Contacts of the strand formed by residues 150 - 156 (chain F) 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 GLY 150 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146F  VAL*     3.5     3.7    -      -       -      -
    147F  ASP*     2.9    40.9    +      -       -      +
    148F  GLU      3.1     2.4    +      -       -      -
    149F  LYS*     1.3    80.2    -      -       -      +
    151F  PRO*     1.3    75.7    -      -       -      +
    152F  GLN*     3.5     3.6    +      -       -      +
    222F  PRO*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 151 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41F  GLN*     3.5    20.5    +      -       +      -
     42F  THR      3.2    30.1    -      -       -      +
     43F  SER*     4.1    15.9    -      -       -      +
     45F  GLY*     4.0    13.5    -      -       -      +
     46F  VAL*     3.8    15.3    -      -       +      -
    145F  GLY      3.4     8.1    -      -       -      +
    146F  VAL*     4.4     6.5    -      -       +      -
    149F  LYS      4.6     2.9    -      -       -      +
    150F  GLY*     1.3    82.5    -      -       -      +
    152F  GLN*     1.3    64.6    -      -       -      +
    222F  PRO*     4.5    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 152 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41F  GLN*     3.8     5.4    -      -       -      -
     46F  VAL*     3.6     7.1    -      -       -      +
    108F  THR*     5.5     0.2    -      -       -      -
    109F  VAL*     3.9    13.7    -      -       +      +
    110F  GLU*     4.1     8.9    +      -       -      +
    143F  PHE      4.0     0.3    -      -       -      +
    144F  GLY*     3.7     0.3    -      -       -      -
    145F  GLY      2.9    34.6    +      -       -      +
    147F  ASP*     3.1    27.7    -      -       -      +
    149F  LYS*     3.8    37.0    +      -       -      +
    150F  GLY      3.5     9.6    +      -       -      +
    151F  PRO*     1.3    79.2    -      -       -      +
    153F  LEU*     1.3    61.8    +      -       -      +
    154F  PHE*     3.7    24.3    -      -       +      -
    164F  GLN*     4.1    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 153 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39F  GLY*     3.6    30.7    -      -       -      +
     40F  ILE      4.1     1.1    -      -       -      +
     41F  GLN*     3.3    16.2    +      -       +      +
     46F  VAL*     4.1    18.6    -      -       +      -
     48F  LEU*     4.2    15.3    -      -       +      -
    142F  LEU*     4.3     8.1    -      -       +      -
    143F  PHE      3.3    21.1    -      -       -      +
    152F  GLN*     1.3    76.3    -      -       -      +
    154F  PHE*     1.3    71.7    +      -       -      +
    164F  GLN*     3.4     7.4    -      -       -      +
    165F  CYS*     2.8    45.9    +      -       +      +
    166F  ASP      4.1    11.2    -      -       -      +
    167F  ALA*     4.3     1.8    -      -       -      -
    168F  ARG*     4.3    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 154 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  VAL*     3.8    16.6    -      -       +      -
    110F  GLU*     3.7    45.1    -      -       +      -
    113F  THR*     3.9    23.6    -      -       +      +
    142F  LEU*     3.3     9.7    -      -       -      +
    143F  PHE*     2.9    34.3    +      -       +      +
    152F  GLN*     3.7    31.4    -      -       +      -
    153F  LEU*     1.3    81.3    -      -       -      +
    155F  HIS*     1.3    60.8    +      -       -      +
    162F  PHE*     3.9    19.1    -      +       -      -
    163F  VAL*     3.3     7.6    -      -       -      -
    164F  GLN*     3.6    42.8    -      -       +      -
    165F  CYS*     5.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 155 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113F  THR*     5.5     0.2    -      -       -      -
    140F  ALA*     4.5     3.6    -      -       +      -
    141F  LEU      3.4     6.8    +      -       -      -
    142F  LEU*     3.8     9.6    -      -       +      +
    143F  PHE*     5.8     0.4    -      -       -      -
    154F  PHE*     1.3    75.4    -      -       -      +
    156F  MET*     1.3    82.0    +      -       -      +
    157F  ASP*     4.1    15.4    -      -       +      +
    161F  THR      5.1     2.5    -      -       -      -
    162F  PHE*     3.2     6.4    -      -       -      +
    163F  VAL*     2.8    42.2    +      -       +      +
    165F  CYS*     4.2     6.5    -      -       -      -
    168F  ARG*     3.3    42.1    +      -       +      +
    170F  ILE*     3.4    33.8    -      -       +      +
     53G  GLN*     5.8     2.6    +      -       -      -
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Residues in contact with MET 156 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88F  LEU*     4.5    10.1    -      -       +      -
    113F  THR*     4.4     2.0    -      -       +      +
    116F  VAL*     4.0    18.6    -      -       +      +
    117F  SER*     2.8    43.5    -      -       -      +
    120F  ALA*     6.3     2.0    -      -       -      -
    137F  PHE*     6.5     0.4    -      -       +      -
    139F  VAL*     5.4     3.8    -      -       +      +
    140F  ALA*     3.3     7.3    -      -       -      +
    141F  LEU*     2.9    63.1    +      -       +      +
    143F  PHE*     4.7     9.8    -      -       +      -
    155F  HIS*     1.3    79.4    -      -       -      +
    157F  ASP*     1.3    76.8    +      -       -      +
    158F  PRO*     5.9     0.7    -      -       +      -
    160F  GLY*     4.4     4.0    -      -       -      +
    161F  THR      3.9    10.8    -      -       -      +
    162F  PHE*     4.0     5.4    -      -       +      -
----------------------------------------------------------
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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