Contacts of the strand formed by residues 129 - 132 (chain N) in PDB entry 6E0P


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 LEU 129 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57N  GLN*     3.6    37.5    -      -       +      +
     59N  VAL*     4.1     7.6    -      -       +      -
     69N  TRP*     5.6     3.1    -      -       +      -
    119N  ALA*     3.8    18.2    -      -       +      -
    120N  ARG      3.5     4.5    -      -       -      -
    121N  LYS*     4.0    11.7    -      -       +      -
    128N  THR*     1.3    75.1    +      -       -      +
    130N  ASP*     1.3    56.6    +      -       -      +
    131N  TYR      3.8     0.2    -      -       -      -
    132N  TRP*     3.6    34.7    +      -       +      +
    194N  TYR*     3.3    14.0    -      -       -      +
    204N  THR*     2.4    28.4    +      -       -      -
    247N  LEU*     3.8    23.8    -      -       +      -
    254N  TYR*     5.9     2.5    -      -       +      -
    256N  PHE*     4.0     9.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 130 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105H  GLU*     5.0     6.4    -      -       -      +
    108H  LYS*     5.9     1.3    +      -       -      -
     54N  TYR*     5.0     3.8    -      -       -      -
    120N  ARG*     2.7    34.2    +      -       -      +
    122N  SER*     4.4    10.4    +      -       -      -
    127N  SER*     5.0     4.0    -      -       -      -
    128N  THR*     2.9    29.2    +      -       -      +
    129N  LEU*     1.3    71.0    -      -       -      +
    131N  TYR*     1.3    83.0    +      -       +      +
    132N  TRP*     4.0     4.4    -      -       -      -
    203N  LYS*     5.8     0.2    -      -       -      -
    204N  THR*     3.2    23.9    +      -       -      +
    207N  TYR*     5.9     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 131 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23N  GLU*     5.8     6.2    -      -       +      +
     24N  VAL*     3.7    47.3    -      -       +      +
     25N  GLN*     6.0     0.2    -      -       -      -
     26N  LEU*     3.8     9.9    -      -       +      +
    119N  ALA*     3.3     1.2    -      -       -      -
    120N  ARG*     2.7    66.6    +      -       +      +
    130N  ASP*     1.3    89.0    -      -       +      +
    132N  TRP*     1.3    63.6    -      -       -      +
    214N  ASP*     4.7    18.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 132 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26N  LEU*     4.2    11.7    +      -       -      +
     59N  VAL*     4.0    21.5    -      -       +      -
     67N  LEU*     5.1     2.5    -      -       +      -
    117N  TYR*     3.6    33.4    -      +       +      -
    118N  CYS      3.5     4.9    -      -       -      -
    119N  ALA*     4.1     8.5    -      -       +      +
    129N  LEU*     3.6    48.7    +      -       +      +
    130N  ASP      4.0     9.6    -      -       -      -
    131N  TYR*     1.3    81.1    -      -       -      +
    133N  GLY*     1.3    69.3    +      -       -      +
    134N  GLN*     4.8     3.3    -      -       -      +
    194N  TYR*     3.8    20.8    -      +       -      -
    201N  SER*     4.1     9.0    +      -       -      +
    202N  PRO*     3.1    60.0    +      -       +      +
    203N  LYS*     4.9     0.9    -      -       -      -
    204N  THR*     4.0     1.7    +      -       -      -
    256N  PHE*     4.3    10.3    -      +       -      -
----------------------------------------------------------
 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