Contacts of the strand formed by residues 70 - 76 (chain m) 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 ILE 70 (chain m).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65m  HIS*     3.8     1.4    -      -       -      -
     66m  VAL*     3.0    25.8    +      -       +      -
     67m  ASP      2.8    32.5    +      -       -      +
     68m  ASN      3.6     0.2    -      -       -      -
     69m  HIS*     1.3   113.4    -      -       +      +
     71m  GLY*     1.3    68.2    -      -       -      +
     88m  MET*     4.7     0.9    -      -       +      -
     92m  CYS*     4.7     2.7    -      -       -      -
    103m  LEU      3.9     6.7    -      -       -      +
    105m  VAL*     3.9    28.7    -      -       +      -
    108m  LEU*     3.6    31.2    -      -       +      -
    134m  ILE*     4.2    13.0    -      -       +      -
    135m  ALA      3.6     3.1    -      -       -      +
    136m  GLY*     4.5     1.1    -      -       -      -
    221m  PHE*     4.2     4.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 71 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46m  LEU*     3.9     6.9    -      -       -      +
     64m  LEU      3.4     7.4    -      -       -      -
     66m  VAL      4.4     0.9    -      -       -      -
     70m  ILE*     1.3    74.3    -      -       -      +
     72m  ILE*     1.3    67.5    +      -       -      +
    134m  ILE*     3.7     1.6    -      -       -      +
    135m  ALA      2.9    33.8    +      -       -      -
    221m  PHE*     3.3    27.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46m  LEU*     3.6     4.6    -      -       -      +
     63m  ILE*     3.3     7.4    -      -       -      +
     64m  LEU*     2.8    68.3    +      -       +      +
     66m  VAL*     4.1     7.0    -      -       +      -
     70m  ILE*     4.8     0.2    -      -       +      -
     71m  GLY*     1.3    79.1    -      -       -      +
     73m  SER*     1.3    60.8    -      -       -      +
     74m  ILE*     4.2     2.0    -      -       +      -
     81m  ALA      5.0     1.6    -      -       -      +
     85m  CYS*     4.1    12.6    -      -       +      -
     88m  MET*     3.4    44.4    -      -       +      -
    132m  LEU*     4.2    21.5    -      -       +      -
    133m  LEU      3.2     7.0    -      -       -      +
    134m  ILE*     4.1    16.2    -      -       +      -
    221m  PHE*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 73 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35m  THR*     2.6    35.4    +      -       -      -
     46m  LEU*     3.9    18.2    -      -       -      -
     48m  ALA*     3.9     8.0    -      -       -      +
     62m  LYS      3.2    12.9    +      -       -      -
     63m  ILE*     4.3     1.7    -      -       -      +
     72m  ILE*     1.3    75.9    -      -       -      +
     74m  ILE*     1.3    64.0    +      -       -      +
    131m  GLY      3.8     0.2    -      -       -      +
    132m  LEU*     3.5     6.1    -      -       -      -
    133m  LEU*     2.8    37.7    +      -       -      +
    161m  ILE*     4.6     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 74 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439M  ALA*     5.3     3.8    -      -       +      -
     35m  THR*     4.3     5.6    -      -       -      +
     61m  LYS      4.2    15.0    -      -       -      +
     62m  LYS*     3.1    41.4    +      -       +      +
     64m  LEU*     3.7    26.9    -      -       +      -
     72m  ILE*     4.2     4.3    -      -       +      -
     73m  SER*     1.3    79.3    -      -       -      +
     75m  ALA*     1.3    64.8    +      -       -      +
     76m  GLY      5.3     1.3    -      -       -      +
     78m  THR*     4.3    23.1    -      -       +      -
     81m  ALA*     3.7    31.4    -      -       +      -
    130m  VAL*     4.5     0.9    -      -       +      -
    131m  GLY      3.7     3.1    -      -       -      -
    132m  LEU*     3.7    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 75 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439M  ALA*     4.3     5.8    -      -       -      -
     29m  VAL*     3.6    29.3    -      -       +      +
     32m  GLY*     4.7     1.1    -      -       -      -
     33m  SER      4.6    11.0    -      -       -      +
     35m  THR*     4.7     0.7    -      -       +      -
     74m  ILE*     1.3    77.7    -      -       -      +
     76m  GLY*     1.3    58.6    +      -       -      +
    130m  VAL*     3.6     2.4    -      -       -      +
    131m  GLY      2.9    31.6    +      -       -      -
    161m  ILE*     3.7    30.1    -      -       +      -
    162m  GLY      4.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain m). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438M  TYR*     3.8     7.8    -      -       -      -
    439M  ALA*     2.9    35.5    +      -       -      +
     28m  ALA      3.6    19.3    -      -       -      -
     32m  GLY*     4.3     1.6    -      -       -      -
     74m  ILE*     5.3     1.9    -      -       -      +
     75m  ALA*     1.3    74.7    -      -       -      +
     77m  LEU*     1.3    67.1    +      -       -      -
     78m  THR*     3.2     2.1    +      -       -      +
    129m  GLY      3.6     7.6    -      -       -      -
    130m  VAL*     4.3     2.2    -      -       -      +
----------------------------------------------------------
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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