Contacts of the strand formed by residues 117 - 124 (chain B) in PDB entry 4HXG


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 117 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  LEU*     4.0    22.2    -      -       +      +
    111B  TRP*     3.5     9.2    -      -       -      -
    112B  ASN*     3.1    42.8    +      -       +      +
    114B  ASP*     2.6    37.2    +      -       -      +
    116B  ARG*     1.3    75.0    -      -       +      +
    118B  LEU*     1.3    60.7    +      -       -      +
    156B  VAL*     4.1    14.7    -      -       +      +
    157B  ILE      3.0     8.1    -      -       -      +
    158B  ASP*     4.7     0.4    -      -       -      -
    165B  ILE*     3.8    31.0    -      -       +      -
    178B  TRP*     4.3    13.8    -      -       +      -
    181B  ASP*     3.0    39.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  ARG*     5.8     0.7    -      -       +      -
     74B  ALA*     4.3    14.8    -      -       +      -
     87B  ILE*     4.2    23.8    -      -       +      -
     89B  VAL*     5.0     0.7    -      -       +      -
    100B  VAL*     5.8     0.4    -      -       +      -
    109B  ILE*     4.9    12.8    -      -       +      -
    110B  GLU      3.5    22.4    -      -       -      +
    111B  TRP*     3.5    35.9    -      -       +      +
    117B  ARG*     1.3    73.9    -      -       -      +
    119B  LEU*     1.3    62.8    +      -       -      +
    120B  ALA      3.9     0.4    -      -       -      -
    155B  TRP      3.5     0.9    -      -       -      +
    156B  VAL*     3.3     5.9    -      -       -      +
    157B  ILE*     2.6    57.8    +      -       +      +
    159B  THR*     3.8    24.5    -      -       +      -
    178B  TRP*     4.1     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  SER*     3.8     2.3    +      -       -      +
    109B  ILE*     3.4     4.8    -      -       -      -
    110B  GLU*     2.9    35.1    +      -       +      +
    118B  LEU*     1.3    72.1    -      -       -      +
    120B  ALA*     1.3    66.9    +      -       -      +
    121B  VAL*     4.0     9.2    +      -       +      -
    154B  PHE*     4.3    13.2    -      -       +      -
    155B  TRP      3.3    16.8    -      -       -      +
    156B  VAL*     4.8     1.8    -      -       +      +
    176B  GLY*     4.0     8.5    -      -       -      +
    177B  ILE*     4.0    37.5    -      -       -      +
    178B  TRP*     3.2    27.3    -      -       +      +
    183B  ILE*     3.9    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  ILE*     5.0     0.2    -      -       +      -
    106B  ILE*     3.7    22.9    -      -       +      -
    108B  SER      3.3     8.5    -      -       -      +
    109B  ILE*     4.3     7.6    -      -       +      -
    118B  LEU      3.9     0.4    +      -       -      -
    119B  LEU*     1.3    74.4    -      -       -      +
    121B  VAL*     1.3    62.7    +      -       -      +
    154B  PHE*     3.5     2.4    -      -       -      -
    155B  TRP*     2.7    50.0    +      -       +      +
    157B  ILE*     3.8    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  ILE*     3.8     2.6    -      -       -      -
    107B  ARG*     3.0    24.6    +      -       +      -
    108B  SER*     3.2    33.1    +      -       -      +
    119B  LEU*     4.4     9.0    -      -       +      -
    120B  ALA*     1.3    76.4    -      -       -      +
    122B  GLY*     1.3    62.6    +      -       -      +
    152B  THR*     3.8    24.2    -      -       +      -
    153B  THR      3.5     4.9    -      -       -      +
    154B  PHE*     3.6    26.9    -      -       +      -
    155B  TRP*     4.5     2.0    -      -       -      -
    174B  SER      4.5     5.8    -      -       -      +
    175B  SER*     4.9     3.6    -      -       -      -
    176B  GLY      4.1    16.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ASN      3.0    17.0    -      -       -      -
    107B  ARG*     4.1     9.7    +      -       -      -
    121B  VAL*     1.3    77.4    -      -       -      +
    123B  PHE*     1.3    60.2    +      -       -      +
    152B  THR*     3.4    11.6    -      -       -      +
    153B  THR*     2.7    39.1    +      -       -      +
    155B  TRP*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ASN*     3.0    73.7    +      -       +      +
    107B  ARG*     3.1    43.7    -      -       +      +
    122B  GLY*     1.3    75.9    -      -       -      +
    124B  LYS*     1.3    64.1    +      -       -      +
    125B  ARG*     3.6    46.0    -      -       +      -
    127B  GLU*     5.3     1.8    -      -       -      -
    150B  GLU*     3.5    22.7    -      -       +      +
    151B  LYS      3.2     9.0    -      -       -      +
    152B  THR*     4.9     0.4    -      -       -      -
    153B  THR*     3.3     7.0    +      -       -      -
    155B  TRP*     4.6     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ASN*     4.9     2.9    -      -       -      +
    123B  PHE*     1.3    76.1    -      -       -      +
    125B  ARG*     1.3    68.9    +      -       -      +
    149B  GLY      4.0     1.7    -      -       -      +
    150B  GLU*     3.3     3.1    -      -       -      -
    151B  LYS*     2.9    41.7    +      -       +      +
    153B  THR*     4.0    18.1    -      -       +      +
    155B  TRP*     6.1     0.4    -      -       +      -
    169B  GLU*     4.6    12.8    -      -       -      +
----------------------------------------------------------
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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