Contacts of the strand formed by residues 785 - 793 (chain D) in PDB entry 3N1G


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 785 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  ASN*     3.8    17.5    +      -       -      -
    181A  HIS*     5.9     1.7    +      -       -      -
    754D  PRO*     3.6     6.6    -      -       -      +
    755D  THR*     2.6    49.5    +      -       -      +
    756D  ASP      4.8     0.2    +      -       -      -
    784D  THR*     1.3    78.8    -      -       -      +
    786D  TYR*     1.3    57.7    +      -       -      +
    806D  ILE*     3.2    21.5    -      -       -      +
    807D  CYS      3.6     5.4    +      -       -      -
    808D  GLU*     3.6    21.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 786 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729D  ILE*     4.0    18.2    -      -       +      -
    752D  TYR*     4.6     8.3    -      +       +      -
    753D  ARG      3.3    24.2    -      -       -      +
    754D  PRO*     3.8    22.6    -      -       +      +
    755D  THR*     3.3     6.2    +      -       -      -
    777D  ILE*     6.3     0.2    -      -       +      -
    780D  LEU*     3.5    37.2    -      -       +      +
    781D  GLN*     2.9    34.1    +      -       -      +
    784D  THR*     3.3    35.6    -      -       +      +
    785D  SER*     1.3    72.3    +      -       -      +
    787D  ASP*     1.3    60.2    +      -       -      +
    788D  ILE*     3.9    15.5    +      -       +      +
    805D  MET      3.6     0.5    -      -       -      +
    806D  ILE*     3.2     5.9    -      -       -      -
    807D  CYS      2.8    36.8    +      -       -      +
    809D  THR*     4.0     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 787 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS*     2.7    37.2    +      -       -      -
     90A  GLU*     4.5     4.7    -      -       -      -
    752D  TYR*     3.1     6.6    -      -       -      -
    753D  ARG*     2.7    52.5    +      -       -      +
    755D  THR*     2.9    29.0    +      -       -      +
    757D  SER      3.8     0.5    -      -       -      +
    763D  TYR*     3.7    21.1    -      -       +      +
    786D  TYR*     1.3    71.8    -      -       -      +
    788D  ILE*     1.3    61.5    +      -       -      +
    804D  VAL*     4.5     5.2    -      -       +      -
    805D  MET      3.5     5.4    -      -       -      +
    806D  ILE*     4.0     7.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 788 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718D  ILE*     3.8    11.2    -      -       +      +
    721D  THR*     4.7     8.3    -      -       +      -
    729D  ILE*     3.8    35.7    -      -       +      -
    731D  LEU*     4.4    14.4    -      -       +      -
    750D  ILE*     4.4     8.1    -      -       +      -
    751D  TYR      3.4     9.0    -      -       -      +
    752D  TYR*     4.4     1.1    -      -       +      -
    777D  ILE*     4.0    25.8    -      -       +      -
    786D  TYR*     4.0    13.7    -      -       +      +
    787D  ASP*     1.3    81.6    -      -       -      +
    789D  LYS*     1.3    64.3    +      -       -      +
    804D  VAL*     3.4     5.4    -      -       -      +
    805D  MET*     2.8    45.5    +      -       +      +
    807D  CYS*     4.2    17.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 789 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  GLU      4.6     3.0    +      -       -      -
     92A  ASN*     4.2    17.8    -      -       -      +
    718D  ILE*     3.9     4.0    -      -       -      -
    750D  ILE*     3.7     1.7    -      -       -      +
    751D  TYR*     2.7    41.2    +      -       +      +
    760D  ASP*     4.6     7.1    +      -       -      +
    763D  TYR*     3.7    42.4    +      -       +      +
    788D  ILE*     1.3    76.5    -      -       -      +
    790D  MET*     1.3    64.1    +      -       -      +
    801D  PHE*     3.6    51.4    -      -       +      -
    802D  SER*     3.6    15.0    -      -       -      +
    803D  ASN      3.8     5.6    -      -       -      +
    804D  VAL*     4.0    19.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 790 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    716D  PRO*     3.7    11.9    -      -       +      +
    718D  ILE*     3.8    13.0    -      -       +      -
    731D  LEU*     4.2     4.9    -      -       -      -
    733D  TRP*     3.3    63.7    -      -       +      -
    748D  PHE*     3.7    31.9    -      -       +      -
    749D  TYR      3.1    15.9    -      -       -      +
    750D  ILE*     4.1    13.5    -      -       +      -
    751D  TYR*     4.2     2.7    -      -       -      -
    789D  LYS*     1.3    77.3    -      -       -      +
    791D  GLN*     1.3    64.7    +      -       -      +
    801D  PHE*     3.5     4.8    -      -       -      -
    802D  SER*     2.8    45.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 791 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    716D  PRO*     3.6    11.0    -      -       -      -
    748D  PHE*     3.2     7.8    -      -       -      +
    749D  TYR*     2.9    33.3    +      -       +      +
    751D  TYR*     2.4    42.5    +      -       +      -
    790D  MET*     1.3    74.3    -      -       -      +
    792D  CYS*     1.3    64.7    +      -       -      +
    798D  GLU*     3.3    27.3    -      -       +      +
    799D  SER*     3.1    32.8    +      -       -      +
    800D  GLU      3.8     4.0    -      -       -      +
    801D  PHE*     3.3    25.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 792 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712D  PRO*     3.7    12.1    -      -       -      -
    714D  ALA      3.9     0.7    -      -       -      -
    715D  GLY*     4.6     1.3    -      -       -      -
    716D  PRO*     3.7     2.1    -      -       +      +
    735D  TYR*     3.5    35.0    -      -       -      -
    745D  ILE*     4.1     9.2    -      -       +      -
    747D  GLY      3.4    12.8    -      -       -      +
    748D  PHE*     3.7    21.1    -      -       +      -
    791D  GLN*     1.3    78.1    -      -       -      +
    793D  PHE*     1.3    65.0    +      -       -      +
    798D  GLU*     3.5     2.1    -      -       -      +
    799D  SER*     2.9    48.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 793 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712D  PRO*     4.1     4.0    -      -       -      -
    745D  ILE*     3.4     4.4    -      -       -      +
    746D  HIS*     2.7    54.8    +      +       +      -
    747D  GLY*     3.0    46.8    +      -       -      -
    748D  PHE      3.5     9.4    -      -       -      -
    749D  TYR*     3.5    59.2    -      +       +      -
    767D  MET*     3.9    15.0    -      -       +      -
    792D  CYS*     1.3    79.2    -      -       -      +
    794D  ASN*     1.3    65.8    +      -       -      +
    797D  GLY      3.2    14.8    -      -       -      +
    798D  GLU*     3.9     7.4    -      -       +      +
----------------------------------------------------------
 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