Contacts of the strand formed by residues 63 - 69 (chain A) in PDB entry 1JYF


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 LEU 63 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LEU*     1.3    88.1    -      -       +      +
     64A  ILE*     1.3    58.6    +      -       -      +
     93A  SER*     3.3    34.1    -      -       -      +
     95A  VAL*     3.2    36.3    -      -       +      -
    117A  GLN*     4.4    15.0    -      -       +      +
    118A  ARG      4.6     4.3    -      -       -      +
    119A  VAL*     3.2    17.7    -      -       +      -
    120A  SER*     2.8    34.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LEU      5.0     3.1    -      -       -      +
     63A  LEU*     1.3    79.9    -      -       -      +
     65A  GLY*     1.3    60.1    +      -       -      +
     66A  VAL*     4.3     2.4    +      -       +      -
     83A  ILE*     3.5    32.5    -      -       +      -
     87A  ALA*     4.4     7.6    -      -       +      -
     92A  ALA*     5.3     3.8    -      -       +      -
     93A  SER      2.9    19.6    +      -       -      +
     94A  VAL*     3.7    16.4    -      -       +      -
     95A  VAL      3.0    24.8    +      -       -      -
    119A  VAL*     3.9     2.6    -      -       -      +
    120A  SER*     5.6     1.8    -      -       -      +
    121A  GLY*     3.7     6.7    -      -       -      +
    123A  ILE*     4.5    11.9    -      -       +      -
    301A  VAL*     4.5     9.6    -      -       +      -
    304A  LEU*     3.7    25.4    -      -       +      -
    305A  LEU*     4.2    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     1.3    75.0    -      -       -      +
     66A  VAL*     1.3    63.5    +      -       -      -
     95A  VAL      3.5     9.4    -      -       -      -
    114A  LEU*     3.7    12.3    -      -       -      -
    119A  VAL*     3.8     7.1    -      -       -      +
    121A  GLY      2.7    16.2    +      -       -      -
    122A  LEU*     3.1    16.7    -      -       -      +
    123A  ILE*     2.8    25.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     4.6     4.0    -      -       +      -
     65A  GLY*     1.3    76.1    -      -       -      -
     67A  ALA*     1.3    67.1    +      -       -      +
     68A  THR*     4.2    14.8    -      -       +      -
     80A  VAL*     4.5    11.9    -      -       +      -
     83A  ILE*     3.9    41.5    -      -       +      -
     94A  VAL*     4.1    14.1    -      -       +      -
     95A  VAL      3.2     6.9    +      -       -      -
     96A  VAL*     3.6    10.8    -      -       +      +
     97A  SER      2.8    29.6    +      -       -      +
    114A  LEU*     3.5     3.5    -      -       -      +
    123A  ILE*     3.2    20.9    -      -       +      +
    125A  ASN*     4.7     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  GLY      4.0     0.4    +      -       -      -
     66A  VAL*     1.3    73.4    -      -       -      +
     68A  THR*     1.3    59.0    +      -       -      +
     97A  SER      3.5     6.1    -      -       -      -
     99A  VAL*     4.8     6.5    -      -       +      -
    107A  CYS*     5.4     3.8    -      -       -      +
    110A  ALA*     4.2    21.1    -      -       +      -
    111A  VAL*     5.3     2.9    -      -       +      +
    114A  LEU*     3.7    16.0    -      -       +      +
    123A  ILE      3.0     6.1    +      -       -      -
    124A  ILE*     3.7    24.2    -      -       +      +
    125A  ASN      3.0    24.9    +      -       -      -
    126A  TYR*     4.1     1.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  VAL*     4.2    11.2    -      -       +      -
     67A  ALA*     1.3    73.7    -      -       -      +
     69A  SER*     1.3    79.2    +      -       -      +
     71A  LEU*     4.3    10.3    -      -       +      -
     76A  PRO*     3.8     7.8    -      -       -      +
     80A  VAL*     4.1    13.5    -      -       +      +
     96A  VAL*     3.8    20.2    -      -       +      -
     97A  SER      3.1    14.6    +      -       -      +
     98A  MET*     3.7     3.5    -      -       +      -
     99A  VAL*     3.0    33.1    +      -       -      +
    125A  ASN*     3.5    29.5    +      -       -      -
    126A  TYR*     4.7     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR*     1.3    96.6    +      -       -      +
     70A  SER*     1.3    71.3    +      -       -      +
     71A  LEU*     3.2     4.7    +      -       -      +
     73A  LEU*     6.0     4.3    -      -       -      -
     76A  PRO*     4.1    14.3    -      -       -      +
     98A  MET*     4.7     1.6    -      -       -      -
     99A  VAL      4.7     3.8    -      -       -      -
    101A  ARG*     6.2     1.6    -      -       -      +
    125A  ASN      3.5     7.2    +      -       -      -
    126A  TYR*     3.2    28.1    -      -       -      -
    127A  PRO*     3.6    13.2    -      -       -      +
----------------------------------------------------------
 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