Contacts of the strand formed by residues 130 - 135 (chain G) in PDB entry 5GAG


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 GLU 130 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86G  LYS*     4.2    17.0    +      -       +      +
     87G  LEU      3.5    12.3    -      -       -      +
     88G  GLN*     4.2    13.2    -      -       +      +
    125G  CYS*     3.3    22.6    -      -       -      +
    126G  PRO*     3.5    24.8    -      -       +      +
    127G  THR*     3.3    28.4    +      -       -      +
    128G  GLN      3.4     2.6    +      -       -      -
    129G  THR*     1.3    82.3    +      -       -      +
    131G  ILE*     1.3    69.0    +      -       -      +
    132G  VAL*     4.0     9.2    -      -       -      +
    165G  ALA*     6.1     1.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 131 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86G  LYS*     3.7     0.2    -      -       -      -
     87G  LEU*     2.9    43.5    +      -       +      +
     88G  GLN*     4.7     0.2    -      -       -      +
     89G  LEU*     4.1    19.7    -      -       +      -
     96G  ALA*     4.1    13.7    -      -       +      -
    103G  ILE*     4.3     9.2    -      -       +      -
    105G  LEU*     3.9    27.8    -      -       +      -
    123G  ALA*     4.6    12.6    -      -       +      -
    124G  GLU      3.9     4.7    -      -       -      +
    125G  CYS*     4.2     9.9    -      -       -      -
    130G  GLU*     1.3    75.5    -      -       -      +
    132G  VAL*     1.3    82.8    +      -       -      +
    133G  LEU*     4.6     8.1    -      -       +      -
    148G  LEU*     4.3    23.8    -      -       +      -
    162G  VAL*     6.0     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 132 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84G  THR*     3.6    29.6    -      -       +      -
     85G  LYS      3.8     2.9    -      -       -      -
     86G  LYS*     3.7    27.4    -      -       +      +
    122G  THR      4.1     0.3    -      -       -      +
    123G  ALA*     3.3     5.7    -      -       -      +
    124G  GLU*     2.9    39.6    +      -       +      +
    126G  PRO*     3.9    25.8    -      -       +      -
    130G  GLU*     4.0     6.7    -      -       -      +
    131G  ILE*     1.3    81.9    -      -       -      +
    133G  LEU*     1.3    67.8    +      -       -      +
    134G  LYS*     4.9     9.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 133 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84G  THR*     3.2    10.9    -      -       -      +
     85G  LYS*     2.9    38.4    +      -       +      +
     87G  LEU*     4.0    13.2    -      -       +      -
    103G  ILE*     4.8     0.4    -      -       +      -
    117G  LEU*     4.2     7.9    -      -       +      -
    121G  ILE*     4.4     5.4    -      -       +      -
    122G  THR      3.9     0.9    -      -       -      -
    123G  ALA*     3.6    25.8    -      -       +      -
    131G  ILE*     4.6     2.7    -      -       +      -
    132G  VAL*     1.3    74.8    -      -       -      +
    134G  LYS*     1.3    60.4    +      -       -      +
    141G  ILE*     3.6    25.8    -      -       +      +
    144G  VAL*     3.6    33.2    -      -       +      -
    145G  ALA*     3.6    26.2    -      -       +      +
    148G  LEU*     4.3     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 134 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82G  GLY*     6.3     0.9    -      -       -      -
     83G  PHE      3.3     6.7    -      -       -      +
     84G  THR*     3.5    29.9    +      -       +      +
    120G  GLY      3.9     0.2    -      -       -      +
    121G  ILE*     3.6     4.5    -      -       -      +
    122G  THR*     2.9    51.6    +      -       -      +
    132G  VAL*     4.9     8.4    -      -       +      +
    133G  LEU*     1.3    77.5    -      -       -      +
    135G  GLY*     1.3    61.8    +      -       -      +
    141G  ILE*     4.0     4.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 135 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  ASN*     4.6     2.2    -      -       -      -
     82G  GLY*     4.3     2.7    -      -       -      -
     83G  PHE*     2.8    35.1    +      -       -      +
    120G  GLY      4.0    13.0    -      -       -      -
    121G  ILE*     4.0    10.8    -      -       -      -
    134G  LYS*     1.3    77.8    -      -       -      +
    136G  ALA*     1.3    64.2    +      -       -      -
    137G  ASP      3.3     5.2    +      -       -      +
    141G  ILE*     3.9     2.3    -      -       -      +
----------------------------------------------------------
 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