Contacts of the strand formed by residues 94 - 102 (chain D) in PDB entry 2C11


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 ASN 94 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79D  LEU      5.4     6.1    +      -       -      +
     82D  GLY*     3.6    21.3    +      -       -      +
     83D  LEU*     3.1    14.9    -      -       +      -
     84D  VAL*     2.8    25.6    +      -       -      -
     93D  ASP*     1.3    70.4    -      -       -      +
     95D  CYS*     1.3    59.0    +      -       -      +
    128D  VAL*     5.1     0.2    -      -       -      -
    129D  PHE      3.4     4.0    -      -       -      +
    130D  PHE*     3.0    43.5    -      -       +      +
    132D  ARG*     2.9    44.3    +      -       -      +
    133D  GLN*     4.7     1.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     3.7     2.0    -      -       -      +
     84D  VAL      3.1    20.6    -      -       -      +
     86D  ALA*     3.5    28.7    -      -       -      -
     89D  ALA*     3.9    19.3    -      -       +      -
     90D  ARG      6.0     0.2    -      -       -      -
     93D  ASP      5.0     2.7    -      -       -      -
     94D  ASN*     1.3    74.5    -      -       -      +
     96D  VAL*     1.3    60.7    +      -       -      +
     97D  PHE      4.9     0.2    -      -       -      -
    128D  VAL*     3.0     8.5    -      -       -      +
    129D  PHE*     2.8    64.6    +      -       -      -
    166D  TYR*     5.8     0.2    -      -       -      -
    172D  LEU*     4.1     6.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72D  MET*     3.9    21.8    -      -       +      -
     75D  LEU*     4.2    13.0    -      -       +      -
     79D  LEU*     4.0    13.5    -      -       +      -
     83D  LEU*     3.7    33.2    -      -       +      +
     84D  VAL      4.2     2.4    +      -       -      -
     86D  ALA*     3.3    16.8    +      -       -      +
     95D  CYS*     1.3    72.5    -      -       -      +
     97D  PHE*     1.3    62.8    +      -       -      +
     98D  SER      4.0     2.5    -      -       -      +
     99D  VAL*     3.8    29.6    -      -       +      -
    126D  ALA*     4.5     2.5    -      -       +      -
    127D  ILE      3.7    11.4    -      -       -      +
    128D  VAL*     4.2     3.8    -      -       +      -
    418D  GLU      4.3     0.5    +      -       -      -
    419D  SER      3.9    12.6    -      -       -      +
    420D  GLN*     5.5     3.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  ALA*     4.3     4.9    -      -       -      -
     95D  CYS*     3.6     3.8    +      -       -      -
     96D  VAL*     1.3    71.3    -      -       -      +
     98D  SER*     1.3    70.9    +      -       -      +
    127D  ILE*     2.9    20.6    +      -       +      +
    129D  PHE*     3.3    44.9    -      +       +      -
    170D  PRO*     3.4    31.9    -      -       +      -
    171D  VAL      5.2     0.2    -      -       -      -
    172D  LEU*     3.7     7.4    -      -       +      -
    344D  PHE*     3.4    30.1    -      +       -      -
    388D  GLY      5.7     0.4    -      -       -      -
    389D  PHE      5.6     0.4    -      -       -      -
    393D  LYS*     3.1    19.3    -      -       -      -
    416D  LEU      5.5     0.2    -      -       -      -
    417D  LEU*     3.2     1.9    -      -       -      +
    418D  GLU*     2.5    64.8    +      -       +      +
    647D  VAL*     4.9     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96D  VAL*     3.5     2.1    -      -       -      +
     97D  PHE*     1.3    89.5    -      -       -      +
     99D  VAL*     1.3    62.1    +      -       -      +
    100D  GLU*     6.1     1.6    -      -       -      -
    125D  LEU      4.1     2.1    +      -       -      -
    126D  ALA*     2.8    11.8    -      -       -      +
    127D  ILE*     2.8    58.1    +      -       -      +
    344D  PHE*     4.0    10.2    -      -       -      -
    416D  LEU      3.5     7.2    -      -       -      -
    417D  LEU*     3.5    20.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  LEU*     4.1     6.1    -      -       +      -
     68D  LEU*     3.5    18.2    -      -       +      +
     71D  VAL*     3.4    32.3    -      -       +      -
     72D  MET*     4.7     2.0    -      -       +      -
     75D  LEU*     4.3     8.7    -      -       +      -
     96D  VAL*     3.8    15.9    -      -       +      -
     98D  SER*     1.3    81.9    -      -       -      +
    100D  GLU*     1.3    63.9    +      -       -      +
    124D  ALA*     4.1    11.9    -      -       +      -
    125D  LEU      3.3     6.1    -      -       -      +
    126D  ALA*     3.5    15.7    -      -       +      -
    416D  LEU*     3.1    39.0    +      -       +      +
    417D  LEU*     4.7     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62D  ASP*     4.8     0.5    -      -       -      +
     63D  LEU*     3.2    13.1    -      -       -      +
     68D  LEU*     4.6     2.2    -      -       -      -
     98D  SER*     6.1     1.6    -      -       -      +
     99D  VAL*     1.3    76.0    -      -       -      +
    101D  LEU*     1.3    68.9    +      -       -      +
    124D  ALA*     3.1     8.1    -      -       -      -
    125D  LEU*     3.0    38.5    +      -       +      +
    341D  LEU      4.0     1.9    -      -       -      +
    342D  GLY*     3.8     2.8    -      -       -      -
    343D  ALA*     2.9    46.7    +      -       +      +
    344D  PHE*     4.1    10.4    +      -       +      -
    348D  ARG*     3.4    28.3    +      -       -      -
    413D  TRP*     5.6     2.1    -      -       +      -
    417D  LEU*     5.4     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59D  LEU      4.7     3.1    -      -       -      +
     60D  PHE*     4.1    15.5    -      -       +      +
     61D  ALA      3.9    20.6    -      -       -      +
     62D  ASP*     4.1     6.5    -      -       -      +
     63D  LEU*     3.3    25.2    -      -       +      +
    100D  GLU*     1.3    90.7    +      -       -      +
    102D  GLN*     1.3    80.0    +      -       -      +
    103D  LEU*     3.6    27.1    +      -       +      +
    104D  PRO*     5.2     2.0    -      -       +      -
    122D  ARG*     3.3    32.1    -      -       -      +
    123D  GLU      3.8     8.5    -      -       -      +
    125D  LEU*     4.6     2.0    -      -       -      +
    348D  ARG*     4.2    14.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 102 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  GLU      3.4     0.8    +      -       -      -
    101D  LEU*     1.3    82.7    -      -       -      +
    103D  LEU*     1.3    94.3    +      -       -      +
    104D  PRO*     3.5     2.6    -      -       -      +
    123D  GLU*     3.2    42.6    +      -       +      +
    124D  ALA*     3.7     7.6    -      -       -      +
    125D  LEU*     3.5    25.0    -      -       -      +
    142D  VAL*     3.9    19.7    -      -       +      -
    159D  ARG*     3.1    28.3    +      -       -      +
----------------------------------------------------------
 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