Contacts of the strand formed by residues 129 - 136 (chain A) in PDB entry 4JDA


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 ILE 129 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ILE*     5.1     4.0    -      -       +      -
     40A  HIS*     3.7    44.4    -      -       +      +
     66A  TRP*     3.4     3.7    -      -       -      -
    122A  VAL*     3.6    20.9    -      -       +      +
    123A  LEU*     3.7     0.9    -      -       -      -
    124A  ASP*     3.2    33.0    +      -       +      -
    127A  LYS*     3.4    31.4    -      -       +      +
    128A  ARG*     1.3    79.5    -      -       -      +
    130A  LEU*     1.3    66.2    +      -       -      +
    147A  VAL*     4.1    17.3    -      -       +      -
    148A  THR      3.1    10.1    -      -       -      +
    149A  SER*     3.9    14.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  TRP*     3.9     6.1    -      -       +      -
     69A  VAL*     3.1    41.1    -      -       +      +
     70A  ARG*     3.9    15.7    -      -       -      +
     72A  PHE*     4.5    19.5    -      -       +      -
    103A  ARG*     5.9     0.2    -      -       -      +
    120A  LEU*     4.2     8.3    -      -       +      -
    122A  VAL      3.5     8.7    -      -       -      +
    123A  LEU*     4.4     9.6    -      -       +      +
    129A  ILE*     1.3    78.0    -      -       -      +
    131A  SER*     1.3    87.4    +      -       -      +
    132A  PHE*     4.0    20.2    -      -       +      -
    147A  VAL*     3.4     0.5    -      -       -      -
    148A  THR*     2.6    46.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LEU*     3.4     6.4    -      -       -      +
    121A  GLU*     2.9    31.2    +      -       -      +
    122A  VAL*     3.1    32.7    +      -       -      +
    130A  LEU*     1.3    82.8    -      -       -      +
    132A  PHE*     1.3    64.0    +      -       -      +
    145A  ARG*     5.4     2.8    -      -       -      +
    146A  SER      2.7    20.9    +      -       -      -
    147A  VAL*     3.5    19.7    -      -       -      +
    148A  THR*     5.6     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     4.1    13.9    -      -       +      -
     79A  LYS*     4.0     3.1    -      -       -      -
    103A  ARG*     3.9    20.0    -      -       -      -
    118A  GLU*     3.6    23.8    -      -       +      -
    119A  ILE      3.2    18.6    -      -       -      +
    121A  GLU*     4.2     2.9    -      -       -      +
    130A  LEU*     4.0    15.7    -      -       +      -
    131A  SER*     1.3    76.8    +      -       -      +
    133A  ARG*     1.3    64.4    +      -       -      +
    134A  VAL*     4.3     7.0    -      -       +      -
    144A  TYR*     3.9    19.3    -      +       -      -
    145A  ARG*     3.1    19.4    -      -       -      +
    146A  SER*     3.2    36.1    +      -       -      +
    148A  THR*     5.7     3.1    -      -       -      -
    170A  GLU*     6.1     0.9    -      -       -      -
    301A  A9S      3.5    34.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  GLU*     3.2     1.6    -      -       -      -
    119A  ILE*     2.7    41.1    +      -       +      +
    121A  GLU*     3.0    37.5    +      -       -      +
    132A  PHE*     1.3    78.1    -      -       -      +
    134A  VAL*     1.3    73.7    +      -       -      +
    135A  LEU*     3.5    17.1    +      -       +      -
    143A  ASN*     5.7     2.5    -      -       -      -
    144A  TYR      3.6     8.1    -      -       -      +
    145A  ARG*     3.7    37.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  SER*     3.6    18.8    -      -       -      +
    117A  VAL      3.6     3.6    -      -       -      +
    118A  GLU*     4.3     1.6    -      -       +      +
    132A  PHE*     4.3    11.0    -      -       +      -
    133A  ARG*     1.3    78.9    -      -       -      +
    135A  LEU*     1.3    60.2    +      -       -      +
    136A  GLY*     3.4    27.8    -      -       -      +
    139A  HIS*     3.8    13.5    -      -       -      +
    141A  LEU      4.5     4.0    -      -       -      +
    142A  ASN*     5.3     0.7    -      -       -      -
    143A  ASN*     4.2    20.3    +      -       -      +
    144A  TYR*     2.7    51.1    +      -       +      +
    301A  A9S      4.7     7.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ILE*     4.1    20.6    -      -       +      -
    117A  VAL*     2.7    26.7    +      -       +      +
    119A  ILE*     3.5    49.1    -      -       +      +
    133A  ARG*     3.5    17.9    +      -       +      -
    134A  VAL*     1.3    77.0    -      -       -      +
    136A  GLY*     1.3    54.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  VAL*     3.0    30.5    +      -       -      +
    134A  VAL*     3.4     8.2    -      -       -      +
    135A  LEU*     1.3    79.8    -      -       -      +
    137A  GLY*     1.3    58.7    +      -       -      -
    139A  HIS*     3.3    15.4    -      -       -      -
----------------------------------------------------------
 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