Contacts of the strand formed by residues 154 - 158 (chain U) in PDB entry 5GJQ


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 154 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448P  LYS*     1.9    55.0    +      -       -      +
    452P  ILE*     5.1     0.5    -      -       -      +
    106U  ILE*     4.6     9.3    -      -       -      +
    140U  SER*     3.0     4.3    -      -       -      -
    141U  VAL*     2.8    37.3    +      -       +      +
    142U  GLU      5.6     2.9    -      -       -      -
    152U  SER*     5.0     3.6    -      -       -      -
    153U  LYS*     1.3    75.8    -      -       -      +
    155U  PHE*     1.3    71.8    +      -       -      +
    156U  GLU*     3.7     2.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 155 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444P  HIS*     2.6    39.9    +      -       +      +
    448P  LYS*     3.8     9.8    -      -       +      +
    101U  LEU*     4.0    32.3    -      -       +      -
    102U  HIS      5.8     0.9    -      -       -      -
    105U  ASP*     3.7    17.0    -      -       +      -
    106U  ILE*     3.0    41.0    -      -       +      +
    109U  ASN*     3.1    31.6    -      -       -      -
    121U  LEU*     4.2    11.0    -      -       +      -
    138U  TYR*     4.1    13.0    -      +       +      -
    139U  ILE      2.8    20.4    -      -       -      +
    140U  SER*     3.7    15.9    -      -       -      -
    154U  THR*     1.3    83.8    +      -       -      +
    156U  GLU*     1.3    57.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 156 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441P  LYS*     5.2    11.2    -      -       -      +
    444P  HIS*     3.7     1.6    -      -       -      -
    138U  TYR*     3.2     5.7    -      -       -      -
    139U  ILE*     2.9    33.8    +      -       +      +
    140U  SER*     4.7     0.4    -      -       -      +
    141U  VAL*     4.8    18.8    -      -       +      -
    154U  THR*     3.7     7.2    +      -       +      +
    155U  PHE*     1.3    71.4    -      -       -      +
    157U  HIS*     1.3    80.8    +      -       +      +
    158U  VAL*     4.2     7.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 157 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440P  ASN*     3.3    34.3    +      -       -      -
    441P  LYS*     3.3    51.7    +      -       +      -
    443P  THR*     4.2     2.5    -      -       -      -
    444P  HIS*     3.1    41.1    -      -       +      +
    136U  GLU*     5.5     2.7    -      -       +      -
    138U  TYR*     3.3    17.5    -      -       +      -
    156U  GLU*     1.3    86.5    -      -       -      +
    158U  VAL*     1.3    64.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 158 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6U  VAL*     5.4     5.8    -      -       +      +
      7U  GLN      2.9    29.6    -      -       -      +
      9U  VAL*     3.3    20.2    -      -       +      -
    136U  GLU*     4.7     6.8    -      -       -      +
    137U  ALA*     2.9    34.8    +      -       +      +
    138U  TYR*     4.8     0.4    -      -       -      -
    139U  ILE*     4.7    19.7    -      -       +      +
    156U  GLU*     4.2    14.1    -      -       +      +
    157U  HIS*     1.3    83.8    -      -       -      +
    159U  THR*     1.3    78.5    +      -       -      +
    160U  SER*     3.9     0.9    +      -       -      -
----------------------------------------------------------
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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