Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 4DEQ


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 ARG 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG      3.5    15.3    -      -       -      +
     33A  SER      3.3     6.3    -      -       -      -
     34A  ARG      3.5    18.4    -      -       -      +
     35A  LEU*     4.5     1.6    -      -       -      -
     36A  ASN*     3.6    10.9    +      -       -      +
     37A  TYR      2.8    39.7    +      -       -      +
     40A  ASN      3.7    18.5    +      -       -      -
     41A  GLY*     3.9     5.2    -      -       -      -
     68A  THR*     3.3     1.9    -      -       -      -
     69A  GLN*     2.7    68.6    +      -       +      +
     70A  GLY      2.9    26.5    +      -       -      +
     71A  ALA*     4.5     4.4    -      -       -      +
     72A  ILE*     5.6     0.6    -      -       -      +
    114A  PRO      3.4    12.1    +      -       -      -
    115A  THR*     4.5     4.2    +      -       -      +
    144A  MET*     1.3    81.1    -      -       -      +
    146A  PHE*     1.3    64.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  MET*     3.2    30.4    -      -       +      +
     18A  ILE*     5.0     0.7    -      -       +      -
     33A  SER*     2.8    47.7    +      -       -      +
     35A  LEU*     3.2    23.9    +      -       -      +
     53A  ILE*     3.8    28.9    -      -       +      -
     54A  GLN      4.6     5.4    -      -       -      -
     55A  VAL*     4.0    29.2    -      -       +      -
     66A  VAL*     4.7     0.9    -      -       +      -
     67A  GLY      3.1    13.7    -      -       -      +
     68A  THR*     4.3     5.8    -      -       +      -
    131A  VAL*     5.5     1.6    -      -       +      -
    133A  ILE*     3.6    32.8    -      -       +      -
    144A  MET*     4.9     4.5    -      -       +      -
    145A  ARG*     1.3    79.2    -      -       -      +
    147A  GLU*     1.3    69.9    +      -       -      +
    148A  VAL*     4.3     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ALA*     3.5    22.5    -      -       +      +
      6A  LEU      4.1     0.2    -      -       -      -
      7A  GLY*     3.2    10.0    +      -       -      -
      8A  MET*     2.8    26.6    +      -       -      +
      9A  GLU*     2.9    35.3    +      -       -      +
     10A  SER      4.5     0.7    +      -       -      -
     35A  LEU*     4.2    13.9    -      -       +      -
     66A  VAL*     3.6     7.3    -      -       -      +
     67A  GLY      3.0    28.9    +      -       -      +
    146A  PHE*     1.3    74.5    -      -       -      +
    148A  VAL*     1.3    84.2    +      -       -      +
    149A  TYR*     3.6    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ALA*     3.5     3.3    -      -       -      -
      6A  LEU*     2.8    48.5    +      -       +      -
      8A  MET*     4.5     4.4    -      -       +      +
     13A  ILE*     5.7     0.9    -      -       +      -
     55A  VAL*     3.8    28.7    -      -       +      -
     57A  LEU*     4.4     7.2    -      -       +      -
     63A  VAL*     3.7    30.5    -      -       +      -
     65A  ALA      3.9     5.2    -      -       -      +
     66A  VAL*     4.4    10.5    -      -       +      -
    131A  VAL*     4.6    10.8    -      -       +      -
    146A  PHE*     4.3    11.4    -      -       +      -
    147A  GLU*     1.3    84.0    +      -       -      +
    149A  TYR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  MET*     3.4    41.3    -      -       -      +
      4A  GLU      3.1     4.3    -      -       -      +
      5A  ALA*     3.6    18.6    -      -       +      -
      6A  LEU*     4.0     3.4    -      -       -      -
     35A  LEU*     4.1    13.0    -      -       -      +
     63A  VAL*     3.6     5.5    -      -       -      +
     64A  THR*     2.9    23.4    +      -       -      +
     65A  ALA*     2.9    28.9    +      -       +      +
     66A  VAL*     4.2     0.9    -      -       -      -
     67A  GLY*     3.7    28.2    -      -       -      -
    117A  VAL*     4.9     5.2    -      -       -      +
    119A  VAL*     4.4    18.9    -      -       +      +
    147A  GLU*     3.6    29.3    -      -       +      +
    148A  VAL*     1.3    75.5    -      -       -      +
    150A  GLY*     1.3    58.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  CYS*     3.4    19.2    +      -       -      -
      4A  GLU*     2.9    33.8    +      -       -      +
      6A  LEU*     3.6    11.1    -      -       -      +
     62A  PHE      3.3    13.7    -      -       -      -
     63A  VAL*     4.1     1.3    -      -       -      -
     64A  THR*     4.0     1.3    -      -       -      -
    149A  TYR*     1.3    75.3    -      -       -      +
    151A  CYS*     1.3    65.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  CYS*     2.0    50.6    -      -       -      -
      4A  GLU*     3.9    16.2    -      -       -      +
      6A  LEU*     3.8    11.2    -      -       -      +
     61A  ARG*     3.8     7.1    -      -       -      +
     62A  PHE*     3.1    27.8    +      -       -      +
    150A  GLY*     1.3    73.1    -      -       -      +
    152A  LYS*     1.3    75.1    +      -       -      +
    155A  ASP*     4.1     9.6    -      -       +      -
    156A  TYR*     3.8    21.3    -      -       -      -
----------------------------------------------------------
 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