Contacts of the strand formed by residues 422 - 427 (chain A) in PDB entry 5FFO


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 ASP 422 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  PHE*     3.6    14.2    -      -       +      -
    347A  LEU*     5.2     1.2    -      -       -      +
    350A  LEU*     4.9     3.5    -      -       -      +
    411A  GLY*     3.7    13.3    -      -       -      -
    412A  ALA      3.8     2.4    +      -       -      -
    413A  THR      2.9    12.7    +      -       -      +
    414A  ASP*     2.9    24.8    -      -       -      +
    415A  ILE*     3.1    21.5    +      -       +      -
    416A  ASP*     3.2    11.4    -      -       -      +
    418A  ASN*     4.1     1.9    +      -       -      -
    420A  TYR      3.6     2.6    -      -       -      +
    421A  PRO*     1.3    74.6    -      -       -      +
    423A  LEU*     1.3    62.6    +      -       -      +
    435A  LEU*     4.4    12.6    -      -       +      -
    436A  TYR      3.6     9.9    -      -       -      +
    437A  ARG*     3.2    12.4    -      -       -      +
    438A  ALA      3.1    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LEU*     4.1    28.3    -      -       +      -
     25A  PHE*     4.3     0.6    -      -       -      -
    345A  ALA*     4.6     1.8    -      -       +      -
    347A  LEU*     3.7    31.4    -      -       +      -
    350A  LEU*     5.5     2.0    -      -       +      -
    359A  ALA*     4.6     4.0    -      -       +      -
    373A  VAL*     4.7     1.8    -      -       +      -
    375A  ILE*     4.3     8.7    -      -       +      -
    391A  LEU*     4.1     9.6    -      -       +      -
    409A  MET*     4.2    11.9    -      -       +      -
    410A  LYS      3.5    17.5    -      -       -      +
    422A  ASP*     1.3    80.0    -      -       -      +
    424A  ILE*     1.3    77.3    +      -       -      +
    425A  VAL*     3.9    18.8    -      -       +      -
    434A  ILE      3.9     0.9    -      -       -      +
    435A  LEU*     3.7     3.3    -      -       -      +
    436A  TYR*     3.1    35.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     3.7    30.5    -      -       +      -
     24A  ASP      3.5    27.8    -      -       -      +
     25A  PHE*     3.7    31.6    -      -       +      -
     36A  LEU*     3.7    33.9    -      -       +      -
     38A  VAL*     5.6     1.6    -      -       +      -
    409A  MET*     3.2    27.4    -      -       -      +
    410A  LYS*     3.3    11.7    +      -       +      +
    423A  LEU*     1.3    76.0    -      -       -      +
    425A  VAL*     1.3    63.9    +      -       -      +
    426A  GLY      4.2     0.2    -      -       -      -
    433A  ALA*     4.7     7.4    -      -       +      -
    434A  ILE      3.8     7.0    -      -       -      +
    435A  LEU*     3.9    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373A  VAL*     4.0     7.2    -      -       +      -
    391A  LEU*     4.4     5.6    -      -       +      -
    405A  PHE*     3.6    26.2    -      -       +      -
    406A  GLY*     3.6    32.3    -      -       -      +
    408A  SER      4.0     2.9    -      -       -      +
    409A  MET*     4.3     4.9    -      -       +      -
    423A  LEU*     3.9    25.8    -      -       +      -
    424A  ILE*     1.3    81.0    -      -       -      +
    426A  GLY*     1.3    62.6    +      -       -      +
    433A  ALA*     3.6     1.4    -      -       -      -
    434A  ILE*     3.1    38.0    +      -       -      +
    436A  TYR*     4.2    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY*     3.4    22.4    -      -       -      -
     23A  VAL*     4.1    11.5    -      -       -      +
    404A  SER      3.3     2.9    -      -       -      +
    406A  GLY      2.8    29.7    +      -       -      -
    407A  TYR*     3.5     6.9    +      -       -      -
    408A  SER*     2.9    16.7    +      -       -      +
    425A  VAL*     1.3    72.8    -      -       -      +
    427A  ALA*     1.3    56.6    +      -       -      -
    428A  PHE      4.0     0.7    -      -       -      -
    432A  ARG      3.9     4.3    -      -       -      -
    433A  ALA*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY      4.0     0.6    +      -       -      -
    395A  TRP*     5.6     1.6    -      -       +      -
    403A  PRO*     3.4    12.1    -      -       +      +
    404A  SER      3.4     7.6    -      -       -      -
    405A  PHE*     3.5    28.7    -      -       +      -
    425A  VAL      4.1     0.2    +      -       -      -
    426A  GLY*     1.3    72.1    -      -       -      -
    428A  PHE*     1.3    64.4    +      -       -      +
    429A  GLY      3.2     4.8    +      -       -      -
    430A  VAL*     3.3    22.2    +      -       +      +
    431A  ASP      3.3     7.8    +      -       -      -
    432A  ARG*     2.9    23.7    +      -       +      +
    434A  ILE*     4.8     4.0    -      -       +      -
----------------------------------------------------------
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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