Contacts of the strand formed by residues 107 - 109 (chain A) in PDB entry 3V4R


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 THR 107 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  TYR*     3.4     5.4    -      -       -      -
    102A  VAL*     2.7    38.5    +      -       -      +
    105A  THR*     3.3    21.5    +      -       -      -
    106A  ASP*     1.3    75.4    -      -       -      +
    108A  PHE*     1.3    62.9    +      -       -      +
    109A  ILE*     4.1     6.3    +      -       +      +
    188B  PHE*     3.9    17.7    -      -       +      +
    194B  ARG*     4.4     0.7    -      -       -      +
    201B  GLU*     5.6     0.5    +      -       -      -
    203B  PHE*     3.5    34.3    -      -       +      -
    211B  CYS*     5.2     2.0    -      -       -      -
    229B  ALA*     4.0    25.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  GLU*     3.4    32.8    -      -       +      -
    100A  ALA      3.3    14.6    -      -       -      -
    101A  TYR*     4.3     1.6    -      -       +      -
    106A  ASP      4.1     0.6    +      -       -      +
    107A  THR*     1.3    71.7    -      -       -      +
    109A  ILE*     1.3    65.5    -      -       -      +
    110A  GLU*     3.7    19.9    +      -       +      -
    289A  ARG*     3.4    26.7    -      -       -      -
    361A  LEU*     4.1     3.4    -      -       +      -
    366A  PHE*     3.4    48.0    -      +       +      -
    187B  ASP*     5.4     3.1    -      -       +      -
    188B  PHE      3.0    17.0    +      -       -      +
    189B  GLN*     3.3    54.7    -      -       +      +
    190B  ARG      4.5     0.9    +      -       -      -
    203B  PHE*     4.1     6.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLN*     3.6    40.6    -      -       +      +
     98A  PRO      3.8     5.2    -      -       -      +
     99A  GLU*     3.3     2.4    -      -       -      -
    100A  ALA*     2.7    46.7    +      -       +      +
    102A  VAL*     3.6    30.5    -      -       +      -
    107A  THR*     4.2    10.8    -      -       +      +
    108A  PHE*     1.3    79.8    -      -       -      +
    110A  GLU*     1.3    64.2    +      -       -      +
    203B  PHE*     4.8     6.1    -      -       +      -
    209B  GLU*     4.3    15.3    -      -       +      +
    229B  ALA*     4.0    12.1    -      -       +      +
    230B  LEU*     3.8    20.2    -      -       +      -
----------------------------------------------------------
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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