Contacts of the strand formed by residues 128 - 132 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73L  GLU*     2.8    24.1    +      -       +      -
     81L  ASN*     3.4    29.5    -      -       -      +
    108L  GLU*     4.7     2.8    +      -       +      -
    109L  VAL      3.7     4.9    +      -       -      -
    110L  LYS*     3.7    27.1    +      -       -      -
    126L  ASP      3.4     3.2    +      -       -      +
    127L  LEU*     1.3    85.6    -      -       +      +
    129L  ILE*     1.3    67.6    +      -       -      +
    130L  ALA*     3.3    32.6    -      -       -      -
    131L  THR*     3.3    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 129 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73L  GLU*     4.4     2.1    -      -       -      -
     78L  ILE*     3.8    29.6    -      -       +      +
     81L  ASN*     2.8    30.1    +      -       +      +
     82L  LEU*     4.5    12.8    -      -       +      -
     85L  LEU*     5.9     1.1    -      -       +      -
    101L  LEU*     5.7     1.8    -      -       +      -
    109L  VAL*     2.9    24.1    +      -       +      +
    110L  LYS      3.4    21.3    -      -       -      +
    111L  ALA*     3.4    11.9    -      -       +      +
    114L  PHE*     4.3    17.5    -      -       +      -
    127L  LEU*     3.2    24.0    -      -       +      +
    128L  HIS*     1.3    79.4    +      -       -      +
    130L  ALA*     1.3    67.0    +      -       +      +
    138L  LEU*     4.9     7.2    -      -       +      -
    140L  MET*     5.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 130 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71L  VAL*     4.0    15.5    -      -       +      -
     73L  GLU*     3.4    12.8    -      -       -      +
     78L  ILE*     4.1    14.4    -      -       +      -
    109L  VAL*     2.9    32.1    +      -       -      +
    128L  HIS*     3.3    11.0    -      -       -      -
    129L  ILE*     1.3    91.1    -      -       +      +
    131L  THR*     1.3    59.7    +      -       -      +
    132L  LEU*     4.4     1.6    -      -       +      -
    138L  LEU*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 131 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71L  VAL*     3.4     6.1    -      -       -      +
     72L  LYS*     3.2    52.9    +      -       -      +
     73L  GLU*     2.8    21.2    +      -       -      +
    107L  LYS      3.9     3.1    -      -       -      -
    108L  GLU*     3.8    25.6    -      -       +      +
    128L  HIS*     3.3    21.3    -      -       +      +
    130L  ALA*     1.3    72.1    -      -       -      +
    132L  LEU*     1.3    62.9    +      -       -      +
    133L  GLU*     4.1     2.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70L  GLY      3.7     2.2    -      -       -      +
     71L  VAL*     3.8    19.1    -      -       +      -
    103L  ALA*     3.6    14.4    -      -       +      +
    104L  GLU*     3.8     5.6    -      -       -      +
    105L  GLY      3.1    12.4    -      -       -      +
    106L  PRO*     3.2     2.9    -      -       -      +
    107L  LYS*     2.9    37.1    +      -       +      +
    109L  VAL*     4.1    14.8    -      -       +      -
    130L  ALA*     4.2     6.1    -      -       +      +
    131L  THR*     1.3    79.3    -      -       -      +
    133L  GLU*     1.3    63.2    +      -       -      +
    136L  GLY      3.4    24.2    -      -       -      +
    137L  ARG      3.8     0.2    -      -       -      -
    138L  LEU*     3.5    49.6    -      -       +      +
----------------------------------------------------------
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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