Contacts of the helix formed by residues 478 - 482 (chain B) in PDB entry 4L0D


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 GLN 478 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427B  PRO      3.5    16.1    -      -       -      +
    428B  THR*     3.7    29.0    +      -       -      +
    429B  ILE      3.9     4.7    -      -       -      +
    430B  THR*     4.5     0.9    -      -       -      +
    431B  CYS*     4.2     5.9    -      -       -      -
    476B  SER      5.4     1.6    -      -       -      +
    477B  ASP*     1.3    76.2    -      -       -      +
    479B  VAL*     1.3    65.9    +      -       -      +
    480B  GLY      3.2     4.6    +      -       -      +
    481B  LYS*     3.6    34.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 479 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425B  VAL*     5.6     1.1    -      -       +      -
    426B  LEU      5.6     0.2    -      -       -      +
    427B  PRO*     4.1    11.5    +      -       +      +
    429B  ILE*     3.2    30.8    +      -       +      +
    430B  THR      3.7     2.5    -      -       -      +
    434B  THR*     3.4    25.8    -      -       +      +
    448B  VAL*     4.3    16.2    -      -       +      -
    459B  VAL*     3.5    26.7    -      -       +      -
    464B  MET*     3.7    17.5    -      -       +      -
    477B  ASP      3.8     0.6    +      -       -      -
    478B  GLN*     1.3    72.6    -      -       -      +
    480B  GLY*     1.3    67.2    +      -       -      +
    482B  VAL*     2.8    20.4    +      -       -      +
    483B  ILE*     3.2    11.4    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 480 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427B  PRO      4.8     3.2    +      -       -      -
    478B  GLN*     3.2     5.8    +      -       -      +
    479B  VAL*     1.3    78.5    -      -       -      +
    481B  LYS*     1.3    61.4    +      -       -      +
    483B  ILE*     3.0    34.5    +      -       -      +
    485B  LYS*     5.3     3.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 481 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  ASN*     6.2     0.2    -      -       -      +
    472B  LYS      5.9     0.2    -      -       -      +
    473B  VAL*     4.2    20.0    -      -       +      -
    477B  ASP*     4.2    27.0    +      -       +      +
    478B  GLN*     3.7    38.1    +      -       -      +
    479B  VAL      2.9     0.4    +      -       -      -
    480B  GLY*     1.3    76.6    -      -       -      +
    482B  VAL*     1.3    60.5    +      -       -      +
    483B  ILE      3.7     1.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 482 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  ASN*     5.1     2.5    -      -       -      +
    431B  CYS*     5.0     1.3    -      -       -      -
    458B  MET      4.7     0.3    -      -       -      +
    459B  VAL*     4.3    10.8    -      -       +      -
    460B  THR*     5.2     1.3    -      -       +      +
    463B  ASN*     3.5    27.5    +      -       +      +
    464B  MET*     3.9    43.5    -      -       +      +
    467B  SER*     3.3    32.8    -      -       -      +
    473B  VAL*     4.2    15.9    -      -       +      -
    478B  GLN      4.9     0.2    +      -       -      -
    479B  VAL      2.8     8.2    +      -       -      +
    481B  LYS*     1.3    79.8    -      -       -      +
    483B  ILE*     1.3    66.6    +      -       -      +
    484B  TYR*     3.6     5.4    +      -       -      -
----------------------------------------------------------
 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