Contacts of the strand formed by residues 42 - 46 (chain C) in PDB entry 1GMO


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 PHE 42 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  THR*     3.1    29.2    -      -       +      -
     39C  ILE*     3.7    19.7    -      -       -      +
     40C  HIS*     2.8    11.3    -      -       -      +
     41C  GLU*     1.3    83.3    -      -       +      +
     43C  LYS*     1.3    61.2    +      -       -      +
     44C  LYS*     3.8     2.5    +      -       -      +
     71C  ALA*     3.9    18.2    -      -       +      -
     74C  CYS*     3.8    24.7    -      -       -      -
     75C  THR*     3.6    24.9    -      -       +      -
     86C  ALA*     5.5     0.2    -      -       -      -
     87C  PHE*     3.8    19.3    -      +       -      -
    119C  TYR*     3.9    23.1    -      -       +      -
    120C  GLU      3.2    24.0    -      -       -      +
    121C  ASN*     3.6    23.3    -      -       +      -
    122C  LYS*     4.1     8.8    -      -       -      -
    176C  TYR*     4.8     3.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  PHE*     1.3    71.0    -      -       -      +
     44C  LYS*     1.3    66.7    +      -       -      +
     45C  SER*     4.2     8.2    +      -       -      +
    104C  MET*     3.9    13.5    -      -       -      +
    118C  LEU      3.4     2.6    -      -       -      +
    119C  TYR*     4.3     1.1    -      -       -      -
    120C  GLU*     2.9    44.9    +      -       +      +
    122C  LYS*     4.6     0.8    -      -       +      +
    125C  ILE*     3.8    20.9    -      -       +      -
    137C  LYS*     3.1    40.1    +      -       -      +
    139C  THR*     4.0    22.0    -      -       +      -
    171C  ASP*     3.2    26.8    +      -       -      +
    173C  GLN*     4.3     9.2    -      -       -      +
    176C  TYR*     4.4    12.6    -      -       +      +
    178C  ARG*     4.4     2.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  PHE      3.8     4.2    +      -       -      +
     43C  LYS*     1.3    73.4    -      -       -      +
     45C  SER*     1.3    65.7    +      -       -      +
     46C  ALA*     3.9    25.3    +      -       -      +
    117C  ASP*     3.6    21.0    +      -       -      -
    118C  LEU      3.1     6.7    -      -       -      +
    119C  TYR*     3.4    43.3    -      -       +      +
    173C  GLN*     2.9    30.1    +      -       -      +
    176C  TYR*     4.9     1.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  LYS*     4.2     9.5    +      -       -      -
     44C  LYS*     1.3    76.1    +      -       -      +
     46C  ALA*     1.3    68.8    +      -       -      +
     48C  THR*     3.2    15.6    +      -       -      -
    110C  LYS*     5.4     8.5    +      -       -      -
    118C  LEU*     2.6    46.7    +      -       -      +
    120C  GLU*     4.5    10.2    +      -       -      -
    173C  GLN*     4.3     7.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LYS*     3.9    23.8    -      -       -      +
     45C  SER*     1.3    72.4    -      -       -      +
     47C  LYS*     1.3    66.0    +      -       +      +
     48C  THR*     2.7    23.9    +      -       -      -
    117C  ASP*     3.4    12.1    -      -       -      +
----------------------------------------------------------
 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