Contacts of the strand formed by residues 79 - 85 (chain X) in PDB entry 1SHT


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 79 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43X  PHE      3.0     7.4    +      -       -      +
     44X  ASP*     2.9    40.6    +      -       -      +
     45X  LEU*     2.9    24.8    +      -       -      +
     74X  VAL*     4.2     5.9    -      -       -      +
     77X  GLU      5.2     2.7    -      -       -      +
     78X  MET*     1.3    78.4    -      -       -      +
     80X  LEU*     1.3    63.6    +      -       -      +
     95X  LEU*     3.6    29.8    +      -       +      +
     96X  THR*     3.3    12.6    -      -       -      +
     97X  GLY*     3.6    19.3    -      -       -      +
    102X  ILE*     6.0     0.2    -      -       -      -
    134X  ALA*     4.4    12.3    +      -       -      +
    139X  THR*     5.3     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45X  LEU*     3.1    15.7    -      -       +      +
     47X  PHE*     4.1    13.9    -      -       +      -
     70X  ALA*     3.6    30.5    -      -       +      -
     74X  VAL*     4.2    13.7    -      -       +      -
     79X  ARG*     1.3    76.4    -      -       -      +
     81X  SER*     1.3    63.5    +      -       -      +
     82X  PHE*     3.6    25.8    -      -       +      -
     93X  LEU*     3.5    26.0    -      -       +      +
     94X  PRO      3.7     2.6    -      -       -      +
     95X  LEU*     3.3     5.2    -      -       -      -
     96X  THR*     2.9    31.1    +      -       -      +
    102X  ILE*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 81 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45X  LEU      2.9     5.4    +      -       -      +
     46X  TYR*     3.8    24.6    -      -       -      -
     47X  PHE*     2.9    27.6    +      -       -      -
     80X  LEU*     1.3    75.8    -      -       -      +
     82X  PHE*     1.3    71.7    +      -       -      +
     83X  ILE*     4.2     2.2    -      -       -      +
     91X  ILE*     4.2     0.5    -      -       -      +
     93X  LEU      2.8    20.8    +      -       -      -
     95X  LEU*     3.6    13.5    -      -       -      -
    130X  GLN*     3.0    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47X  PHE*     3.7    20.6    -      +       +      -
     49X  LEU*     5.0     1.3    -      -       +      -
     66X  VAL*     3.5    21.5    -      -       +      -
     70X  ALA*     5.1     1.1    -      -       +      -
     80X  LEU*     3.6    27.8    -      -       +      -
     81X  SER*     1.3    79.2    -      -       -      +
     83X  ILE*     1.3    58.2    +      -       -      +
     91X  ILE*     3.7     2.6    -      -       -      -
     92X  ILE*     2.9    36.7    +      -       +      -
     93X  LEU*     3.0    39.9    +      -       +      +
    102X  ILE*     4.0     5.6    -      -       +      -
    105X  GLY*     3.7    34.5    -      -       -      -
    106X  LEU*     3.7    27.6    -      -       +      -
    109X  LEU*     3.9    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46X  TYR*     4.7     4.5    -      -       +      -
     47X  PHE      2.9    14.3    +      -       -      +
     48X  VAL*     4.2    11.7    -      -       +      -
     49X  LEU*     2.8    35.0    +      -       -      +
     81X  SER*     4.2     2.9    -      -       -      +
     82X  PHE*     1.3    78.1    -      -       -      +
     84X  VAL*     1.3    69.1    +      -       -      +
     90X  THR      3.3     9.9    -      -       -      +
     91X  ILE*     4.2    16.4    -      -       +      -
    123X  GLY*     3.9    26.7    -      -       -      +
    126X  LEU*     3.9    10.5    -      -       +      -
    127X  ALA*     3.5    41.5    -      -       +      +
    130X  GLN*     3.8    15.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49X  LEU*     3.2    16.4    -      -       +      +
     51X  LYS*     3.7    25.8    -      -       +      +
     59X  TRP*     4.3     9.2    -      -       +      -
     83X  ILE*     1.3    81.7    -      -       -      +
     85X  PHE*     1.3    62.4    +      -       -      +
     88X  GLN      4.1     0.6    -      -       -      +
     89X  ALA*     3.2     3.8    -      -       -      +
     90X  THR*     2.9    46.1    +      -       -      +
     92X  ILE*     3.9    30.3    -      -       +      +
    109X  LEU*     3.9    19.3    -      -       +      -
    112X  VAL*     4.5     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 85 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48X  VAL*     3.8    25.6    -      -       +      -
     49X  LEU      2.9    15.5    +      -       -      -
     50X  ASP*     3.5    37.7    -      -       +      -
     51X  LYS*     2.9    28.6    +      -       -      -
     52X  SER      3.8     0.7    +      -       -      -
     84X  VAL*     1.3    77.4    -      -       -      +
     86X  SER*     1.3    61.9    +      -       -      +
     88X  GLN      3.4     5.8    -      -       -      +
     89X  ALA*     4.0    16.2    -      -       +      -
    118X  THR*     3.8    18.6    -      -       +      -
    119X  TYR      3.6    16.4    -      -       -      +
    120X  ILE*     3.4    57.9    -      -       +      -
    123X  GLY*     4.2     3.6    -      -       -      -
    146X  LEU      4.8     0.7    -      -       -      -
    147X  THR*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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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