Contacts of the strand formed by residues 128 - 132 (chain A) in PDB entry 5D4E


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 HIS 128 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLU*     3.2    24.9    +      -       -      -
     81A  ASN*     3.6    22.6    -      -       -      +
    108A  GLU*     4.3     8.9    -      -       +      +
    109A  VAL      3.8     6.7    +      -       -      -
    110A  LYS*     3.6    26.3    +      -       -      +
    126A  ASP      3.3     3.8    +      -       -      +
    127A  LEU*     1.3    90.5    -      -       -      +
    129A  ILE*     1.3    65.6    +      -       -      +
    130A  ALA      3.3    25.4    +      -       -      -
    131A  THR*     3.2    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLU*     4.1     5.0    -      -       -      +
     78A  ILE*     4.3    19.6    -      -       +      +
     81A  ASN*     3.0    27.9    +      -       +      +
     82A  LEU*     4.1    16.6    -      -       +      -
     85A  LEU*     5.9     1.3    -      -       +      -
    101A  LEU*     4.1     6.5    -      -       +      -
    109A  VAL*     3.1    16.1    +      -       +      +
    110A  LYS      3.9    15.9    -      -       -      +
    111A  ALA*     4.3     3.6    -      -       +      -
    114A  PHE*     3.5    35.4    -      -       +      -
    127A  LEU*     4.0    11.9    -      -       +      +
    128A  HIS*     1.3    83.7    +      -       -      +
    130A  ALA*     1.3    70.3    +      -       +      +
    138A  LEU*     5.0     2.0    -      -       +      -
    140A  MET*     4.2    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  VAL*     4.1    11.7    -      -       +      -
     73A  GLU*     3.3    12.1    -      -       -      +
     78A  ILE*     4.1    10.8    -      -       +      -
    109A  VAL*     2.9    30.9    +      -       +      +
    128A  HIS*     3.3     6.6    -      -       -      -
    129A  ILE*     1.3    82.2    -      -       +      +
    131A  THR*     1.3    60.9    +      -       -      +
    132A  LEU*     3.8    18.4    +      -       +      -
    138A  LEU*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLY      4.9     0.2    -      -       -      -
     71A  VAL*     3.8     1.2    -      -       -      -
     72A  LYS*     3.2    39.0    +      -       +      +
     73A  GLU*     2.7    18.3    +      -       -      -
    107A  LYS      4.0     2.7    -      -       -      -
    108A  GLU*     3.9    19.5    -      -       +      +
    128A  HIS*     3.2    21.8    +      -       -      -
    130A  ALA*     1.3    69.8    -      -       -      +
    132A  LEU*     1.3    71.0    +      -       -      +
    133A  GLU*     4.0     0.9    +      -       -      +
    606C  VAL      5.7     0.2    -      -       -      +
    644C  VAL*     4.6    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLY      3.5     3.8    -      -       -      +
     71A  VAL*     3.9    23.8    -      -       +      -
    103A  ALA*     3.8    13.7    -      -       +      +
    104A  GLU*     3.9     6.1    -      -       -      +
    105A  GLY      3.5    12.6    -      -       -      +
    106A  PRO*     3.3     2.9    -      -       -      +
    107A  LYS*     2.9    37.4    +      -       +      +
    109A  VAL*     4.0    15.5    -      -       +      -
    130A  ALA*     4.0    14.1    -      -       +      -
    131A  THR*     1.3    83.1    -      -       -      +
    133A  GLU*     1.3    61.3    +      -       -      +
    136A  GLY      3.7    16.8    -      -       -      +
    137A  ARG      3.8     2.0    -      -       -      -
    138A  LEU*     3.5    41.1    -      -       +      +
----------------------------------------------------------
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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