Contacts of the strand formed by residues 2116 - 2121 (chain A) in PDB entry 5W0P


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 THR2116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2045A  VAL*     3.6    35.0    -      -       +      -
   2046A  VAL      3.6    10.5    -      -       -      +
   2047A  LEU*     3.5    11.0    -      -       -      +
   2108A  LEU      4.7     2.2    -      -       -      +
   2109A  LEU*     3.7    25.9    -      -       +      +
   2112A  LEU*     3.2    35.3    -      -       +      +
   2113A  GLY      3.3    11.1    +      -       -      -
   2114A  ASP      3.2     7.7    -      -       -      +
   2115A  ASN*     1.3    78.9    -      -       -      +
   2117A  TYR*     1.3    71.0    +      -       -      +
   2118A  PRO*     4.5     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR2117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2045A  VAL*     3.5     4.6    -      -       -      -
   2046A  VAL*     2.8    36.2    +      -       -      +
   2048A  VAL*     4.3    13.5    -      -       +      -
   2091A  VAL*     3.6    32.8    -      -       +      +
   2092A  TYR*     3.5    34.3    -      +       +      -
   2094A  PRO*     3.7    30.5    -      -       +      +
   2114A  ASP      4.9     3.6    +      -       -      -
   2115A  ASN*     3.0    42.9    +      -       +      -
   2116A  THR*     1.3    75.4    -      -       -      +
   2118A  PRO*     1.3    73.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO2118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2044A  GLY      3.9     6.7    -      -       -      +
   2045A  VAL*     4.0     6.2    -      -       +      -
   2089A  VAL*     5.9     0.7    -      -       -      +
   2091A  VAL*     4.7     6.9    -      -       -      +
   2098A  MET*     4.4    16.3    -      -       +      +
   2101A  LEU*     3.8    21.8    -      -       +      -
   2105A  GLN*     3.6    26.0    -      -       +      +
   2109A  LEU*     4.7    14.4    -      -       +      -
   2116A  THR      4.5     2.0    -      -       -      +
   2117A  TYR*     1.3    94.7    -      -       +      +
   2119A  PHE*     1.3    64.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE2119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2025A  ILE*     4.3     8.3    -      -       +      -
   2026A  TYR      4.1     1.1    -      -       -      -
   2027A  LEU*     3.7    23.3    -      -       +      -
   2042A  VAL*     4.0    13.8    -      -       +      +
   2043A  ASP*     4.3     0.5    -      -       -      -
   2044A  GLY*     3.3    35.6    +      -       -      +
   2045A  VAL*     3.3    20.2    -      -       -      -
   2046A  VAL*     3.7    17.9    -      -       +      -
   2060A  VAL*     3.7    42.8    -      -       +      -
   2089A  VAL*     5.1     7.6    -      -       +      -
   2091A  VAL*     4.7     4.9    -      -       +      -
   2098A  MET*     4.2     7.4    -      -       -      -
   2105A  GLN*     2.8    17.9    +      -       -      -
   2117A  TYR      4.5     0.2    -      -       -      -
   2118A  PRO*     1.3    77.2    -      -       -      +
   2120A  LEU*     1.3    63.6    +      -       -      +
   2121A  LEU*     3.7    22.4    -      -       +      -
   2150A  VAL*     4.6     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU2120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2041A  PRO*     4.0    28.7    -      -       +      -
   2042A  VAL      3.5    18.2    -      -       -      +
   2043A  ASP*     4.2    12.8    -      -       +      -
   2089A  VAL*     4.0    13.0    -      -       -      +
   2098A  MET*     3.9    25.1    -      -       +      +
   2100A  VAL      5.8     2.9    -      -       -      +
   2102A  THR*     5.1    12.3    -      -       +      -
   2105A  GLN*     4.9     2.9    -      -       -      +
   2119A  PHE*     1.3    78.2    -      -       -      +
   2121A  LEU*     1.3    70.2    +      -       -      +
   2122A  THR*     4.1    14.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU2121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2041A  PRO*     3.4     3.1    -      -       -      +
   2042A  VAL*     2.9    46.4    +      -       +      +
   2060A  VAL*     4.0    20.0    -      -       +      +
   2061A  THR      3.5    26.7    -      -       -      +
   2062A  LEU*     3.9    25.1    -      -       +      +
   2087A  SER*     4.7     9.9    -      -       -      +
   2088A  ARG      5.0     0.4    -      -       -      -
   2089A  VAL*     3.7    22.9    -      -       +      +
   2119A  PHE*     3.7    28.5    -      -       +      -
   2120A  LEU*     1.3    81.4    -      -       -      +
   2122A  THR*     1.3    64.2    +      -       -      +
   2123A  PHE*     4.1     1.6    -      -       -      -
   2150A  VAL*     4.2     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page


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