Contacts of the helix formed by residues 2912 - 2933 (chain F) in PDB entry 6X34


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 THR2912 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2910F  THR      3.9     0.2    +      -       -      -
   2911F  LEU*     1.3    78.4    -      -       -      +
   2913F  ALA*     1.3    65.4    +      -       -      +
   2914F  LYS*     3.4     8.5    -      -       -      -
   2915F  GLU*     4.0    11.4    -      -       -      +
   2916F  LYS*     3.2    23.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA2913 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2912F  THR*     1.3    73.3    -      -       -      +
   2914F  LYS*     1.3    64.3    +      -       -      +
   2916F  LYS*     3.5     5.7    +      -       -      +
   2917F  ALA*     3.4    20.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS2914 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2912F  THR*     3.4     4.3    -      -       -      -
   2913F  ALA*     1.3    80.2    -      -       -      +
   2915F  GLU*     1.3    60.9    +      -       -      +
   2917F  ALA*     3.4    17.8    +      -       -      +
   2918F  ARG*     4.4     1.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU2915 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2911F  LEU*     4.4    10.3    -      -       +      -
   2912F  THR*     3.6    21.0    +      -       -      +
   2913F  ALA      3.3     0.4    -      -       -      -
   2914F  LYS*     1.3    80.2    -      -       -      +
   2916F  LYS*     1.3    61.6    +      -       -      +
   2917F  ALA      3.4     0.5    +      -       -      -
   2918F  ARG*     3.7    14.9    +      -       -      +
   2919F  ASP*     4.6     2.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS2916 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2879F  ALA*     5.5     0.5    -      -       -      +
   2908F  TYR      5.7     2.5    -      -       -      +
   2911F  LEU*     4.9     8.5    -      -       +      +
   2912F  THR      3.2    19.2    +      -       -      +
   2913F  ALA*     3.5     7.1    +      -       -      +
   2914F  LYS      3.3     0.4    -      -       -      -
   2915F  GLU*     1.3    73.8    -      -       -      +
   2917F  ALA*     1.3    57.9    +      -       -      +
   2918F  ARG      3.2     1.3    -      -       -      -
   2919F  ASP*     3.4     6.8    +      -       +      +
   2920F  ARG*     3.0    31.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA2917 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2913F  ALA      3.4    10.7    +      -       -      +
   2914F  LYS*     3.6    14.6    -      -       -      +
   2915F  GLU      3.2     1.4    -      -       -      -
   2916F  LYS*     1.3    77.9    -      -       -      +
   2918F  ARG*     1.3    61.1    +      -       -      +
   2920F  ARG*     4.3     6.0    -      -       -      +
   2921F  GLU*     3.1    26.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG2918 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2914F  LYS      4.4     1.5    +      -       -      +
   2915F  GLU      3.7    11.9    +      -       -      +
   2916F  LYS      3.2     0.8    -      -       -      -
   2917F  ALA*     1.3    81.3    -      -       -      +
   2919F  ASP*     1.3    60.8    +      -       -      +
   2921F  GLU*     3.9     7.5    +      -       -      +
   2922F  LYS*     3.9    11.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP2919 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2879F  ALA*     3.4    40.6    -      -       +      +
   2882F  TYR*     4.8    10.5    -      -       +      +
   2883F  HIS*     5.1     8.3    -      -       +      +
   2915F  GLU      4.6     1.5    +      -       -      +
   2916F  LYS*     3.4    10.3    +      -       -      +
   2917F  ALA      3.3     0.2    -      -       -      -
   2918F  ARG*     1.3    76.8    -      -       -      +
   2920F  ARG*     1.3    64.7    +      -       -      +
   2921F  GLU      3.3     0.8    +      -       -      -
   2922F  LYS*     3.5     6.6    +      -       -      +
   2923F  ALA      3.4    15.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG2920 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2875F  ALA*     5.6     2.0    -      -       +      +
   2879F  ALA*     3.9    11.4    -      -       +      +
   2916F  LYS*     3.0    20.4    +      -       +      +
   2917F  ALA*     4.3     5.4    -      -       -      +
   2919F  ASP*     1.3    74.9    -      -       -      +
   2921F  GLU*     1.3    59.8    +      -       -      +
   2923F  ALA*     3.9     2.7    -      -       -      +
   2924F  GLN*     2.9    31.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU2921 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2917F  ALA      3.1    19.9    +      -       -      +
   2918F  ARG*     4.2     6.1    -      -       -      +
   2919F  ASP      3.3     0.4    -      -       -      -
   2920F  ARG*     1.3    78.9    -      -       -      +
   2922F  LYS*     1.3    57.5    +      -       -      +
   2924F  GLN*     3.5     4.4    +      -       -      +
   2925F  GLU*     3.0    30.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS2922 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2882F  TYR*     5.8     6.7    -      -       +      -
   2918F  ARG      3.9     9.2    +      -       -      +
   2919F  ASP*     3.5     9.0    +      -       -      +
   2920F  ARG      3.3     0.4    -      -       -      -
   2921F  GLU*     1.3    78.5    -      -       -      +
   2923F  ALA*     1.3    62.5    +      -       -      +
   2925F  GLU*     3.6     5.8    +      -       -      +
   2926F  LEU*     3.4    21.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA2923 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2875F  ALA*     3.4    35.1    -      -       +      +
   2878F  LEU*     3.9    20.9    -      -       +      -
   2879F  ALA*     3.9     4.7    -      -       +      +
   2919F  ASP      3.4    14.4    +      -       -      +
   2920F  ARG*     3.5     3.3    +      -       -      +
   2921F  GLU      3.3     0.2    -      -       -      -
   2922F  LYS*     1.3    77.6    -      -       -      +
   2924F  GLN*     1.3    65.0    +      -       -      +
   2926F  LEU*     3.4     5.8    +      -       -      +
   2927F  LEU*     3.2    23.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN2924 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2875F  ALA*     4.9     6.6    -      -       +      +
   2920F  ARG      2.9    18.2    +      -       -      +
   2921F  GLU*     4.1     5.2    -      -       -      +
   2923F  ALA*     1.3    74.5    -      -       -      +
   2925F  GLU*     1.3    60.5    +      -       -      +
   2927F  LEU*     4.0     5.6    -      -       -      +
   2928F  LYS*     2.9    32.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU2925 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2862F  LEU*     6.4     1.1    -      -       -      -
   2921F  GLU      3.0    18.8    +      -       -      +
   2922F  LYS*     3.9     6.7    -      -       -      +
   2923F  ALA      3.3     0.2    -      -       -      -
   2924F  GLN*     1.3    78.7    -      -       -      +
   2926F  LEU*     1.3    61.0    +      -       -      +
   2928F  LYS*     4.1     4.8    -      -       -      +
   2929F  PHE*     3.2    24.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU2926 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2812F  SER*     5.4    12.8    -      -       -      -
   2922F  LYS      3.4    14.3    +      -       -      +
   2923F  ALA*     3.9     5.6    -      -       -      +
   2924F  GLN      3.3     0.4    -      -       -      -
   2925F  GLU*     1.3    77.1    -      -       -      +
   2927F  LEU*     1.3    63.3    +      -       -      +
   2929F  PHE*     3.6     5.2    +      -       -      +
   2930F  LEU*     3.3    22.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU2927 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2871F  LEU*     5.3    18.4    -      -       +      +
   2875F  ALA*     5.6     4.5    -      -       +      -
   2923F  ALA      3.2    16.5    +      -       -      +
   2924F  GLN*     4.0     6.1    -      -       -      +
   2926F  LEU*     1.3    74.9    -      -       -      +
   2928F  LYS*     1.3    66.1    +      -       -      +
   2930F  LEU*     3.4     5.2    +      -       -      +
   2931F  GLN*     3.1    24.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS2928 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2862F  LEU*     4.5    18.6    -      -       +      +
   2865F  VAL*     4.2    26.0    -      -       +      +
   2924F  GLN      2.9    18.8    +      -       -      +
   2925F  GLU*     4.1     4.7    -      -       -      +
   2926F  LEU      3.4     0.2    -      -       -      -
   2927F  LEU*     1.3    78.3    -      -       -      +
   2929F  PHE*     1.3    59.8    +      -       -      +
   2931F  GLN*     3.6     5.2    +      -       -      +
   2932F  MET*     3.1    24.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE2929 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2758F  PHE*     5.2    15.9    -      -       +      -
   2925F  GLU      3.2    18.6    +      -       -      +
   2926F  LEU*     4.0     5.8    -      -       -      +
   2927F  LEU      3.3     0.2    -      -       -      -
   2928F  LYS*     1.3    76.7    -      -       -      +
   2930F  LEU*     1.3    62.2    +      -       -      +
   2932F  MET*     3.6     6.1    +      -       -      +
   2933F  ASN*     3.4    21.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU2930 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2926F  LEU      3.3    15.9    +      -       -      +
   2927F  LEU*     3.9     6.1    -      -       -      +
   2929F  PHE*     1.3    76.8    -      -       -      +
   2931F  GLN*     1.3    62.0    +      -       -      +
   2933F  ASN*     3.3     8.7    +      -       -      -
   2934F  GLY      3.3     0.2    +      -       -      -
   2935F  TYR*     2.8    48.4    +      -       +      +
   2937F  VAL*     5.9     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN2931 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2927F  LEU      3.1    17.4    +      -       -      +
   2928F  LYS*     4.1     5.4    -      -       -      +
   2930F  LEU*     1.3    76.8    -      -       -      +
   2932F  MET*     1.3    63.7    +      -       -      +
   2934F  GLY*     3.3    11.3    +      -       -      +
   2935F  TYR      4.0     9.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET2932 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2828F  GLU      4.5     0.5    -      -       -      +
   2829F  GLY*     3.4     1.7    -      -       -      -
   2830F  GLU*     2.9    37.6    +      -       +      +
   2928F  LYS      3.1    18.6    +      -       -      +
   2929F  PHE*     3.9     7.2    -      -       -      +
   2930F  LEU      3.2     0.2    -      -       -      -
   2931F  GLN*     1.3    78.5    -      -       -      +
   2933F  ASN*     1.3    56.7    +      -       -      +
   2934F  GLY      3.2     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN2933 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2754F  PHE*     6.2     4.0    -      -       +      -
   2825F  LYS*     5.3     3.8    -      -       -      +
   2827F  ARG      3.6     7.4    -      -       -      +
   2829F  GLY*     3.7    17.5    +      -       -      -
   2929F  PHE      3.4    13.2    +      -       -      +
   2930F  LEU*     3.3     6.8    +      -       -      +
   2931F  GLN      3.3     0.8    -      -       -      -
   2932F  MET*     1.3    76.9    -      -       -      +
   2934F  GLY*     1.3    60.6    +      -       -      +
   2935F  TYR*     3.4     4.6    +      -       +      +
----------------------------------------------------------
 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