Contacts of the strand formed by residues 50 - 55 (chain H) in PDB entry 1W4R


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 50 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  VAL*     3.8    31.2    -      -       +      -
     43H  PHE*     4.2     2.0    -      -       -      -
     44H  GLN*     3.8    30.0    -      -       +      +
     48H  TYR      3.6    17.2    +      -       -      +
     49H  LYS*     1.3    77.1    -      -       -      +
     51H  LEU*     1.3    61.9    +      -       -      +
     52H  VAL*     5.7     1.1    -      -       +      -
     74H  GLU*     3.4    27.7    -      -       -      +
     91H  VAL*     4.0     8.1    -      -       -      +
     93H  VAL*     3.2    19.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  VAL*     5.5     0.2    -      -       -      +
     50H  CYS*     1.3    76.4    -      -       -      +
     52H  VAL*     1.3    77.5    +      -       -      +
     53H  ILE*     4.0    20.4    -      -       +      -
     74H  GLU*     3.7    22.4    -      -       -      +
     76H  LEU*     4.1    22.2    -      -       +      -
     84H  VAL*     4.6     2.5    -      -       +      +
     87H  GLU*     4.3    11.2    -      -       +      +
     88H  ALA*     3.8    36.3    -      -       +      +
     91H  VAL*     3.8    17.7    -      -       +      -
     93H  VAL      2.9     6.1    +      -       -      +
     94H  ILE*     3.3     5.0    -      -       +      +
     95H  GLY      2.8    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  LEU*     4.5     9.6    -      -       +      -
     37H  MET*     3.8    38.1    -      -       +      -
     40H  VAL*     4.4    18.8    -      -       +      -
     50H  CYS*     5.7     0.9    -      -       +      -
     51H  LEU*     1.3    82.1    -      -       -      +
     53H  ILE*     1.3    71.0    +      -       -      +
     54H  LYS*     5.6     2.5    -      -       +      -
     74H  GLU*     2.9    20.2    +      -       -      +
     75H  ALA*     3.4    12.9    -      -       +      -
     76H  LEU      2.9    24.8    +      -       -      -
     95H  GLY*     3.2    12.1    -      -       -      +
     97H  ASP*     5.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51H  LEU*     4.0    17.3    -      -       +      -
     52H  VAL*     1.3    80.0    -      -       -      +
     54H  LYS*     1.3    64.8    +      -       -      +
     76H  LEU*     3.3    14.1    -      -       +      +
     78H  ALA*     4.1    11.7    -      -       +      -
     81H  LEU*     3.9    23.8    -      -       +      -
     84H  VAL*     3.6    26.0    -      -       +      -
     94H  ILE*     3.9    24.7    -      -       +      -
     95H  GLY      2.8    10.6    +      -       -      +
     96H  ILE*     3.4     5.9    -      -       +      +
     97H  ASP*     2.8    28.5    +      -       -      +
    102H  PHE*     3.9    14.4    -      -       +      -
    108H  PHE*     4.2    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52H  VAL*     4.3     2.9    -      -       +      -
     53H  ILE*     1.3    74.8    -      -       -      +
     55H  TYR*     1.3    80.8    +      -       -      +
     56H  ALA*     4.1    11.9    +      -       -      +
     58H  ASP      3.5    16.0    +      -       -      -
     59H  THR*     5.2     3.2    -      -       -      +
     75H  ALA*     4.6    12.1    -      -       +      +
     76H  LEU      3.0    14.0    +      -       -      +
     77H  PRO*     3.2    20.8    -      -       +      +
     78H  ALA      2.9    25.8    +      -       -      +
     97H  ASP*     3.9    20.2    -      -       +      +
    102H  PHE*     4.0     5.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 55 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54H  LYS*     1.3    82.9    +      -       -      +
     56H  ALA*     1.3    63.6    +      -       -      +
     57H  LYS*     3.3    40.5    +      -       +      +
     58H  ASP*     3.3    23.9    +      -       +      +
     78H  ALA      3.4    14.4    -      -       -      -
     79H  CYS*     4.5    11.9    -      -       -      -
     97H  ASP      3.7     5.9    +      -       -      -
     98H  GLU*     4.1    25.6    -      -       +      +
    101H  PHE*     3.4    54.6    +      +       +      -
    102H  PHE*     3.7    14.5    -      +       +      -
    173H  GLU*     2.5    36.1    +      -       -      -
    175H  ILE*     4.5     2.5    -      -       +      -
----------------------------------------------------------
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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