Contacts of the strand formed by residues 451 - 458 (chain A) in PDB entry 4QQN


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 451 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  LEU*     4.2    11.2    -      -       +      -
    382A  ILE*     4.3     5.4    -      -       +      -
    436A  ILE*     3.4    42.0    -      -       +      -
    437A  LYS*     3.7    52.0    -      -       +      +
    448A  ASP      4.0     0.2    -      -       -      +
    449A  LEU      3.7    13.7    -      -       -      -
    450A  GLU*     1.3    75.5    -      -       -      +
    452A  SER*     1.3    71.6    +      -       -      +
    453A  SER*     4.6     3.8    -      -       -      -
    520A  VAL*     5.0     4.0    -      -       +      -
    521A  THR*     3.2     6.1    -      -       -      +
    522A  VAL*     2.9    60.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451A  PHE*     1.3    77.8    -      -       -      +
    453A  SER*     1.3    64.2    +      -       -      +
    519A  LYS*     4.0    18.9    +      -       -      -
    520A  VAL      3.2     5.4    -      -       -      -
    521A  THR*     2.4    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435A  GLY      4.6     1.4    +      -       -      -
    436A  ILE*     3.4    45.8    +      -       -      +
    451A  PHE*     4.6     1.1    -      -       -      -
    452A  SER*     1.3    77.3    -      -       -      +
    454A  ASP*     1.3    74.8    +      -       -      +
    455A  PHE      3.8     0.2    +      -       -      -
    519A  LYS*     3.5     5.0    -      -       -      -
    520A  VAL*     2.8    41.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  CYS*     5.4     0.9    -      -       -      -
    453A  SER*     1.3    84.6    +      -       -      +
    455A  PHE*     1.3    59.7    +      -       -      +
    518A  GLY      3.4     7.1    -      -       -      +
    519A  LYS*     3.5    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  LEU*     3.8    25.1    -      -       +      -
    434A  CYS*     4.0    19.1    -      -       +      -
    436A  ILE*     4.1    11.4    -      -       +      -
    453A  SER      4.0     9.0    -      -       -      -
    454A  ASP*     1.3    75.5    -      -       -      +
    456A  THR*     1.3    66.5    +      -       -      +
    457A  LEU*     3.8    35.9    -      -       +      -
    468A  ILE*     5.6     2.9    -      -       +      -
    516A  LEU      4.7     0.7    -      -       -      -
    517A  LYS*     3.3     5.3    -      -       -      +
    518A  GLY*     2.9    55.4    +      -       -      +
    519A  LYS      3.4    26.0    -      -       -      -
    520A  VAL*     3.9     5.2    -      -       +      -
    536A  LEU*     3.9    17.9    -      -       +      -
    537A  THR      4.4     0.2    -      -       -      -
    538A  LEU*     4.2    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    433A  PRO      5.3     0.5    -      -       -      +
    434A  CYS*     3.5    22.5    -      -       -      +
    455A  PHE*     1.3    78.3    +      -       -      +
    457A  LEU*     1.3    67.0    +      -       -      +
    458A  LYS*     3.9     3.4    +      -       +      +
    515A  ALA*     3.6    32.5    -      -       +      -
    516A  LEU      3.2     7.4    -      -       -      +
    517A  LYS*     3.9    21.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  LEU*     3.7    26.0    -      -       +      +
    385A  VAL*     4.3     2.5    -      -       -      +
    386A  ALA*     3.9    28.5    -      -       +      +
    431A  SER*     3.8    12.3    -      -       -      +
    432A  GLU      3.9    10.3    -      -       -      +
    434A  CYS*     3.7    19.7    -      -       +      -
    455A  PHE*     3.8    27.8    -      -       +      -
    456A  THR*     1.3    73.1    -      -       -      +
    458A  LYS*     1.3    57.5    -      -       -      +
    459A  ILE*     3.2     7.6    +      -       +      -
    468A  ILE*     4.0    16.4    -      -       +      -
    516A  LEU*     2.6    53.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431A  SER*     3.3     0.6    -      -       -      -
    432A  GLU*     3.0    54.5    +      -       +      +
    456A  THR*     3.9     5.8    +      -       +      +
    457A  LEU*     1.3    67.9    -      -       -      +
    459A  ILE*     1.3    66.8    +      -       -      +
    460A  THR*     3.6     3.8    -      -       +      +
    513A  GLY*     6.2     0.9    -      -       -      -
    514A  GLU      3.6     7.0    -      -       -      +
    515A  ALA*     4.8     2.9    -      -       -      +
----------------------------------------------------------
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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