Contacts of the strand formed by residues 37 - 42 (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 ALA 37 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35F  SER      4.6     2.2    -      -       -      +
     36F  THR*     1.3    76.4    +      -       -      +
     38F  ILE*     1.3    65.9    +      -       -      +
     49F  ALA      3.4    11.9    -      -       -      +
     50F  VAL*     3.7    15.5    -      -       +      +
     77F  ALA*     4.7     8.3    -      -       +      -
     78F  MET      4.8     2.5    -      -       -      +
    142F  LEU*     4.2     7.2    -      -       +      -
    168F  ARG      3.8     0.3    -      -       -      +
    169F  ALA*     3.1     8.7    -      -       -      +
    170F  ILE*     2.6    54.4    +      -       +      +
    202F  LEU*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 38 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36F  THR*     5.0     1.6    -      -       -      +
     37F  ALA*     1.3    80.0    -      -       -      +
     39F  GLY*     1.3    62.2    +      -       -      +
     40F  ILE*     4.1    12.6    -      -       +      -
     47F  CYS      3.8     0.5    -      -       -      +
     48F  LEU*     3.5     3.1    -      -       -      +
     49F  ALA*     2.8    43.6    +      -       +      +
    142F  LEU*     4.1     4.3    -      -       -      -
    168F  ARG      3.5     2.7    -      -       -      -
    169F  ALA*     4.2    13.9    -      -       +      -
    177F  ALA*     4.5     7.0    -      -       +      -
    181F  LEU*     4.1    17.5    -      -       +      -
    198F  SER*     3.5    39.1    +      -       -      +
    201F  ILE*     3.8    35.4    -      -       +      -
    202F  LEU*     4.3    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 39 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38F  ILE*     1.3    76.7    -      -       -      +
     40F  ILE*     1.3    65.0    +      -       -      +
     47F  CYS      3.2     8.7    -      -       -      -
     48F  LEU*     4.1    12.6    -      -       -      -
    142F  LEU*     3.9     4.5    -      -       -      +
    153F  LEU*     3.6    12.7    -      -       -      +
    167F  ALA*     3.1     4.9    -      -       -      +
    168F  ARG      2.9    34.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 40 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38F  ILE*     4.1     4.7    -      -       +      -
     39F  GLY*     1.3    79.9    -      -       -      +
     41F  GLN*     1.3    66.3    +      -       -      +
     42F  THR*     3.7    10.3    +      -       -      +
     45F  GLY      3.9     0.7    -      -       -      +
     46F  VAL*     3.3     9.3    -      -       -      +
     47F  CYS*     2.9    41.7    +      -       -      -
    153F  LEU*     4.1     0.6    -      -       -      +
    166F  ASP      3.7     2.7    -      -       -      +
    167F  ALA*     4.4     2.2    -      -       +      -
    181F  LEU*     4.0    22.0    -      -       +      -
    185F  TYR*     4.0    19.3    -      -       +      -
    189F  MET*     5.0     4.3    -      -       +      -
    194F  ALA*     3.3    34.9    -      -       +      +
    197F  SER*     4.4     8.7    -      -       -      -
    198F  SER*     3.2    26.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 41 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  ILE*     1.3    70.0    -      -       -      +
     42F  THR*     1.3    73.6    +      -       -      +
     46F  VAL*     4.2     7.0    -      -       +      -
    151F  PRO*     3.5    31.4    +      -       +      +
    152F  GLN*     4.2     1.1    -      -       -      -
    153F  LEU*     3.3    21.4    +      -       +      +
    164F  GLN*     3.7    19.2    +      -       -      +
    165F  CYS      3.0    21.4    -      -       -      +
    166F  ASP*     2.7    33.5    +      -       -      +
    185F  TYR*     3.2    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 42 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  ILE*     3.7    14.4    +      -       -      +
     41F  GLN*     1.3    88.5    +      -       -      +
     43F  SER*     1.3    59.2    +      -       -      +
     44F  GLU*     3.0    20.9    -      -       +      +
     45F  GLY      2.7    38.9    +      -       -      +
    151F  PRO*     3.2    13.0    -      -       -      +
    185F  TYR*     4.9     0.3    -      -       -      -
    189F  MET*     3.2    36.3    -      -       +      +
    190F  THR      4.0     7.0    +      -       -      -
    191F  LEU*     4.1     5.4    -      -       -      +
    194F  ALA*     4.1     7.4    -      -       -      +
----------------------------------------------------------
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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