Contacts of the strand formed by residues 450 - 454 (chain D) in PDB entry 4Z2C


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 450 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419D  CYS*     3.9     9.1    -      -       -      +
    428D  GLU*     3.1    27.6    +      -       -      +
    430D  PHE*     3.5    14.4    -      -       +      -
    445D  ARG*     2.8    52.4    +      -       +      +
    446D  ASN*     3.7     5.7    +      -       -      +
    447D  ARG*     4.4     0.3    -      -       -      -
    448D  GLU      3.6     1.8    -      -       -      -
    449D  PHE*     1.3   108.6    -      -       +      +
    451D  ALA*     1.3    61.1    +      -       -      +
    600D  MET*     3.1    45.9    +      -       +      +
    602D  PRO*     4.1     2.8    -      -       -      +
    605D  ARG*     3.5     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 451 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416D  LEU*     4.6     1.3    -      -       +      -
    417D  ALA      3.3    15.9    -      -       -      +
    418D  ASP*     3.7     2.9    -      -       -      -
    419D  CYS*     3.6    17.2    -      -       +      +
    428D  GLU      2.9     7.8    +      -       -      +
    429D  LEU*     3.5    10.0    -      -       +      -
    430D  PHE*     2.9    25.1    +      -       -      +
    445D  ARG*     4.4     0.7    -      -       -      +
    450D  GLN*     1.3    74.4    -      -       -      +
    452D  ILE*     1.3    67.3    +      -       -      +
    498D  TYR*     3.6    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 452 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416D  LEU*     3.3    10.5    -      -       -      +
    417D  ALA*     3.2    29.8    +      -       +      +
    429D  LEU*     4.4     0.2    -      -       -      -
    430D  PHE*     3.6    26.9    -      -       +      +
    432D  VAL*     4.1    17.9    -      -       +      -
    438D  GLY*     4.8     6.3    -      -       -      +
    441D  ALA*     4.0    21.3    -      -       +      +
    442D  LYS*     4.0    18.2    -      -       +      +
    445D  ARG*     3.7    22.2    -      -       +      -
    450D  GLN      5.1     0.2    -      -       -      -
    451D  ALA*     1.3    85.3    -      -       -      +
    453D  LEU*     1.3    65.1    +      -       -      +
    454D  PRO*     3.8     4.5    -      -       +      +
    600D  MET*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 453 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413D  PRO*     5.4     3.1    -      -       +      -
    415D  LYS*     4.6     4.3    -      -       +      -
    416D  LEU*     3.7    33.9    -      -       +      +
    429D  LEU*     3.7    23.6    -      -       +      -
    430D  PHE      2.9     9.7    +      -       -      -
    431D  ILE*     3.4    12.5    -      -       +      +
    432D  VAL      2.9    25.0    +      -       -      +
    451D  ALA      4.3     0.2    +      -       -      -
    452D  ILE*     1.3    75.8    -      -       -      +
    454D  PRO*     1.3    87.8    -      -       +      +
    455D  ILE*     3.8     1.1    +      -       +      -
    478D  SER*     4.1    24.5    -      -       -      +
    479D  LEU*     4.3    24.9    -      -       +      +
    482D  ALA*     4.5     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 454 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415D  LYS*     4.0    16.5    -      -       +      +
    416D  LEU*     4.0     9.0    -      -       -      +
    432D  VAL*     3.1    10.8    -      -       +      +
    434D  GLY*     4.4    21.1    -      -       -      +
    435D  ASP*     4.8     6.3    -      -       +      +
    438D  GLY*     5.0    10.5    -      -       -      -
    452D  ILE*     3.8     8.7    -      -       +      +
    453D  LEU*     1.3   114.6    -      -       +      +
    455D  ILE*     1.3    58.3    +      -       -      +
    456D  ARG*     3.8     3.8    -      -       +      +
    475D  GLU*     4.0     7.8    -      -       -      +
    478D  SER*     5.1     0.3    +      -       -      -
----------------------------------------------------------
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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