Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 1QP4


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 SER 61 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR*     2.9    26.4    +      -       -      -
     60A  LYS*     1.3    77.3    +      -       -      +
     62A  ILE*     1.3    61.1    +      -       -      +
     90A  TYR*     3.7     1.8    -      -       -      -
     91A  THR*     2.9    31.4    -      -       -      +
     93A  ILE*     4.7    13.9    -      -       -      -
    114A  LYS      6.0     0.4    -      -       -      -
    116A  VAL*     3.6     5.6    -      -       -      -
    117A  ASP*     2.8    32.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  SER*     1.3    74.8    -      -       -      +
     63A  GLY*     1.3    76.9    +      -       -      +
     85A  CYS*     4.0    22.9    -      -       -      -
     90A  TYR*     3.1    36.8    -      -       +      -
     91A  THR      2.7    11.7    +      -       -      +
     92A  LEU*     3.3    13.1    -      -       +      +
     93A  ILE*     2.9    25.9    +      -       -      +
    116A  VAL*     4.5     4.0    -      -       -      -
    117A  ASP*     4.8     0.2    -      -       +      -
    118A  GLY      3.7    13.9    -      -       -      +
    120A  LEU*     3.4    33.7    -      -       +      +
    302A  PHE*     4.6     6.7    -      -       +      -
    305A  LEU*     3.9    19.3    -      -       +      -
    306A  LEU*     5.7     0.2    -      -       +      -
    309A  ILE*     4.9     3.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE*     1.3    75.8    -      -       -      +
     64A  LEU*     1.3    54.5    +      -       -      -
     93A  ILE*     3.6     7.0    -      -       -      -
    111A  MET*     4.2    10.5    -      -       -      -
    116A  VAL*     4.0     9.3    -      -       -      +
    118A  GLY      3.1    11.7    +      -       -      -
    119A  LEU*     2.9    21.9    -      -       -      +
    120A  LEU      2.6    32.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE*     4.0     0.8    +      -       +      -
     63A  GLY*     1.3    70.5    -      -       -      -
     65A  LEU*     1.3    63.9    +      -       -      +
     66A  ALA*     3.3     4.5    +      -       +      +
     78A  ILE*     3.5    28.9    -      -       +      -
     81A  VAL*     4.3    27.4    -      -       +      -
     92A  LEU*     3.7    16.2    -      -       +      -
     93A  ILE      2.8    14.6    +      -       -      +
     94A  LEU*     3.9    14.0    -      -       +      +
     95A  GLY*     2.7    34.8    +      -       -      +
    111A  MET*     4.1     3.0    -      -       -      +
    120A  LEU*     3.4    27.8    -      -       +      +
    122A  MET*     4.1    21.3    -      -       +      -
    145A  MET*     4.8     2.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  GLY      3.7     1.0    +      -       -      -
     64A  LEU*     1.3    71.7    -      -       -      +
     66A  ALA*     1.3    62.1    +      -       -      +
     95A  GLY      3.8     7.6    -      -       -      +
     97A  ALA*     4.2    16.6    -      -       +      -
    104A  GLN*     4.6     9.4    -      -       +      +
    107A  TYR*     3.9    25.1    -      -       +      -
    108A  LEU*     3.6    39.5    -      -       +      +
    111A  MET*     4.7    12.3    -      -       +      -
    119A  LEU*     4.9     3.8    -      -       +      -
    120A  LEU      2.8    13.1    +      -       -      +
    121A  VAL*     4.5    12.8    -      -       +      -
    122A  MET      3.0    25.3    +      -       -      -
    123A  CYS*     3.9    19.9    -      -       -      -
    130A  LEU*     6.0     0.9    -      -       +      -
    134A  LEU*     5.1     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU*     3.3    18.8    +      -       +      +
     65A  LEU*     1.3    77.9    -      -       -      +
     67A  THR*     1.3    62.4    +      -       -      +
     68A  SER      4.5     2.5    -      -       -      +
     74A  PHE*     6.4     0.4    -      -       +      -
     78A  ILE*     4.5    10.5    -      -       +      -
     94A  LEU*     4.6     1.6    -      -       +      -
     95A  GLY      2.7    11.2    +      -       -      +
     96A  ASN*     3.3    18.3    -      -       -      +
     97A  ALA*     2.8    29.1    +      -       -      +
    122A  MET*     3.5    20.9    -      -       +      -
    123A  CYS*     5.1     2.5    -      -       -      -
----------------------------------------------------------
 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