Contacts of the helix formed by residues 55 - 71 (chain B) in PDB entry 4HFG


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 55 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU      2.6    29.5    +      -       -      -
     14A  SER*     3.1    20.9    +      -       -      +
     16A  LEU*     3.0    33.9    +      -       -      +
     17A  SER      4.5     2.7    -      -       -      +
     18A  ASN*     3.1    32.5    -      -       -      +
     19A  SER*     3.9     5.2    -      -       -      +
     51B  ALA*     4.2    13.0    -      -       +      +
     52B  LYS*     2.9    31.2    +      -       +      +
     54B  ASN*     1.3    84.5    -      -       -      +
     56B  LYS*     1.3    64.6    +      -       -      +
     57B  LEU      3.3     2.5    -      -       -      -
     58B  THR*     3.1    21.2    +      -       -      -
     59B  PHE*     3.5    26.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  LEU*     2.9    44.4    +      -       +      +
     49B  ARG      3.8     7.7    +      -       -      -
     50B  LYS      4.4     0.2    -      -       -      -
     51B  ALA*     2.7    29.4    +      -       +      +
     52B  LYS      3.2    12.4    +      -       -      +
     53B  SER*     4.0     8.4    +      -       -      +
     54B  ASN      3.8     0.6    -      -       -      -
     55B  ARG*     1.3    76.3    -      -       -      +
     57B  LEU*     1.3    64.0    +      -       -      +
     59B  PHE*     3.0    24.9    +      -       -      +
     60B  LEU      3.7     2.1    +      -       -      -
     91B  HIS*     3.1    30.8    +      -       +      +
     92B  VAL*     4.1     8.8    -      -       +      +
     95B  GLU*     3.7    35.4    -      -       -      +
     96B  ALA*     4.0    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  SER*     3.4    23.9    +      -       -      +
     25A  THR*     4.7     3.8    -      -       -      +
     53B  SER      5.1     0.2    +      -       -      -
     55B  ARG      3.3     0.6    -      -       -      -
     56B  LYS*     1.3    78.0    -      -       -      +
     58B  THR*     1.3    64.6    +      -       -      +
     60B  LEU*     2.9    13.6    +      -       +      +
     61B  TYR*     3.0    48.5    +      -       +      +
     92B  VAL*     4.2    12.2    -      -       +      +
     96B  ALA*     4.7     4.6    -      -       +      +
     99B  GLY      5.5     0.4    -      -       -      +
    100B  CYS*     4.5    16.2    -      -       +      -
    103B  PRO*     4.3    15.9    -      -       +      -
    104B  LEU*     3.5    38.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LEU*     3.9    18.8    -      -       +      +
     17A  SER      2.6    29.9    +      -       -      +
     18A  ASN      3.5     0.3    -      -       -      -
     19A  SER*     3.2    21.5    +      -       -      -
     22A  SER*     4.4     8.4    -      -       -      -
     23B  VAL*     3.8    22.4    -      -       +      -
     55B  ARG*     3.1    10.1    +      -       -      -
     57B  LEU*     1.3    76.9    -      -       -      +
     59B  PHE*     1.3    57.9    +      -       -      +
     61B  TYR*     3.2    11.4    +      -       +      +
     62B  LEU*     2.9    27.0    +      -       -      +
    202B  SO4      4.1     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     4.2    31.6    -      -       +      -
     16A  LEU*     4.9     7.0    -      -       +      -
     44B  TRP*     3.0    43.4    +      +       +      +
     47B  GLU*     3.8    19.3    -      -       +      -
     48B  LEU*     3.4    42.8    -      -       +      -
     51B  ALA*     3.5    22.0    -      -       +      -
     55B  ARG*     3.5    31.4    -      -       -      -
     56B  LYS*     3.0    17.3    +      -       -      +
     58B  THR*     1.3    77.9    -      -       -      +
     60B  LEU*     1.3    55.3    +      -       -      +
     62B  LEU*     3.3     5.0    +      -       -      +
     63B  ALA      3.0    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  TRP*     3.9    24.9    -      -       +      -
     48B  LEU*     5.4     0.2    -      -       +      -
     56B  LYS      4.9     0.2    -      -       -      +
     57B  LEU*     2.9    10.0    +      -       +      +
     59B  PHE*     1.3    74.9    -      -       +      +
     61B  TYR*     1.3    60.9    +      -       -      +
     63B  ALA*     3.6     4.3    -      -       +      +
     64B  ASN*     2.8    30.3    +      -       -      +
     85B  LEU*     4.0     9.4    -      -       +      -
     88B  ALA*     4.3     5.6    -      -       +      +
     89B  PHE*     3.8    38.8    -      -       +      -
     92B  VAL*     3.6    34.1    -      -       +      -
    104B  LEU*     3.7    31.6    -      -       +      -
    107B  LEU*     4.0     9.1    -      -       +      +
    111B  TRP*     5.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  SER      5.2     0.2    -      -       -      -
     22A  SER*     4.0     9.6    -      -       -      -
     24A  GLN*     3.0    47.7    +      -       +      +
     25A  THR*     3.9    16.6    +      -       -      -
     28A  LEU*     3.9    14.4    -      -       -      +
     23B  VAL*     3.9    17.5    -      -       +      +
     57B  LEU*     3.0    44.3    +      -       +      +
     58B  THR*     3.2    15.9    +      -       +      +
     60B  LEU*     1.3    75.8    -      -       -      +
     62B  LEU*     1.3    59.8    +      -       -      +
     64B  ASN*     3.4     7.6    +      -       +      +
     65B  ASP*     3.1    18.0    +      -       -      +
    103B  PRO*     3.2    31.3    +      -       -      +
    107B  LEU*     3.9    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     3.7    30.1    -      -       +      -
     16A  LEU*     4.0     7.0    -      -       +      -
     23B  VAL*     3.9    37.8    -      -       +      +
     26B  LEU*     3.9    24.7    -      -       +      -
     27B  SER*     4.1     3.1    -      -       -      +
     30B  LEU*     4.3     8.5    -      -       +      -
     44B  TRP*     4.0    15.0    -      -       +      +
     58B  THR      2.9    13.5    +      -       -      +
     59B  PHE*     3.4     7.9    -      -       -      +
     61B  TYR*     1.3    73.3    -      -       -      +
     63B  ALA*     1.3    66.8    +      -       -      +
     65B  ASP*     3.1     2.4    +      -       -      -
     66B  VAL*     2.9    45.0    +      -       +      +
     81B  PHE*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  TRP*     3.8     9.4    -      -       +      +
     59B  PHE      3.0    14.4    +      -       -      +
     60B  LEU*     3.6    15.3    -      -       +      +
     62B  LEU*     1.3    75.9    -      -       -      +
     64B  ASN*     1.3    64.7    +      -       -      +
     66B  VAL*     4.5     1.1    -      -       -      -
     67B  ILE*     3.0    37.8    +      -       +      +
     81B  PHE*     3.8    38.4    -      -       +      -
     85B  LEU*     4.7     2.2    -      -       +      -
    111B  TRP*     4.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  GLN*     4.3    14.1    -      -       -      +
    204A  UNX      4.2    13.7    -      -       -      -
     60B  LEU      2.8    17.4    +      -       -      +
     61B  TYR*     3.4     9.1    +      -       -      +
     62B  LEU      3.1     0.2    -      -       -      -
     63B  ALA*     1.3    78.1    -      -       -      +
     65B  ASP*     1.3    65.8    +      -       -      +
     67B  ILE*     4.1     0.7    -      -       -      +
     68B  GLN*     2.8    47.7    +      -       -      +
    107B  LEU*     4.1    22.1    -      -       +      +
    110B  ILE*     5.3     0.9    -      -       -      +
    111B  TRP*     2.7    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ASN*     5.4     1.6    +      -       -      -
     65A  ASP*     5.4     2.1    -      -       -      +
     23B  VAL*     4.0    13.0    -      -       +      +
     24B  GLN*     3.5    31.0    +      -       -      +
     27B  SER*     2.8    29.8    +      -       -      +
     61B  TYR      3.1    10.9    +      -       -      +
     62B  LEU      3.7     5.4    -      -       -      +
     64B  ASN*     1.3    84.6    +      -       -      +
     66B  VAL*     1.3    62.2    +      -       -      +
     68B  GLN*     4.2     2.2    -      -       -      -
     69B  ASN*     3.1    53.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  SER*     3.4    20.9    -      -       -      +
     30B  LEU*     3.8    26.2    -      -       +      -
     31B  ILE*     3.9     5.9    -      -       +      +
     62B  LEU*     2.9    29.2    +      -       +      +
     63B  ALA*     3.9     4.5    -      -       -      +
     65B  ASP*     1.3    72.9    -      -       -      +
     67B  ILE*     1.3    60.8    +      -       -      +
     69B  ASN      3.8     0.2    -      -       -      -
     70B  SER*     2.8    35.5    +      -       -      -
     77B  PHE*     3.5    45.8    -      -       +      -
     81B  PHE*     4.1    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ALA*     3.0    25.6    +      -       +      +
     64B  ASN*     4.1     2.0    -      -       -      +
     66B  VAL*     1.3    76.0    -      -       -      +
     68B  GLN*     1.3    64.3    +      -       -      +
     70B  SER*     2.8    20.7    +      -       -      -
     71B  LYS*     3.4    10.7    +      -       -      +
     77B  PHE*     4.3     5.2    -      -       -      +
     78B  THR*     4.1    16.4    -      -       -      +
     81B  PHE*     3.6    45.3    -      -       +      -
     85B  LEU*     4.1     6.7    -      -       +      -
    111B  TRP*     4.1    16.8    -      -       +      -
    116B  VAL*     3.5    29.2    -      -       +      -
    117B  TYR*     3.9    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ASN*     5.4     0.6    +      -       -      -
    114A  ARG*     4.0    17.7    +      -       -      +
     64B  ASN*     2.8    48.6    +      -       -      +
     65B  ASP*     4.3     2.9    -      -       -      +
     67B  ILE*     1.3    78.7    -      -       -      +
     69B  ASN*     1.3    70.4    +      -       -      +
     71B  LYS*     3.3    21.8    +      -       -      +
     72B  ARG      4.7     0.7    +      -       -      -
    110B  ILE*     3.9    11.5    -      -       -      +
    111B  TRP*     4.2     3.4    -      -       -      +
    114B  ARG*     2.7    46.5    +      -       -      +
    116B  VAL*     3.8    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ARG*     5.6     1.6    +      -       -      -
    110A  ILE*     3.8    14.7    -      -       +      +
    114A  ARG*     2.7    34.5    +      -       -      +
    208A  UNX      3.4    23.0    -      -       -      -
     24B  GLN*     5.9     0.4    -      -       -      +
     27B  SER*     4.7     0.2    +      -       -      -
     31B  ILE*     3.7    17.8    -      -       +      +
     65B  ASP*     3.1    40.4    +      -       -      +
     68B  GLN*     1.3    80.7    -      -       -      +
     70B  SER*     1.3    62.3    +      -       -      +
     71B  LYS      3.4     0.2    -      -       -      -
     72B  ARG*     3.4    23.2    +      -       -      +
     73B  LYS*     4.5     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  ILE*     3.8    11.4    -      -       -      +
     66B  VAL      2.8    18.3    +      -       -      -
     67B  ILE*     2.8    16.5    +      -       -      -
     69B  ASN*     1.3    76.4    -      -       -      +
     71B  LYS*     1.3    56.5    +      -       -      +
     72B  ARG      3.2     1.1    -      -       -      -
     73B  LYS*     2.8    28.5    +      -       -      +
     74B  GLY      3.0    15.9    +      -       -      +
     77B  PHE*     3.6    26.3    -      -       -      +
     78B  THR*     4.5     5.0    +      -       -      -
    207B  UNX      3.5    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  ILE*     3.4     7.2    -      -       -      +
     68B  GLN*     3.3    19.1    -      -       -      +
     69B  ASN      3.4     0.8    -      -       -      -
     70B  SER*     1.3    78.2    +      -       -      +
     72B  ARG*     1.3    59.4    +      -       -      +
     73B  LYS      3.0     6.1    +      -       -      -
     74B  GLY*     3.3    17.1    +      -       -      +
     75B  PRO*     6.3     0.2    -      -       +      -
     78B  THR*     3.2    34.4    +      -       -      +
    115B  SER      4.2     5.0    +      -       -      -
    116B  VAL*     2.6    55.0    +      -       +      +
----------------------------------------------------------
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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