Contacts of the strand formed by residues 110 - 112 (chain E) in PDB entry 4PEI


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 MET 110 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  TYR*     3.6    37.5    -      -       +      -
     23E  TYR*     3.4    25.8    -      -       +      +
     46E  MET*     6.0     0.2    -      -       -      -
     48E  THR*     5.9     0.2    -      -       -      -
     70E  PHE*     3.9    10.3    -      -       -      -
     73E  TYR*     3.8    32.8    -      -       +      -
     80E  ALA*     3.9     5.2    -      -       +      -
     84E  THR*     3.4     7.6    -      -       -      +
     86E  PHE*     3.8    10.3    -      -       +      -
    105E  PHE*     3.3     6.1    -      -       -      -
    106E  VAL*     3.0    40.2    +      -       +      +
    107E  CYS*     3.0    24.5    +      -       -      +
    108E  PHE      4.0     1.8    -      -       -      +
    109E  ASN*     1.3    82.6    -      -       -      +
    111E  TYR*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83E  LEU*     4.8     0.2    -      -       +      -
     84E  THR      2.7    10.3    +      -       -      -
     85E  LEU*     3.4    25.4    -      -       +      -
     86E  PHE*     2.9    29.7    +      -       -      -
    102E  ASN      4.5     1.9    +      -       -      -
    103E  GLY*     3.9    12.9    -      -       -      -
    104E  GLY*     3.4    30.1    -      -       -      -
    105E  PHE*     3.8    20.9    -      +       +      -
    109E  ASN      4.0     0.4    -      -       -      -
    110E  MET*     1.3    71.5    -      -       -      +
    112E  TYR*     1.3    75.9    +      -       -      +
    113E  LEU*     4.0    13.7    -      -       +      -
    117E  SER*     5.2     1.7    +      -       -      -
    119E  ILE*     4.0    23.2    -      -       +      +
    269E  LEU*     4.1     7.4    -      -       +      -
    271E  TYR*     3.9    13.3    -      +       -      -
    326E  ILE*     3.4    39.9    -      -       +      +
    340E  ARG*     5.5     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86E  PHE*     3.4    40.2    -      +       +      -
     87E  ILE*     4.0     1.1    -      -       -      -
     88E  GLY*     3.5    13.9    -      -       -      -
     97E  LEU*     3.6    41.6    +      -       +      +
    100E  LEU*     3.4    31.0    -      -       +      -
    103E  GLY*     3.0     5.2    -      -       -      -
    104E  GLY      2.8    42.9    +      -       -      +
    106E  VAL*     4.8     4.3    -      -       +      -
    111E  TYR*     1.3    80.4    -      -       -      +
    113E  LEU*     1.3    64.5    +      -       -      +
    114E  GLY*     3.1    42.4    +      -       -      -
    115E  VAL*     3.7     4.9    +      -       -      +
    130E  SER*     3.5    20.9    +      -       -      -
----------------------------------------------------------
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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