Contacts of the strand formed by residues 42 - 48 (chain d) 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 42 (chain d).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36d  PHE      3.9     0.7    -      -       -      +
     38d  MET*     3.2    41.9    +      -       +      -
     39d  SER*     3.7    29.3    +      -       -      +
     40d  GLU      3.7     1.6    -      -       -      -
     41d  LYS*     1.4    87.1    -      -       +      +
     43d  LEU*     1.3    68.8    +      -       -      +
     64d  VAL*     5.4     1.1    -      -       +      -
     75d  LEU*     3.6    27.4    -      -       +      +
     77d  PRO*     3.9    27.4    -      -       +      -
     80d  ALA*     4.0    12.3    -      -       +      -
    104d  LEU*     3.6    18.4    -      -       +      -
    105d  ALA      3.4     9.6    -      -       -      +
    183d  ILE*     4.4     0.2    -      -       -      -
    188d  ILE*     3.9     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15d  VAL*     3.8    26.0    -      -       +      -
     35d  MET*     4.0     7.6    -      -       +      -
     36d  PHE      3.5    28.5    -      -       -      +
     37d  LYS*     4.0    13.7    -      -       -      +
     42d  ILE*     1.3    75.4    -      -       -      +
     44d  LEU*     1.3    59.0    -      -       -      +
     45d  LEU*     4.1    12.0    -      -       +      +
    103d  LEU      3.8     0.5    -      -       -      +
    104d  LEU*     3.4     7.8    -      -       -      +
    105d  ALA*     2.8    34.8    +      -       +      +
    181d  ARG*     3.8    22.7    -      -       +      -
    183d  ILE*     3.7    17.7    -      -       +      +
    188d  ILE*     3.7    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35d  MET*     3.5     0.2    -      -       -      -
     36d  PHE*     2.9    50.6    +      -       +      +
     38d  MET*     3.7    32.3    -      -       +      -
     42d  ILE      4.3     0.2    -      -       -      -
     43d  LEU*     1.3    72.7    -      -       -      +
     45d  LEU*     1.3    64.0    +      -       -      +
     46d  CYS*     3.7     5.8    +      -       +      -
     56d  PHE*     5.3     2.7    -      -       +      -
     57d  ALA*     4.2    24.5    -      -       +      +
     60d  ILE*     4.3    12.3    -      -       +      -
     84d  THR*     5.4     0.9    -      -       +      -
    102d  LEU*     3.7    30.1    -      -       +      -
    103d  LEU      3.5    15.5    -      -       -      +
    104d  LEU*     4.0    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 45 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4d  LEU*     3.5    35.9    -      -       +      +
     15d  VAL*     4.1    24.7    -      -       +      -
     16d  ALA      4.3     6.5    -      -       -      +
     17d  SER*     3.9     9.2    -      -       -      -
     34d  LYS      3.6     4.5    -      -       -      -
     35d  MET*     3.4    40.8    -      -       +      +
     43d  LEU*     4.1    16.4    -      -       +      +
     44d  LEU*     1.3    74.8    -      -       -      +
     46d  CYS*     1.3    59.4    +      -       -      +
    102d  LEU*     3.1     8.5    -      -       -      +
    103d  LEU*     2.8    51.5    +      -       +      +
    105d  ALA*     5.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 46 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2d  GLU*     5.0     0.2    -      -       -      +
     34d  LYS*     3.2    23.3    +      -       -      +
     36d  PHE*     4.7     6.1    -      -       +      -
     44d  LEU*     3.7     6.2    +      -       +      +
     45d  LEU*     1.3    75.3    -      -       -      +
     47d  VAL*     1.3    73.2    +      -       -      +
     53d  THR*     3.7    29.2    -      -       -      +
     56d  PHE*     4.6    10.1    -      -       -      -
     57d  ALA*     4.5    13.5    -      -       +      -
    100d  VAL*     3.6    33.9    -      -       -      -
    101d  ASN      3.8     3.8    -      -       -      -
    102d  LEU*     4.4     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 47 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1d  MET*     5.5     3.1    -      -       -      -
      2d  GLU*     3.4    44.9    -      -       +      +
      4d  LEU*     3.7    33.2    -      -       +      -
     34d  LYS*     3.8     9.9    -      -       +      -
     46d  CYS*     1.3    84.6    -      -       -      +
     48d  GLY*     1.3    63.8    +      -       -      +
     53d  THR*     3.3     8.5    -      -       -      -
    100d  VAL*     3.4     5.4    -      -       -      -
    101d  ASN*     2.8    47.9    +      -       +      +
    132d  HIS*     4.9     7.4    -      -       +      -
    133d  GLY*     5.4     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 48 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2d  GLU*     3.1    26.5    +      -       -      +
     47d  VAL*     1.3    78.0    -      -       -      +
     49d  GLU*     1.3    66.3    +      -       -      +
     50d  ALA      3.8     0.3    +      -       -      -
     53d  THR*     3.3     4.2    -      -       -      +
     99d  HIS*     3.7     6.5    -      -       -      -
    100d  VAL*     4.8     0.2    -      -       -      -
    101d  ASN*     4.9     3.8    -      -       -      -
----------------------------------------------------------
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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