Contacts of the strand formed by residues 109 - 114 (chain D) in PDB entry 3DC1


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 MET 109 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  LYS*     4.2    43.4    +      -       +      +
     91D  GLN*     4.3     9.2    -      -       +      -
     92D  ILE*     4.8     9.6    -      -       +      -
     97D  PRO*     3.8    28.5    -      -       +      -
     99D  THR*     3.2    25.0    +      -       -      +
    100D  ILE*     4.1    22.1    -      -       +      +
    107D  GLY      3.4     1.5    +      -       -      -
    108D  GLN*     1.3    86.1    -      -       -      +
    110D  ASP*     1.3    61.5    +      -       -      +
    247D  LEU*     4.8     5.2    -      -       +      -
    275D  THR*     3.8    27.8    -      -       +      -
    276D  GLY      4.0     6.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 110 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  LYS*     3.8    16.6    +      -       -      +
    109D  MET*     1.3    78.5    -      -       -      +
    111D  LEU*     1.3    75.1    +      -       -      +
    275D  THR*     3.3     9.6    -      -       -      +
    276D  GLY      3.0    29.9    +      -       -      +
    278D  LYS*     3.6    39.0    -      -       +      +
    281D  ILE*     3.8    21.3    -      -       +      +
    282D  GLU*     4.9     1.7    +      -       -      +
    285D  ILE*     5.0     5.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 111 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  ALA*     4.7     5.2    -      -       -      +
     84D  LEU*     3.3    36.3    -      -       +      +
     87D  LEU*     3.6    45.3    -      -       +      -
     88D  LYS*     3.8    23.2    -      -       +      +
     91D  GLN*     3.9    13.7    -      -       +      -
    110D  ASP*     1.3    91.0    +      -       -      +
    112D  CYS*     1.3    70.3    +      -       -      +
    113D  VAL      4.5     0.2    -      -       -      +
    273D  PHE*     3.8    14.1    -      -       +      -
    274D  LEU      3.2    10.1    -      -       -      +
    275D  THR*     3.4    21.1    -      -       +      +
    281D  ILE*     4.3     5.0    -      -       -      +
    285D  ILE*     4.9     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 112 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77D  SER      4.6     0.4    -      -       -      -
     78D  ALA*     3.7    13.2    -      -       -      +
    111D  LEU*     1.3    78.2    -      -       -      +
    113D  VAL*     1.3    84.4    +      -       -      +
    114D  THR*     3.7     6.6    +      -       +      -
    273D  PHE*     3.0     4.9    -      -       -      +
    274D  LEU*     2.6    45.3    +      -       +      +
    281D  ILE*     4.0    16.8    -      -       +      -
    284D  VAL*     4.9     2.9    -      -       +      -
    285D  ILE*     3.6    22.4    -      -       +      -
    288D  ILE*     3.9    20.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 113 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77D  SER      4.2     1.4    -      -       -      +
     78D  ALA      2.6    23.4    +      -       -      +
     79D  GLY*     3.8    14.6    -      -       -      -
     83D  LEU*     3.7    32.5    -      -       +      -
     84D  LEU*     4.0    13.7    -      -       +      -
     87D  LEU*     4.1    13.7    -      -       +      -
    112D  CYS*     1.3    86.6    -      -       -      +
    114D  THR*     1.3    61.2    +      -       -      +
    271D  ILE*     4.2    10.1    -      -       +      -
    272D  GLY      3.6     8.1    -      -       -      +
    273D  PHE*     4.2     1.1    -      -       -      +
    288D  ILE*     4.5     1.9    -      -       -      +
    295D  PRO*     3.4    29.1    -      -       +      +
    300D  GLN*     3.6    12.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 114 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112D  CYS*     4.0    13.0    -      -       -      +
    113D  VAL*     1.3    79.5    -      -       -      +
    115D  SER*     1.3    59.7    +      -       -      +
    116D  GLY      2.7    28.8    +      -       -      -
    117D  SER*     3.9     4.3    -      -       -      -
    119D  GLN*     3.4     8.3    -      -       -      +
    120D  GLY*     4.0    23.7    +      -       -      +
    270D  ARG      3.6     0.2    -      -       -      +
    271D  ILE*     3.3     6.6    -      -       -      -
    272D  GLY      2.4    45.3    +      -       -      +
    273D  PHE*     4.0     2.8    +      -       -      -
    274D  LEU*     4.4     8.9    -      -       +      +
    284D  VAL*     5.0     2.7    -      -       +      -
    288D  ILE*     4.0    20.0    -      -       +      -
    295D  PRO*     4.1     7.7    -      -       -      +
----------------------------------------------------------
 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