Contacts of the strand formed by residues 43 - 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 VAL 43 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ILE      3.4    17.3    -      -       -      +
     38D  LEU*     4.0    19.5    -      -       +      -
     39D  ALA*     4.3     0.9    -      -       -      +
     42D  GLY*     1.3    78.1    -      -       -      +
     44D  LEU*     1.3    69.1    +      -       -      +
    137D  ILE*     3.6    33.6    -      -       +      +
    138D  GLY      4.9     1.3    -      -       -      +
    145D  PHE*     3.8    15.5    -      -       +      -
    146D  GLN      4.8     4.7    -      -       -      +
    147D  LEU*     4.7     8.7    -      -       +      -
    186D  LEU*     4.4     5.9    -      -       -      +
    215D  THR*     3.5     1.6    -      -       -      -
    216D  LEU*     2.8    50.4    +      -       +      +
----------------------------------------------------------
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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  LEU*     5.4     1.8    -      -       +      -
     36D  GLY*     3.1     5.4    -      -       -      -
     37D  ILE*     3.0    66.4    +      -       +      +
     43D  VAL*     1.3    82.6    -      -       -      +
     45D  LEU*     1.3    75.0    +      -       -      +
     46D  ALA*     4.2     1.8    -      -       +      +
    137D  ILE*     4.9     1.6    -      -       -      -
    186D  LEU*     4.7     3.8    -      -       +      -
    189D  ALA*     3.7    22.0    -      -       +      +
    190D  LEU*     4.1    14.4    -      -       +      -
    193D  ALA*     3.9    24.9    -      -       +      -
    213D  ILE*     4.1    10.8    -      -       +      -
    214D  ALA      3.2    13.9    -      -       -      +
    215D  THR*     3.8    13.0    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     34D  CYS*     4.9     0.4    -      -       -      -
     35D  LEU      3.4    11.0    -      -       -      +
     36D  GLY*     4.2     6.1    -      -       -      -
     44D  LEU*     1.3    74.1    -      -       -      +
     46D  ALA*     1.3    63.1    +      -       -      +
     65D  ILE*     4.0    21.1    -      -       +      -
     74D  CYS*     4.0     7.2    -      -       -      +
     75D  SER*     3.7    33.2    -      -       -      +
    135D  LEU*     3.7    31.9    -      -       +      +
    137D  ILE*     3.6    46.8    -      -       +      +
    147D  LEU*     4.7     0.7    -      -       +      -
    212D  GLU      4.5     0.2    -      -       -      -
    213D  ILE*     3.4     2.4    -      -       -      +
    214D  ALA*     2.8    36.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 46 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  CYS*     3.6     0.8    -      -       -      -
     35D  LEU*     2.9    44.0    +      -       +      +
     44D  LEU*     4.2    10.1    -      -       +      -
     45D  LEU*     1.3    77.5    -      -       -      +
     47D  ALA*     1.3    61.0    +      -       -      +
    193D  ALA*     4.3     4.5    -      -       +      -
    197D  LEU*     3.5    24.7    -      -       +      +
    212D  GLU      3.2     8.5    -      -       -      +
    213D  ILE*     4.2    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  THR      3.3    10.1    -      -       -      +
     34D  CYS*     3.9    18.6    -      -       +      -
     46D  ALA*     1.3    76.5    -      -       -      +
     48D  GLU*     1.3    67.7    +      -       -      +
     49D  ARG*     3.6     0.4    +      -       +      -
     64D  LYS*     4.3    21.1    -      -       +      +
     65D  ILE*     5.0     5.2    -      -       +      -
     75D  SER*     4.4     2.0    -      -       -      +
    197D  LEU*     4.4     5.3    -      -       -      +
    211D  VAL*     3.5     3.7    -      -       -      -
    212D  GLU*     2.9    40.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  GLY*     4.0     1.7    -      -       -      -
     33D  THR*     2.7    48.9    +      -       -      +
     47D  ALA*     1.3    70.9    -      -       -      +
     49D  ARG*     1.3    70.0    +      -       -      +
     50D  ARG*     2.5    41.9    +      -       -      +
     64D  LYS*     3.3    28.2    +      -       -      +
    166D  ASN*     4.8     4.0    +      -       -      +
    197D  LEU*     4.7     8.3    -      -       +      +
    201D  MET*     5.4    14.0    -      -       +      -
    210D  LYS      3.7     8.7    -      -       -      +
    211D  VAL*     4.9     1.8    -      -       -      +
----------------------------------------------------------
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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