Contacts of the strand formed by residues 144 - 150 (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 GLY 144 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139D  TRP*     3.2    22.7    -      -       -      -
    140D  ASP      3.0    36.4    +      -       -      -
    141D  LYS      4.8     0.2    -      -       -      -
    142D  HIS      3.7     1.0    -      -       -      -
    143D  TYR*     1.3    74.4    -      -       -      +
    145D  PHE*     1.3    66.4    +      -       -      -
    146D  GLN*     3.3     8.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 145 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LEU*     3.6    28.8    -      -       +      +
     39D  ALA      4.5     2.5    -      -       -      +
     40D  ASN*     4.1    15.5    -      -       -      -
     41D  ASP*     3.9     7.6    -      -       -      -
     42D  GLY*     3.4    41.1    -      -       -      +
     43D  VAL*     3.8    13.9    -      -       +      -
    138D  GLY      3.5     3.1    -      -       -      -
    139D  TRP*     4.0    19.1    -      +       +      -
    143D  TYR      3.4     6.9    +      -       -      +
    144D  GLY*     1.3    73.3    -      -       -      -
    146D  GLN*     1.3    64.4    +      -       -      +
    216D  LEU*     3.5    26.7    -      -       +      -
    217D  THR*     4.0     2.5    -      -       -      -
    218D  ARG*     3.9    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 146 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LEU*     4.3     6.7    -      -       -      -
     43D  VAL*     4.8     2.8    -      -       -      +
    107D  CYS*     3.6     9.6    -      -       +      -
    108D  GLU*     4.5     3.8    +      -       -      +
    136D  TYR      3.7     0.4    -      -       -      +
    137D  ILE*     3.4     6.2    -      -       -      +
    138D  GLY      2.9    31.3    +      -       -      +
    140D  ASP*     2.5    39.3    +      -       -      +
    143D  TYR*     3.6    30.1    -      -       +      +
    144D  GLY      3.3    10.2    +      -       -      +
    145D  PHE*     1.3    81.7    -      -       -      +
    147D  LEU*     1.3    61.3    +      -       -      +
    148D  TYR*     2.5    45.6    +      -       +      +
     57E  ARG*     4.1     3.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  GLY*     3.4    32.1    -      -       -      +
     37D  ILE      4.4     1.3    -      -       -      +
     38D  LEU*     4.6     8.6    -      -       +      +
     43D  VAL*     4.7     8.5    -      -       +      -
     45D  LEU*     4.7     3.6    -      -       +      -
    135D  LEU*     4.5    10.5    -      -       +      -
    136D  TYR      3.2    17.9    -      -       -      +
    137D  ILE*     3.6    17.7    -      -       +      -
    146D  GLN*     1.3    76.8    -      -       -      +
    148D  TYR*     1.3    73.5    +      -       -      +
    158D  GLY*     3.4     4.3    -      -       -      -
    159D  TRP*     3.0    40.2    +      -       +      +
    160D  LYS      4.3     2.2    -      -       -      +
    161D  ALA*     3.9    20.6    -      -       -      +
    162D  THR*     4.0    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 148 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  CYS*     4.1     7.0    -      -       +      -
    108D  GLU*     3.6    37.7    -      -       +      +
    111D  VAL*     4.1    19.1    -      -       +      -
    135D  LEU*     3.4     9.4    -      -       -      +
    136D  TYR*     2.9    49.2    +      -       +      +
    146D  GLN*     2.5    48.3    +      -       +      -
    147D  LEU*     1.3    78.9    -      -       -      +
    149D  GLN*     1.3    63.5    +      -       -      +
    156D  TYR*     4.1    15.0    -      +       -      -
    157D  GLY      3.3     7.9    -      -       -      +
    158D  GLY*     3.6    24.5    -      -       -      -
    159D  TRP*     4.7     1.1    -      -       -      +
     57E  ARG*     3.4    15.9    +      -       -      -
     58E  THR*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 149 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134D  LEU      3.1    13.2    -      -       -      +
    135D  LEU*     3.6    12.8    -      -       +      -
    136D  TYR*     4.5     1.6    -      -       -      -
    148D  TYR*     1.3    78.2    -      -       -      +
    150D  SER*     1.3    67.6    +      -       -      +
    151D  ASP*     4.0    19.0    +      -       -      +
    155D  ASN      4.1     0.2    -      -       -      +
    156D  TYR*     3.1     4.2    -      -       -      -
    157D  GLY      2.9    30.3    +      -       -      -
    159D  TRP*     3.1    34.2    +      -       +      +
    162D  THR*     3.4    18.0    +      -       -      +
    163D  CYS      4.5     1.4    +      -       -      -
    164D  ILE*     3.2    36.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 150 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115D  CYS*     3.5    25.1    -      -       -      -
    118D  LYS*     2.7    27.3    +      -       -      -
    133D  SER*     3.0     9.0    +      -       -      -
    134D  LEU*     3.0    35.4    +      -       -      +
    136D  TYR*     3.0    23.2    +      -       -      -
    149D  GLN*     1.3    78.6    -      -       -      +
    151D  ASP*     1.3    64.2    +      -       -      +
    155D  ASN      3.5     3.6    -      -       -      -
    156D  TYR*     4.0     2.5    -      -       -      -
----------------------------------------------------------
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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