Contacts of the strand formed by residues 6 - 14 (chain B) in PDB entry 3FHX


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 ARG 6 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     3.3    49.1    -      -       -      +
    287A  MET*     5.9     2.4    +      -       -      +
    290A  GLU*     6.2     2.2    -      -       -      +
      4B  GLU*     3.8    35.0    +      -       +      +
      5B  CYS*     1.3    72.2    -      -       -      +
      7B  VAL*     1.3    61.8    +      -       -      +
     34B  GLU*     3.4    30.9    +      -       +      +
     36B  ASP*     3.7    12.1    +      -       -      -
     76B  LYS      3.9    13.0    -      -       -      +
     77B  TYR*     3.7    18.5    -      -       +      +
     78B  ASP*     2.7    44.3    +      -       -      +
     79B  TYR      3.0     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  CYS      4.3     2.0    -      -       -      +
      6B  ARG*     1.3    79.1    -      -       -      +
      8B  LEU*     1.3    71.1    +      -       -      +
     28B  LEU*     4.6     3.6    -      -       +      -
     33B  PHE*     4.2    29.8    -      -       +      -
     34B  GLU      3.0     6.3    +      -       -      -
     35B  ILE*     3.4    24.6    -      -       +      +
     36B  ASP*     2.8    30.7    +      -       -      +
     77B  TYR*     3.6     4.2    -      -       -      -
     79B  TYR*     3.4    25.4    -      -       +      +
     81B  LEU*     4.3     7.2    -      -       +      -
    242B  LEU*     4.0    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     4.1     7.4    -      -       +      -
      7B  VAL*     1.3    71.2    -      -       -      +
      9B  SER*     1.3    53.4    +      -       -      +
     10B  ILE*     3.9    25.5    +      -       +      -
     36B  ASP      3.7    11.2    -      -       -      +
     38B  VAL*     3.8    22.0    -      -       +      -
     66B  TYR*     5.4     4.0    -      -       +      -
     69B  LEU*     4.7     6.5    -      -       +      -
     77B  TYR*     3.4    39.3    -      -       +      +
     79B  TYR      2.9    11.7    +      -       -      +
     80B  VAL*     3.3    11.6    -      -       +      +
     81B  LEU      2.7    32.8    +      -       -      +
     97B  ILE*     4.6     7.9    -      -       +      -
    101B  LEU*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     3.7     0.6    +      -       -      -
      8B  LEU*     1.3    73.0    -      -       -      +
     10B  ILE*     1.3    59.4    +      -       -      +
     11B  GLN*     2.8    24.8    +      -       -      -
     21B  ASN*     2.6    30.9    +      -       -      +
     24B  ALA*     4.8     0.5    -      -       -      +
     35B  ILE*     3.4    28.5    -      -       -      +
     36B  ASP      2.9    12.3    +      -       -      -
     37B  ALA*     3.5     0.4    -      -       -      -
     38B  VAL*     2.8    23.8    +      -       -      -
     81B  LEU*     3.2    12.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LEU*     3.9    22.6    +      -       +      +
      9B  SER*     1.3    69.3    -      -       -      +
     11B  GLN*     1.3    66.2    +      -       -      +
     38B  VAL*     3.2    37.9    -      -       +      +
     40B  SER*     4.5     2.6    -      -       -      -
     62B  LEU*     4.3    13.7    -      -       +      -
     80B  VAL*     5.1     4.9    -      -       +      -
     81B  LEU      2.9     7.5    +      -       -      -
     82B  THR*     3.7    25.2    -      -       +      -
     83B  GLY      4.0     2.1    +      -       -      -
     84B  TYR      5.6     0.2    -      -       -      +
     85B  THR*     5.8     0.3    +      -       -      -
     90B  PHE*     3.8    30.9    -      -       +      -
     94B  VAL*     4.6    23.3    -      -       +      -
     97B  ILE*     4.9    12.6    -      -       +      -
     98B  VAL*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  SER*     2.8    22.6    +      -       -      +
     10B  ILE*     1.3    81.1    -      -       -      +
     12B  SER*     1.3    59.8    +      -       -      +
     20B  GLY*     3.8    15.3    -      -       -      -
     21B  ASN*     3.1    31.5    +      -       -      +
     24B  ALA*     3.8    13.7    -      -       -      +
     38B  VAL      3.2     3.2    +      -       -      -
     39B  ASN*     3.3     0.2    -      -       -      -
     40B  SER*     2.7    33.5    +      -       -      -
     81B  LEU*     3.4    28.1    -      -       -      +
     82B  THR      4.5     2.2    -      -       -      -
     83B  GLY*     3.8    26.4    -      -       -      +
     84B  TYR      5.2     6.2    +      -       -      +
    235B  ALA*     3.9    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  GLN*     1.3    77.6    -      -       -      +
     13B  HIS*     1.3    60.6    +      -       -      +
     14B  VAL*     5.4     0.2    -      -       -      -
     19B  VAL*     3.8     4.3    -      -       -      +
     20B  GLY*     3.4     7.7    -      -       -      -
     21B  ASN*     2.6    31.8    +      -       -      +
     40B  SER*     3.1     9.1    +      -       -      -
     41B  VAL*     3.0    18.8    -      -       -      +
     84B  TYR*     4.1    14.6    +      -       -      +
    313B  PXL      3.0    42.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ALA*     2.8    36.3    +      -       +      +
     39A  ASN*     3.4    23.6    +      -       -      -
     11B  GLN      4.0     0.2    +      -       -      -
     12B  SER*     1.3    73.3    -      -       -      +
     14B  VAL*     1.3    84.0    +      -       -      +
     19B  VAL      5.3     0.2    -      -       -      -
     21B  ASN*     4.8     1.6    -      -       +      +
     22B  ARG*     3.2    31.1    +      -       +      +
     39B  ASN*     3.4    31.8    +      -       +      +
     41B  VAL*     3.0    25.0    +      -       -      +
     42B  GLN*     3.3    18.1    -      -       +      -
     43B  PHE      3.1    15.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  HIS*     1.3   103.1    +      -       -      +
     15B  ILE*     1.3    65.6    +      -       -      +
     16B  ARG      3.1    22.0    -      -       -      +
     17B  GLY      3.4    18.6    -      -       -      +
     19B  VAL*     3.9    29.8    -      -       +      -
     22B  ARG*     3.4    10.5    -      -       +      +
     43B  PHE*     3.1    13.9    -      -       +      +
     45B  ASN*     3.9    24.5    -      -       -      +
     46B  HIS*     4.1     1.8    -      -       -      +
    313B  PXL      4.5     8.7    -      -       +      -
----------------------------------------------------------
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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