +      +
    140A  THR*     1.3    79.1    -      -       -      +
    142A  THR*     1.3    58.5    +      -       -      +
    143A  VAL*     4.0     2.9    -      -       +      -
    162A  ASN*     3.4     5.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE      3.9     0.2    -      -       -      +
      6A  VAL*     3.6     2.1    -      -       -      -
      7A  ASP*     2.9    37.8    +      -       -      +
      9A  ASP*     2.8    21.3    +      -       -      -
    141A  VAL*     1.3    73.0    -      -       -      +
    143A  VAL*     1.3    64.3    +      -       -      +
    156A  ALA*     3.2    39.4    -      -       +      +
    159A  SER*     4.0     2.7    -      -       -      -
    160A  LYS*     3.7    19.4    -      -       +      +
    161A  PRO*     3.4     4.9    -      -       -      +
    162A  ASN      2.9    17.3    +      -       -      -
    163A  GLY*     3.1    14.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ILE*     3.5    26.9    -      -       +      -
      5A  PHE      3.1     7.9    -      -       -      +
      6A  VAL*     4.0    15.7    -      -       +      -
    126A  ALA*     3.8    21.3    -      -       +      +
    129A  ILE*     5.1     4.3    -      -       +      -
    130A  LYS*     3.8    27.4    -      -       +      -
    141A  VAL*     4.0     7.4    -      -       +      -
    142A  THR*     1.3    79.7    -      -       -      +
    144A  GLY*     1.3    65.9    +      -       -      +
    145A  VAL*     4.2     2.0    -      -       +      -
    156A  ALA*     3.9     9.6    -      -       -      -
    163A  GLY      2.9    11.6    +      -       -      +
    164A  LEU*     3.4     5.0    -      -       +      -
    165A  GLY*     2.8    24.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL      3.7     0.7    -      -       -      +
      4A  ILE*     3.4     3.5    -      -       -      -
      5A  PHE      2.8    32.9    +      -       -      -
    143A  VAL*     1.3    74.5    -      -       -      +
    145A  VAL*     1.3    62.6    +      -       -      +
    152A  ALA*     3.5    26.9    -      -       -      +
    155A  ILE*     3.7     6.1    -      -       -      -
    156A  ALA*     3.8     3.8    -      -       -      +
    165A  GLY      3.3     6.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     4.4    11.9    -      -       +      -
      3A  VAL      3.3    10.1    -      -       -      +
      4A  ILE*     4.5     7.2    -      -       +      -
    119A  PHE*     3.9    23.5    -      -       +      -
    122A  GLY*     4.5    14.4    -      -       -      -
    123A  ILE*     4.5     5.4    -      -       +      -
    126A  ALA*     3.6    30.7    -      -       +      -
    143A  VAL*     4.2     2.0    -      -       +      -
    144A  GLY*     1.3    77.3    -      -       -      +
    146A  ALA*     1.3    64.0    +      -       -      +
    155A  ILE*     4.0     1.7    -      -       -      +
    164A  LEU*     4.1    10.5    -      -       +      -
    165A  GLY      2.8    14.6    +      -       -      +
    166A  VAL*     3.5     9.2    -      -       +      -
    167A  ILE      3.0    25.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.8     1.4    -      -       -      -
      3A  VAL*     2.8    33.7    +      -       -      +
    119A  PHE*     4.0     7.9    -      -       -      -
    144A  GLY      4.2     0.4    -      -       -      -
    145A  VAL*     1.3    76.9    -      -       -      +
    147A  PRO*     1.3    74.3    -      -       +      +
    148A  ASN      3.2     2.7    +      -       -      +
    151A  LEU*     3.7    14.6    -      -       +      +
    152A  ALA*     3.5    29.4    -      -       -      +
    155A  ILE*     5.0     0.4    -      -       +      -
    167A  ILE*     3.6    10.8    -      -       +      +
----------------------------------------------------------
 Back to top of page


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