Contacts of the strand formed by residues 144 - 150 (chain j) 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 144 (chain j).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139j  TRP*     3.2    22.0    -      -       -      -
    140j  ASP      3.0    34.9    +      -       -      -
    141j  LYS      4.7     0.4    -      -       -      -
    142j  HIS      3.6     1.2    -      -       -      -
    143j  TYR*     1.3    74.7    -      -       -      +
    145j  PHE*     1.3    65.4    +      -       -      -
    146j  GLN*     3.2     7.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 145 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38j  LEU*     3.7    28.5    -      -       +      +
     39j  ALA      4.9     2.2    -      -       -      +
     40j  ASN      4.1    14.6    -      -       -      -
     41j  ASP*     3.9     6.7    -      -       -      -
     42j  GLY*     3.6    28.5    -      -       -      +
     43j  VAL*     3.7    20.0    -      -       +      -
    138j  GLY      3.5     2.7    -      -       -      -
    139j  TRP*     3.9    18.4    -      +       +      -
    143j  TYR      3.4     5.9    +      -       -      +
    144j  GLY*     1.3    72.8    -      -       -      -
    146j  GLN*     1.3    66.6    +      -       -      +
    216j  LEU*     3.4    33.9    -      -       +      -
    217j  THR*     4.0     3.6    -      -       -      -
    218j  ARG*     3.9    28.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 146 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38j  LEU*     4.2     7.2    -      -       -      -
     43j  VAL*     4.3     2.6    -      -       -      +
    107j  CYS*     3.7     9.9    -      -       +      +
    108j  GLU*     4.8     1.2    -      -       -      +
    136j  TYR      3.7     0.6    -      -       -      +
    137j  ILE*     3.4     6.9    -      -       -      +
    138j  GLY      2.9    30.8    +      -       -      +
    140j  ASP*     2.5    37.9    +      -       -      +
    143j  TYR*     3.5    30.5    -      -       +      +
    144j  GLY      3.2    12.4    +      -       -      +
    145j  PHE*     1.3    82.1    -      -       -      +
    147j  LEU*     1.3    61.3    -      -       -      +
    148j  TYR*     2.4    45.6    +      -       +      +
     57k  ARG*     3.8     4.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 147 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36j  GLY*     3.3    37.7    -      -       -      +
     37j  ILE      4.2     2.2    -      -       -      +
     38j  LEU*     4.4     8.9    -      -       +      +
     43j  VAL*     4.3     9.0    -      -       +      -
     45j  LEU*     4.7     0.2    -      -       +      -
    135j  LEU*     4.6     9.4    -      -       +      -
    136j  TYR      3.2    17.5    -      -       -      +
    137j  ILE*     3.6    18.6    -      -       +      -
    146j  GLN*     1.3    76.6    -      -       -      +
    148j  TYR*     1.3    72.1    +      -       -      +
    158j  GLY*     3.5     4.3    -      -       -      -
    159j  TRP      3.0    35.3    +      -       -      +
    160j  LYS      4.2     3.1    -      -       -      +
    161j  ALA*     3.9    20.2    -      -       -      +
    162j  THR*     4.1    15.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 148 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107j  CYS*     4.0    20.2    -      -       +      -
    108j  GLU*     3.5    33.2    +      -       +      +
    111j  VAL*     4.2    14.4    -      -       +      -
    135j  LEU*     3.3     9.2    -      -       -      +
    136j  TYR*     2.9    47.5    +      -       +      +
    146j  GLN*     2.4    46.6    +      -       +      -
    147j  LEU*     1.3    78.0    -      -       -      +
    149j  GLN*     1.3    62.5    +      -       -      +
    156j  TYR*     4.1    13.5    -      +       +      -
    157j  GLY      3.3    11.0    -      -       -      -
    158j  GLY*     3.7    20.2    -      -       -      -
    159j  TRP*     4.5     3.1    -      -       -      +
     57k  ARG*     3.5    13.5    +      -       -      -
     58k  THR*     4.1    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 149 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134j  LEU      3.2    11.7    -      -       -      +
    135j  LEU*     3.7     9.4    -      -       +      -
    136j  TYR*     4.5     2.9    -      -       -      -
    148j  TYR*     1.3    77.9    -      -       -      +
    150j  SER*     1.3    69.0    +      -       -      +
    151j  ASP*     3.9    16.7    +      -       -      +
    155j  ASN      4.1     0.2    -      -       -      +
    156j  TYR*     3.0     6.7    -      -       -      +
    157j  GLY      2.8    29.5    +      -       -      +
    159j  TRP*     3.1    33.4    +      -       +      +
    162j  THR*     3.2    16.6    +      -       -      -
    163j  CYS      4.3     2.4    +      -       -      -
    164j  ILE*     3.3    34.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 150 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115j  CYS*     3.5    24.7    -      -       -      -
    118j  LYS*     2.6    26.9    +      -       -      -
    133j  SER*     3.2     8.5    +      -       -      -
    134j  LEU*     2.9    36.8    +      -       -      +
    136j  TYR*     3.0    24.3    +      -       -      -
    149j  GLN*     1.3    76.9    -      -       -      +
    151j  ASP*     1.3    64.6    +      -       -      +
    155j  ASN      3.4     4.7    -      -       -      -
    156j  TYR*     4.0     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page


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