Contacts of the strand formed by residues 107 - 110 (chain A) in PDB entry 5D4D


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 LYS 107 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ALA*     3.9    13.0    -      -       +      +
    104A  GLU      3.6    22.0    -      -       -      +
    105A  GLY      2.9     7.9    +      -       -      +
    106A  PRO*     1.3    75.5    -      -       -      +
    108A  GLU*     1.3    71.2    +      -       -      +
    109A  VAL*     3.8    22.7    -      -       +      -
    113A  ASP*     2.9    34.7    +      -       -      +
    131A  THR*     3.8     1.4    -      -       -      +
    132A  LEU*     2.9    32.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  LYS*     1.3    84.2    -      -       -      +
    109A  VAL*     1.3    64.0    +      -       -      +
    110A  LYS*     3.2    38.2    +      -       -      +
    113A  ASP*     4.3     1.9    -      -       -      +
    128A  HIS*     4.2     8.7    +      -       +      -
    130A  ALA      3.6     4.9    -      -       -      -
    131A  THR*     4.1    20.2    -      -       +      +
    644C  VAL*     5.5     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  LEU*     3.6    38.4    -      -       +      -
    103A  ALA*     3.7    23.8    -      -       +      -
    107A  LYS*     3.8    13.7    -      -       +      -
    108A  GLU*     1.3    68.9    -      -       -      +
    110A  LYS*     1.3    60.6    +      -       -      +
    113A  ASP*     3.6    11.0    -      -       +      +
    128A  HIS*     4.4     0.2    +      -       -      -
    129A  ILE*     2.8    37.3    +      -       +      +
    130A  ALA*     2.9    21.7    +      -       +      +
    132A  LEU*     3.7    25.6    -      -       +      -
    138A  LEU*     4.8     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  LEU*     4.4     1.6    -      -       -      +
    108A  GLU*     3.5    35.4    +      -       -      +
    109A  VAL*     1.3    84.4    -      -       -      +
    111A  ALA*     1.3    66.8    +      -       -      +
    112A  ARG*     3.1    23.6    -      -       +      +
    113A  ASP*     2.9    22.3    +      -       -      +
    125A  PRO      3.6    13.7    -      -       -      +
    126A  ASP*     4.2    12.5    +      -       -      +
    127A  LEU      3.3     7.2    -      -       -      +
    128A  HIS*     3.5    40.9    +      -       -      +
    129A  ILE*     4.2     5.9    -      -       -      +
----------------------------------------------------------
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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