Contacts of the strand formed by residues 123 - 131 (chain A) in PDB entry 6DU3


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 VAL 123 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  GLU*     4.1     1.1    -      -       -      -
    120A  ILE      2.9    30.0    +      -       -      +
    121A  ASP      3.2     8.3    -      -       -      +
    122A  GLY*     1.3    82.1    -      -       -      +
    124A  VAL*     1.3    68.6    +      -       -      +
    125A  HIS*     3.4    35.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PRO*     3.6    33.9    -      -       +      -
    118A  VAL      3.8     5.8    -      -       -      +
    119A  GLU*     4.0    17.0    -      -       +      +
    122A  GLY      4.2     1.9    +      -       -      +
    123A  VAL*     1.3    79.4    -      -       -      +
    125A  HIS*     1.3    71.1    +      -       -      +
    126A  GLN*     4.3     9.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PHE*     3.6    28.9    -      +       +      -
    117A  PRO*     3.5     0.7    -      -       -      +
    118A  VAL*     2.9    33.6    +      -       -      +
    120A  ILE*     4.3    21.3    +      -       +      +
    123A  VAL*     3.4    45.8    +      -       +      +
    124A  VAL*     1.3    74.9    +      -       -      +
    126A  GLN*     1.3    68.7    +      -       -      +
    127A  VAL*     3.6     0.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PHE*     3.9    17.0    -      -       -      +
    115A  ILE*     3.4    27.9    -      -       +      +
    116A  ILE      3.8     0.2    -      -       -      -
    117A  PRO*     3.6    20.1    -      -       -      +
    124A  VAL*     4.3    16.6    +      -       -      +
    125A  HIS*     1.3    75.9    -      -       -      +
    127A  VAL*     1.3    59.7    +      -       -      +
    128A  TYR*     3.6    33.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  SER*     3.5    28.5    -      -       -      +
    105A  SER      3.7     6.3    -      -       -      +
    106A  PHE*     3.6    37.5    -      -       +      -
    115A  ILE*     3.3     5.0    -      -       -      -
    116A  ILE*     2.9    38.8    +      -       +      +
    118A  VAL*     3.8    24.7    -      -       +      -
    126A  GLN*     1.3    71.6    -      -       -      +
    128A  TYR*     1.3    62.5    +      -       -      +
    129A  VAL*     3.7     5.5    -      -       +      +
    158A  TYR*     4.0    11.7    -      -       +      -
    860C  LEU*     3.7    15.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  HIS      3.7     1.4    -      -       -      +
    104A  SER*     3.1    22.6    -      -       -      -
    105A  SER      2.9    22.9    +      -       -      +
    106A  PHE      4.0     4.3    -      -       -      -
    107A  LYS      3.7     1.6    -      -       -      -
    108A  PRO*     3.4    36.2    -      -       +      +
    109A  VAL*     3.4    53.2    -      -       +      +
    112A  ALA*     4.3     3.4    -      -       +      -
    114A  PHE      3.8     3.1    -      -       -      -
    115A  ILE*     3.6    30.7    -      -       +      -
    126A  GLN*     3.6    36.3    -      -       +      +
    127A  VAL*     1.3    72.1    -      -       -      +
    129A  VAL*     1.3    59.4    +      -       -      +
    130A  LEU*     4.1     0.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  VAL*     3.9    24.7    -      -       +      -
    103A  HIS      3.6     1.8    -      -       -      -
    104A  SER*     3.7    19.3    -      -       -      +
    112A  ALA*     4.0     1.6    -      -       -      +
    113A  ASP*     3.0    27.0    +      -       -      +
    114A  PHE*     2.8    53.0    +      -       +      +
    116A  ILE*     4.7     5.2    -      -       +      -
    127A  VAL*     3.7    14.6    -      -       +      +
    128A  TYR*     1.3    75.2    -      -       -      +
    130A  LEU*     1.3    65.4    +      -       -      +
    162A  VAL*     4.3    20.9    -      -       +      -
----------------------------------------------------------
 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
----------------------------------------------------------
    102A  VAL*     3.2     9.1    -      -       -      +
    103A  HIS*     2.7    44.0    +      -       +      +
    109A  VAL*     4.1    25.6    -      -       +      -
    110A  ASN      5.1     0.7    -      -       -      +
    111A  ASN      4.1     6.3    -      -       -      +
    112A  ALA*     4.0    18.6    -      -       -      -
    113A  ASP*     3.6    11.2    -      -       -      +
    128A  TYR      5.6     0.2    -      -       -      +
    129A  VAL*     1.3    78.5    -      -       -      +
    131A  LYS*     1.3    61.6    +      -       -      +
    225A  TRP*     3.7    12.6    -      -       +      -
    226A  PHE      4.0     5.2    -      -       -      +
    227A  ASP*     4.0    22.2    -      -       +      -
    229A  MET*     4.0    24.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  LEU      4.2     3.8    -      -       -      -
    102A  VAL*     4.5     2.2    -      -       +      -
    113A  ASP*     2.9    35.5    +      -       +      +
    114A  PHE*     3.7    33.8    -      -       +      -
    130A  LEU*     1.3    72.0    -      -       -      +
    132A  ARG*     1.3    64.8    +      -       -      +
    133A  PRO*     3.5     3.5    -      -       -      +
    135A  VAL*     3.7    18.6    -      -       +      -
    136A  ASP*     2.8    34.7    +      -       -      -
    166A  LEU*     4.0    15.3    -      -       +      -
    225A  TRP*     3.5     9.0    -      -       -      -
    229A  MET*     4.6     7.1    -      -       -      +
----------------------------------------------------------
 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