Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 2HW6


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 119 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  GLU*     3.0    41.2    +      -       -      -
     83A  GLN*     6.0     0.4    -      -       -      +
    118A  THR*     3.7    18.4    +      -       -      -
    119A  ARG*     3.6    42.3    -      -       -      +
     44B  PHE*     5.5     1.8    -      -       -      -
     50B  LEU*     5.8     0.2    -      -       -      +
     62B  LYS*     4.5     3.4    -      -       -      +
     79B  ILE*     3.3    31.1    -      -       +      +
     80B  ILE      3.2    15.7    -      -       -      +
     81B  GLU*     4.3     5.6    -      -       -      -
     82B  LYS*     3.5     5.2    -      -       -      +
    115B  GLU*     3.4     5.4    -      -       -      +
    116B  ASP*     2.9    34.7    +      -       -      +
    118B  THR*     1.3    88.8    +      -       -      +
    120B  PHE*     1.3    64.7    +      -       -      +
    121B  TYR*     2.6    32.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  LYS      3.6     0.6    -      -       -      +
     79B  ILE*     3.2     8.3    -      -       -      +
     80B  ILE*     2.9    40.8    +      -       +      +
     82B  LYS*     3.6    26.2    -      -       +      -
     87B  SER*     3.5    34.3    -      -       -      -
     88B  ARG*     3.8    24.7    -      -       +      -
     91B  VAL*     3.8    24.5    -      -       +      -
     92B  PHE*     5.6     2.2    -      -       +      -
    113B  PHE*     3.5    29.8    -      +       +      -
    114B  PHE      3.6     1.8    -      -       -      -
    115B  GLU*     3.1    31.4    -      -       +      -
    119B  ARG*     1.3    74.1    -      -       -      +
    121B  TYR*     1.3    63.9    +      -       -      +
    122B  LEU*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     4.3     2.1    +      -       -      -
     44B  PHE*     3.6    49.8    -      +       +      +
     77B  VAL*     4.4     3.1    -      -       +      -
     78B  LYS      3.6     2.9    -      -       -      -
     79B  ILE*     3.5    35.9    -      -       +      -
    112B  GLU      3.8     0.2    -      -       -      +
    113B  PHE*     3.5     5.9    -      -       -      -
    114B  PHE*     2.6    70.3    +      +       +      +
    116B  ASP*     2.8    39.3    +      -       -      -
    119B  ARG*     2.6    42.4    +      -       +      -
    120B  PHE*     1.3    72.3    -      -       -      +
    122B  LEU*     1.3    64.1    +      -       -      +
    123B  VAL*     3.7     3.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77B  VAL*     3.2     3.1    -      -       -      +
     78B  LYS*     2.7    45.8    +      -       +      +
     80B  ILE*     3.8    29.2    -      -       +      -
     91B  VAL*     4.1     7.6    -      -       +      -
     94B  GLU*     5.0    10.3    -      -       -      +
     95B  VAL*     4.1    15.0    -      -       +      -
     98B  LEU*     4.3    12.1    -      -       +      -
    110B  LEU*     3.8    13.5    -      -       +      -
    112B  GLU      3.9     0.4    -      -       -      -
    113B  PHE*     3.6    27.8    -      -       +      -
    120B  PHE*     4.2     3.6    -      -       +      -
    121B  TYR*     1.3    71.2    -      -       -      +
    123B  VAL*     1.3    63.2    +      -       -      +
    124B  PHE*     3.4    33.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  PHE*     5.0     4.5    -      -       +      -
     48B  TYR*     3.6    44.4    -      -       +      +
     75B  TYR*     3.7    34.8    -      -       +      -
     76B  ALA      4.1     1.8    -      -       -      -
     77B  VAL*     4.1    16.8    -      -       +      +
    110B  LEU*     3.5     3.9    -      -       -      +
    111B  ILE*     2.7    36.5    +      -       +      -
    112B  GLU*     2.8    29.3    +      -       +      +
    113B  PHE      6.0     0.2    -      -       -      -
    114B  PHE*     5.8     2.7    -      -       +      +
    121B  TYR*     4.7     5.6    -      -       +      +
    122B  LEU*     1.3    70.5    -      -       -      +
    124B  PHE*     1.3    53.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  VAL*     6.2     0.2    -      -       +      -
     75B  TYR*     3.2     9.2    -      -       -      +
     76B  ALA*     2.8    42.2    +      -       +      +
     78B  LYS*     4.1    16.8    -      -       +      -
     94B  GLU*     5.7     1.3    -      -       -      -
     98B  LEU*     4.0    16.6    -      -       +      -
    108B  LEU*     3.7    33.9    -      -       +      -
    109B  GLU      3.2    25.8    -      -       -      +
    110B  LEU*     3.6    18.6    -      -       +      -
    111B  ILE*     4.0     3.4    -      -       -      -
    122B  LEU*     3.4    50.7    -      -       +      -
    123B  VAL*     1.3    73.2    -      -       -      +
    125B  GLU*     1.3    67.0    +      -       -      +
    190B  CYS*     6.2     0.4    -      -       +      -
    191B  ASP      5.2     9.6    -      -       -      -
    192B  PHE*     4.4    16.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  TYR*     4.5     5.6    -      -       -      -
     76B  ALA*     4.0     5.2    -      -       -      +
    108B  LEU*     3.6    22.1    -      -       +      +
    109B  GLU*     3.0    42.7    +      -       -      +
    111B  ILE*     3.4    19.1    -      -       +      +
    124B  PHE*     1.3    77.1    -      -       -      +
    126B  LYS*     1.3    62.5    +      -       -      +
    127B  LEU*     3.8    11.8    +      -       +      +
    188B  LYS*     2.7    39.0    +      -       -      +
----------------------------------------------------------
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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