Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 3QPV


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 LYS 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ASN*     3.6    25.1    +      -       -      +
     33A  SER*     4.3    19.3    -      -       -      +
     34A  PRO      3.0     6.2    +      -       -      +
     35A  THR*     3.6    20.4    -      -       +      +
     36A  VAL*     2.9    26.3    +      -       -      +
    144A  ASP      4.1     0.8    +      -       -      -
    145A  PHE*     1.3    79.8    -      -       -      +
    147A  ALA*     1.3    60.6    +      -       -      +
    227A  GLN*     3.5    34.5    +      -       -      +
    228A  ASP*     2.9    39.7    +      -       -      +
    231A  GLN*     4.6     2.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR*     4.8     0.4    -      -       -      -
     36A  VAL*     3.4     8.5    -      -       +      +
     38A  VAL*     5.2     5.2    -      -       +      -
    136A  ILE*     5.9     1.1    -      -       +      -
    137A  LEU*     4.0    27.4    -      -       +      -
    140A  ALA*     4.1    15.5    -      -       +      -
    145A  PHE      3.9     0.2    +      -       -      -
    146A  LYS*     1.3    79.1    -      -       -      +
    148A  PHE*     1.3    60.9    +      -       -      +
    149A  PHE*     4.4    10.0    -      -       +      -
    210A  SER*     4.0     8.1    +      -       -      +
    227A  GLN*     3.5    19.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR*     4.3    12.1    -      -       +      -
     36A  VAL      3.0     7.0    +      -       -      +
     37A  ILE*     3.4    16.0    -      -       +      +
     38A  VAL*     2.9    24.7    +      -       -      +
    147A  ALA*     1.3    75.1    -      -       -      +
    149A  PHE*     1.3    63.4    +      -       -      +
    150A  ILE*     3.7    30.5    -      -       +      -
    210A  SER*     3.3    12.8    -      -       -      -
    211A  LEU*     3.8    19.1    -      -       -      -
    212A  ILE*     3.8    20.4    -      -       +      -
    223A  VAL*     6.1     0.4    -      -       +      -
    224A  ASN      5.3     1.1    -      -       -      -
    226A  VAL*     5.5     4.7    -      -       +      -
    231A  GLN*     3.3    46.7    -      -       +      +
    234A  ILE*     4.0    15.7    -      -       +      -
    235A  VAL*     4.0    19.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     3.4    43.7    -      -       +      +
     40A  VAL*     4.1     4.3    -      -       +      -
    133A  ARG*     3.8    37.2    -      -       +      -
    136A  ILE*     5.3     1.6    -      -       +      -
    137A  LEU*     3.5    31.0    -      -       +      -
    147A  ALA*     4.4    11.4    -      -       +      -
    148A  PHE*     1.3    75.8    -      -       -      +
    150A  ILE*     1.3    64.6    +      -       -      +
    151A  GLU      4.2     0.4    -      -       -      -
    200A  LEU*     3.7    21.1    -      -       +      -
    209A  LEU*     3.5    33.7    -      -       +      -
    210A  SER      2.7    19.2    +      -       -      -
    211A  LEU*     3.0     8.5    -      -       +      +
    212A  ILE*     2.9    26.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     3.6    24.7    -      -       +      -
     38A  VAL      2.9     8.3    +      -       -      -
     39A  MET*     3.3    32.6    -      -       +      +
     40A  VAL*     2.7    29.7    +      -       -      +
     50A  ILE*     4.5     7.2    -      -       +      -
     54A  LEU*     3.9    17.7    -      -       +      -
    148A  PHE*     3.7    22.0    -      -       +      -
    149A  PHE*     1.3    76.5    -      -       -      +
    151A  GLU*     1.3    57.6    +      -       -      +
    212A  ILE*     3.4    15.5    -      -       +      -
    214A  VAL*     4.3    13.0    -      -       +      -
    234A  ILE*     4.1     1.3    -      -       +      -
    238A  LEU*     3.8    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     3.2    22.5    -      -       +      +
    149A  PHE      4.2     0.4    -      -       -      -
    150A  ILE*     1.3    75.8    -      -       -      +
    152A  SER*     1.3    59.7    +      -       -      +
    153A  VAL*     3.9    11.4    +      -       +      -
    197A  TYR*     2.5    29.5    +      -       -      +
    199A  PRO*     3.2    16.5    -      -       -      +
    200A  LEU*     2.9    42.7    +      -       +      +
    212A  ILE      3.0     8.6    +      -       -      +
    213A  LYS*     3.0    25.8    +      -       -      +
    214A  VAL*     2.7    36.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  MET*     5.9     1.3    -      -       -      +
     40A  VAL      3.0    14.0    +      -       -      +
     41A  GLY*     4.1     6.9    -      -       -      -
     42A  LEU      4.8     0.2    +      -       -      -
     45A  ARG*     2.5    50.0    +      -       -      +
     47A  LYS*     4.4     8.5    -      -       -      +
     50A  ILE*     4.7    12.7    -      -       -      +
    150A  ILE      4.2     0.6    +      -       -      -
    151A  GLU*     1.3    73.5    -      -       -      +
    153A  VAL*     1.3    63.2    +      -       -      +
    197A  TYR*     4.4     1.4    +      -       -      -
    214A  VAL*     3.4     6.0    +      -       -      -
    700A  ADP      3.5    21.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  GLU*     3.9    17.0    -      -       +      -
    152A  SER*     1.3    76.9    +      -       -      +
    154A  CYS*     1.3    66.2    +      -       -      +
    155A  ASP*     4.2    18.8    -      -       -      +
    197A  TYR*     3.9    20.9    -      -       +      +
    199A  PRO*     5.4     1.8    -      -       +      -
    213A  LYS*     4.1    20.9    -      -       +      +
    214A  VAL      2.8    13.8    +      -       -      +
    215A  ILE*     3.5    13.1    -      -       +      -
    216A  ASP*     3.0    27.4    +      -       -      +
    217A  VAL      4.7     0.5    +      -       -      -
    700A  ADP      5.4     0.5    +      -       -      -
----------------------------------------------------------
 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