Contacts of the strand formed by residues 884 - 888 (chain A) in PDB entry 3H0G


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 VAL 884 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  ASN*     3.2    31.7    -      -       +      +
    637A  HIS*     3.9     4.6    +      -       -      -
    641A  LYS*     4.2     2.4    -      -       -      +
    877A  ASP*     5.8     3.1    -      -       -      +
    879A  LEU*     5.0     9.4    -      -       +      -
    880A  ASP      3.9     9.0    -      -       -      +
    881A  ALA*     3.4    19.5    +      -       -      +
    882A  THR      3.5     2.4    +      -       -      -
    883A  LEU*     1.3    84.9    -      -       -      +
    885A  GLU*     1.3    70.8    +      -       -      +
    958A  PRO*     3.8    28.0    -      -       +      +
    959A  LEU      3.1    18.2    -      -       -      +
    960A  PRO*     4.1    16.8    -      -       +      -
   1059A  ALA*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 885 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  ASN*     5.0     0.9    -      -       -      +
    524A  LYS*     5.5     1.1    -      -       -      +
    637A  HIS*     3.6    23.3    -      -       +      +
    641A  LYS*     2.9    45.5    -      -       -      +
    884A  VAL*     1.3    86.5    -      -       -      +
    886A  TYR*     1.3    75.5    +      -       +      +
    887A  GLN*     3.1     8.0    +      -       -      +
    959A  LEU      3.1    19.9    +      -       -      +
    961A  VAL      5.2     0.2    -      -       -      +
    962A  ASN*     2.9    43.0    +      -       +      +
    965A  ARG*     3.0    18.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 886 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  ASN*     4.8     5.2    -      -       -      +
    524A  LYS*     4.2    19.6    -      -       -      +
    632A  GLN*     3.0    38.3    +      -       +      +
    633A  GLY*     4.6     9.4    +      -       -      -
    884A  VAL      4.3     0.4    -      -       -      -
    885A  GLU*     1.3    81.9    -      -       +      +
    887A  GLN*     1.3    59.5    +      -       -      +
    956A  ARG*     3.4    49.3    +      -       +      -
    957A  TRP      3.4    12.6    -      -       -      +
    958A  PRO*     3.4    19.7    -      -       +      +
    962A  ASN*     5.5     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 887 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    885A  GLU      3.7     6.4    -      -       -      +
    886A  TYR*     1.3    75.8    -      -       -      +
    888A  VAL*     1.3    87.4    +      -       -      +
    889A  PHE*     5.0     2.9    -      -       +      -
    955A  ALA      3.9     0.3    -      -       -      +
    956A  ARG*     3.3     9.8    -      -       -      +
    957A  TRP      2.5    35.9    +      -       -      +
    959A  LEU*     4.3    13.6    -      -       +      +
    961A  VAL      4.4     1.4    -      -       -      +
    962A  ASN*     3.1    25.9    +      -       -      +
    963A  VAL      3.5    11.9    +      -       -      -
    964A  GLN*     3.2    39.1    +      -       -      +
   1024A  LEU*     3.7    26.8    -      -       +      +
   1028A  LYS*     4.5     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 888 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    887A  GLN*     1.3   103.7    +      -       -      +
    889A  PHE*     1.3    71.6    +      -       -      +
    890A  ASP*     3.5    19.7    +      -       -      +
    955A  ALA*     4.2    16.4    -      -       +      -
    956A  ARG*     4.6    12.6    -      -       +      -
    964A  GLN*     4.1    15.9    -      -       +      +
   1024A  LEU*     4.1     7.1    -      -       -      +
   1028A  LYS*     4.2     4.1    -      -       +      -
----------------------------------------------------------
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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