Contacts of the strand formed by residues 888 - 891 (chain C) in PDB entry 3N1Q


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 TRP 888 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834C  TYR*     5.0     0.2    -      -       -      -
    844C  MET*     2.9    45.0    -      -       +      +
    845C  LEU      3.3    19.1    -      -       -      -
    846C  LYS*     3.7    17.3    -      -       +      -
    847C  TRP*     3.4     7.8    -      -       -      -
    882C  VAL*     5.6     0.7    -      -       -      +
    886C  LYS*     4.0    11.1    -      -       -      +
    887C  GLN*     1.3    81.1    -      -       -      +
    889C  HIS*     1.3    77.9    +      -       -      +
    890C  MET*     3.6    25.6    -      -       +      -
    834D  TYR*     3.3    25.3    +      +       +      -
    836D  GLU*     3.0    58.6    +      -       +      +
    837D  ALA      3.8    12.1    -      -       -      -
    838D  VAL*     3.8    18.4    -      -       +      -
    844D  MET*     4.4     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 889 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    844C  MET*     3.4     4.2    -      -       -      -
    845C  LEU*     3.1    43.3    +      -       +      +
    847C  TRP*     3.7    14.6    -      -       +      -
    864C  ILE*     4.6    11.2    -      -       +      -
    880C  ASP*     3.3    25.9    +      -       +      +
    881C  VAL      5.5     0.9    -      -       -      -
    882C  VAL*     3.3    30.2    -      -       +      +
    888C  TRP*     1.3    89.1    +      -       -      +
    890C  MET*     1.3    92.0    +      -       -      +
    891C  ILE*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 890 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    838C  VAL*     3.7    14.1    -      -       +      -
    842C  GLN*     3.5    39.9    -      -       +      +
    843C  ILE      3.7     7.0    -      -       -      +
    844C  MET*     3.8    20.9    -      -       +      +
    888C  TRP*     3.6    17.3    -      -       +      -
    889C  HIS*     1.3    94.6    +      -       -      +
    891C  ILE*     1.3    64.0    +      -       -      +
    892C  GLY*     3.8     1.9    +      -       -      +
    838D  VAL*     3.7    38.1    -      -       +      +
    844D  MET*     4.2     8.3    -      -       +      -
    890D  MET*     4.2     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 891 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    841C  THR      3.8     0.6    -      -       -      +
    842C  GLN*     3.1     8.3    -      -       -      +
    843C  ILE*     2.9    38.4    +      -       +      +
    845C  LEU*     4.1     7.4    -      -       +      -
    864C  ILE*     3.8    23.3    -      -       +      -
    866C  TYR*     3.9    45.8    -      -       +      -
    880C  ASP*     4.3     5.2    -      -       -      +
    889C  HIS*     3.8    19.1    -      -       +      +
    890C  MET*     1.3    74.5    -      -       -      +
    892C  GLY*     1.3    63.1    +      -       -      +
    894C  LEU*     3.9    21.0    -      -       +      +
    902C  ILE*     4.2    24.5    -      -       +      -
----------------------------------------------------------
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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