Contacts of the strand formed by residues 42 - 49 (chain F) in PDB entry 8GCH


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 CYS 42 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     5.2     1.6    -      -       -      -
     32F  SER*     3.6     0.2    -      -       -      -
     33F  LEU*     2.8    43.0    +      -       +      -
     40F  HIS*     3.3    16.1    +      -       -      -
     41F  PHE*     1.3    97.2    -      -       +      +
     43F  GLY*     1.3    56.8    +      -       -      +
     57F  HIS*     5.0     1.3    -      -       -      -
     58F  CYS*     2.0    53.8    -      -       -      -
    193G  GLY      3.9     5.4    -      -       -      -
    195G  SER*     3.4    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 43 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  GLN*     3.7    10.5    -      -       -      -
     31F  VAL      3.4    11.4    -      -       -      -
     33F  LEU*     3.5     5.6    -      -       -      +
     40F  HIS*     4.6     4.3    -      -       -      -
     42F  CYS*     1.3    74.3    -      -       -      +
     44F  GLY*     1.3    58.3    +      -       -      -
     54F  THR*     2.9    22.2    +      -       -      -
    140F  GLY*     6.3     0.9    -      -       -      -
    193G  GLY      4.0     3.8    +      -       -      -
    194G  ASP*     4.2     2.2    +      -       -      -
    195G  SER      2.7    12.3    +      -       -      -
    196G  GLY*     3.2    10.9    -      -       -      -
    197G  GLY*     3.8     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 44 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  GLN*     3.5     9.8    +      -       -      +
     31F  VAL*     2.9    43.1    +      -       -      +
     33F  LEU*     4.7     0.9    -      -       -      -
     43F  GLY*     1.3    74.3    -      -       -      -
     45F  SER*     1.3    64.5    +      -       -      -
     52F  VAL*     4.1     4.3    -      -       -      -
     53F  VAL      3.3    13.7    -      -       -      -
     54F  THR*     4.4     1.1    -      -       -      -
    196G  GLY      3.5     4.9    +      -       -      -
    197G  GLY*     3.9     1.2    -      -       -      -
    198G  PRO*     4.2     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 45 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  TRP*     3.1     9.9    -      -       -      -
     44F  GLY*     1.3    76.6    +      -       -      -
     46F  LEU*     1.3    65.0    +      -       -      +
     47F  ILE*     3.6     1.4    +      -       -      +
     52F  VAL*     3.4     4.9    -      -       -      +
     53F  VAL*     2.8    39.2    +      -       -      +
    121F  VAL*     4.1    20.9    -      -       -      -
    196G  GLY      5.4     0.2    -      -       -      -
    197G  GLY      4.4     1.2    -      -       -      -
    198G  PRO*     3.1    34.4    -      -       -      +
    209G  LEU*     3.9    12.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28F  PRO      4.2     4.0    -      -       -      +
     29F  TRP*     2.8    12.1    +      -       -      +
     31F  VAL*     3.7    24.2    -      -       +      +
     45F  SER*     1.3    73.1    -      -       -      +
     47F  ILE*     1.3    58.9    +      -       -      +
     48F  ASN      3.4    20.9    -      -       -      +
     51F  TRP      3.7     3.4    -      -       -      +
     52F  VAL*     3.4    21.5    -      -       +      -
     66F  VAL*     5.5     0.9    -      -       +      -
     68F  ALA*     4.4     4.0    -      -       +      -
     83F  LEU*     5.6     0.4    -      -       +      -
    108F  LEU*     4.4    14.4    -      -       +      -
    112F  ALA*     4.5     7.6    -      -       +      -
    114F  PHE*     3.9     9.4    -      -       +      -
    118F  VAL*     3.5    32.1    -      -       +      -
    119F  SER      3.8    15.3    -      -       -      +
    120F  ALA*     3.3     2.8    -      -       -      -
    121F  VAL*     2.9    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  CYS*     5.6     0.9    -      -       -      +
     45F  SER      4.0     4.0    -      -       -      +
     46F  LEU*     1.3    75.1    -      -       -      +
     48F  ASN*     1.3    69.3    +      -       -      +
     51F  TRP*     3.1    23.6    +      -       +      +
     53F  VAL*     3.6    34.8    -      -       +      -
    105F  LEU*     4.1     7.0    -      -       +      -
    120F  ALA*     3.4    15.4    -      -       -      +
    121F  VAL*     4.1    22.1    -      -       +      +
    123F  LEU*     4.0    24.5    -      -       +      -
    209G  LEU*     5.1     1.1    -      -       +      -
    238G  VAL*     3.8    15.9    -      -       +      -
    242G  LEU*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 48 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46F  LEU*     3.4    22.5    -      -       -      +
     47F  ILE*     1.3    84.8    +      -       -      +
     49F  GLU*     1.3    61.8    +      -       -      +
     50F  ASN*     3.0    29.2    +      -       -      +
     51F  TRP*     3.1    25.7    +      -       -      +
    114F  PHE*     3.5    14.9    -      -       -      -
    120F  ALA*     3.7     2.4    -      -       -      +
    242G  LEU*     3.3    32.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 49 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48F  ASN*     1.3    75.4    -      -       -      +
     50F  ASN*     1.3    65.1    +      -       -      +
     51F  TRP      3.8     0.2    -      -       -      -
    108F  LEU*     3.6     5.0    -      -       -      +
    111F  ALA*     3.3    12.1    -      -       +      -
    112F  ALA*     2.8    51.7    +      -       -      +
    114F  PHE*     3.6    38.0    -      -       +      +
----------------------------------------------------------
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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