Contacts of the strand formed by residues 424 - 430 (chain A) in PDB entry 5FPQ


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 ARG 424 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324A  LEU      2.8    12.2    +      -       -      +
    325A  GLN*     3.2    25.1    -      -       +      +
    326A  VAL*     2.8    32.2    +      -       -      +
    422A  GLY      3.9     1.4    +      -       -      -
    423A  ALA*     1.3    71.6    -      -       -      +
    425A  VAL*     1.3    56.2    +      -       -      +
    426A  TYR*     3.1    30.4    +      -       +      +
    486A  THR      4.0     7.3    +      -       -      -
    487A  GLY      3.1    29.5    +      -       -      -
    488A  ASP*     3.9    10.9    +      -       -      +
    502A  PRO*     4.5    16.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  VAL*     3.3    11.9    -      -       +      +
    328A  VAL*     4.1    17.7    -      -       +      -
    415A  ALA*     3.8    31.9    -      -       +      +
    418A  LEU*     4.2     6.5    -      -       +      -
    419A  ALA*     3.8    27.1    -      -       -      +
    423A  ALA*     3.7    15.6    +      -       +      +
    424A  ARG*     1.3    79.3    -      -       -      +
    426A  TYR*     1.3    61.4    +      -       -      +
    502A  PRO*     3.3     8.2    -      -       -      +
    503A  TYR*     2.6    50.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  VAL      2.9    14.6    +      -       -      +
    327A  LEU*     3.4    17.2    -      -       +      +
    328A  VAL*     2.8    29.5    +      -       -      +
    424A  ARG*     3.1    38.3    +      -       +      -
    425A  VAL*     1.3    76.3    -      -       -      +
    427A  ALA*     1.3    61.1    +      -       -      +
    483A  PHE*     4.4     5.8    -      +       -      -
    487A  GLY      3.5    21.5    -      -       -      -
    488A  ASP*     3.6    16.6    +      -       -      -
    489A  PRO*     3.7    26.2    -      -       +      -
    490A  ASN*     4.4     0.4    -      -       -      -
    500A  TRP*     3.5    36.3    -      +       +      +
    501A  PRO      3.8    14.4    -      -       -      -
    502A  PRO*     3.8    20.8    -      -       +      +
    503A  TYR      4.3     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328A  VAL*     2.9    19.7    -      -       +      +
    329A  GLY*     5.5     0.4    -      -       -      -
    426A  TYR*     1.3    74.4    -      -       -      +
    428A  TYR*     1.3    60.7    +      -       -      +
    500A  TRP*     3.1    13.8    +      -       -      +
    503A  TYR*     3.9    26.0    -      -       +      +
    509A  GLN      4.8     1.4    +      -       -      -
    510A  TYR*     3.2    19.4    -      -       +      +
    511A  VAL      3.0    19.9    +      -       -      -
    524A  LEU*     4.4    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  VAL*     5.6     0.7    -      -       +      -
    228A  GLN*     3.3    36.0    -      -       +      +
    229A  SER*     4.5     0.9    +      -       -      -
    327A  LEU*     4.1    13.5    -      -       +      -
    328A  VAL*     3.0    22.5    +      -       -      -
    329A  GLY*     3.2    38.3    -      -       -      -
    330A  VAL*     3.3    18.4    +      -       -      +
    427A  ALA*     1.3    74.7    -      -       -      +
    429A  VAL*     1.3    69.1    +      -       -      +
    430A  PHE*     3.7    19.7    -      +       +      -
    450A  GLU*     4.4    11.0    +      -       +      +
    480A  TRP*     3.6    32.0    -      +       -      -
    500A  TRP*     3.7    12.8    -      +       +      -
    510A  TYR*     4.3     1.6    -      -       -      -
    511A  VAL      3.1    12.3    -      -       -      +
    513A  LEU*     3.7    23.6    -      -       +      -
    524A  LEU*     4.9     3.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  VAL*     3.3    16.4    -      -       +      +
    331A  VAL      4.4     2.9    -      -       -      +
    332A  LYS*     4.3    18.2    -      -       +      -
    428A  TYR*     1.3    79.5    -      -       -      +
    430A  PHE*     1.3    58.1    +      -       -      +
    431A  GLU*     3.6    24.0    +      -       +      +
    510A  TYR*     3.2    37.0    -      -       +      +
    511A  VAL      2.8     8.8    +      -       -      +
    512A  SER*     3.3     5.0    -      -       -      -
    513A  LEU      2.7    30.5    +      -       -      -
    524A  LEU*     4.1    13.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  VAL      2.8    16.7    +      -       -      +
    331A  VAL*     4.0     7.0    -      -       +      -
    332A  LYS*     3.0    24.6    +      -       -      +
    428A  TYR*     3.7    10.2    -      +       +      -
    429A  VAL*     1.3    72.0    -      -       -      +
    431A  GLU*     1.3    57.5    +      -       -      +
    432A  HIS*     3.1    25.4    -      -       +      -
    445A  VAL*     3.8    14.7    -      -       +      +
    449A  TYR      3.8     6.3    -      -       -      -
    450A  GLU*     3.5    37.0    -      -       +      -
    453A  PHE*     3.7    24.7    -      +       -      -
    454A  ILE*     5.8     0.4    -      -       +      -
    472A  PHE*     3.5    30.5    -      +       -      -
    476A  LEU*     3.7    16.6    -      -       +      -
    513A  LEU*     3.6    21.3    -      -       +      -
----------------------------------------------------------
 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