Contacts of the strand formed by residues 441 - 451 (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 VAL 441 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  PHE*     3.7    32.3    -      -       +      -
      2A  ASN*     3.7    39.0    -      -       +      +
    351A  ASP*     4.3    15.7    -      -       +      +
    420A  TYR*     3.3    13.4    +      -       +      +
    440A  PRO*     1.3    72.2    -      -       -      +
    442A  ILE*     1.3    65.7    +      -       -      +
    443A  THR*     3.9     5.0    +      -       -      +
    484A  GLY*     3.6    19.6    -      -       -      -
    485A  LYS      4.2     0.9    +      -       -      -
    488A  LEU*     6.0     0.2    -      -       -      +
    578A  ILE*     3.1     3.4    -      -       +      +
    580A  ASN*     3.9    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440A  PRO      4.8     2.0    -      -       -      +
    441A  VAL*     1.3    76.6    -      -       -      +
    443A  THR*     1.3    63.4    +      -       -      +
    444A  VAL*     3.9     1.7    +      -       +      +
    482A  ALA*     4.2    21.5    -      -       +      -
    483A  ASP      3.4    11.0    -      -       -      +
    488A  LEU*     3.5    32.3    -      -       +      -
    492A  LEU*     4.3    15.7    -      -       +      -
    494A  PHE*     5.0     4.9    -      -       +      -
    564A  LEU*     4.7    13.2    -      -       +      -
    577A  PRO*     3.9    27.8    -      -       +      -
    578A  ILE      2.8    13.3    +      -       -      +
    579A  LEU*     3.5    24.9    -      -       +      +
    580A  ASN      3.0    22.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441A  VAL*     3.9     7.0    +      -       -      +
    442A  ILE*     1.3    73.5    -      -       -      +
    444A  VAL*     1.3    63.5    +      -       -      +
    445A  ASN*     4.3    17.2    +      -       -      +
    482A  ALA*     3.5     2.3    -      -       -      -
    483A  ASP*     2.9    37.0    +      -       -      +
    580A  ASN*     4.2    17.3    +      -       +      +
    583A  THR*     5.0     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 444 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  ILE*     4.8     1.8    -      -       +      +
    443A  THR*     1.3    76.3    -      -       -      +
    445A  ASN*     1.3    75.2    +      -       -      +
    446A  ALA      4.1     1.7    +      -       -      +
    480A  LEU*     4.3    10.8    -      -       +      -
    481A  LYS      3.6    10.3    -      -       -      +
    482A  ALA*     4.5     6.3    -      -       +      +
    494A  PHE*     5.0     9.2    -      -       +      -
    562A  TYR*     3.7    38.7    +      -       +      +
    579A  LEU*     4.0    25.8    -      -       +      -
    583A  THR*     3.7    32.7    +      -       -      +
    584A  PRO*     4.6     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  THR*     4.3    14.8    +      -       -      +
    444A  VAL*     1.3    79.5    +      -       -      +
    446A  ALA*     1.3    61.2    +      -       -      +
    447A  GLY      4.2     0.5    +      -       -      -
    479A  CYS      4.4     0.3    -      -       -      +
    480A  LEU*     4.2     1.6    +      -       -      -
    481A  LYS*     3.0    60.7    +      -       -      +
    534A  MET*     5.2     5.5    -      -       +      +
    583A  THR*     6.2     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  VAL*     4.0     2.8    +      -       -      +
    445A  ASN*     1.3    73.4    -      -       -      +
    447A  GLY*     1.3    59.6    -      -       -      +
    479A  CYS      3.9     4.0    -      -       -      -
    480A  LEU*     4.1    10.5    -      -       +      -
    560A  MET*     4.5     4.0    -      -       +      -
    562A  TYR*     3.5    42.5    +      -       +      +
    587A  ILE*     3.5    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  ASN      4.2     0.6    +      -       -      -
    446A  ALA*     1.3    76.0    -      -       -      +
    448A  LEU*     1.3    63.4    +      -       -      +
    449A  GLU*     5.8     0.2    -      -       -      -
    478A  PHE*     3.8     0.5    -      -       -      -
    479A  CYS*     3.1    37.5    +      -       -      +
    534A  MET*     6.3     0.2    -      -       -      -
    560A  MET*     3.8    12.8    -      -       -      +
    587A  ILE*     3.8     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447A  GLY*     1.3    74.1    -      -       -      +
    449A  GLU*     1.3    71.4    +      -       -      +
    450A  VAL*     4.6     5.2    -      -       +      -
    476A  VAL*     4.7    13.0    -      -       +      -
    477A  ARG      4.1     4.9    -      -       -      +
    478A  PHE*     4.0    22.9    -      -       +      -
    498A  LEU*     5.8     1.8    -      -       +      -
    558A  ILE*     4.0    20.4    -      -       +      +
    560A  MET*     4.1    24.9    -      -       +      -
    587A  ILE*     4.0    19.4    -      -       +      +
    588A  SER      4.2     1.8    -      -       -      -
    589A  ARG*     3.9    47.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447A  GLY      5.8     0.2    -      -       -      -
    448A  LEU*     1.3    80.8    -      -       -      +
    450A  VAL*     1.3    65.1    +      -       -      +
    451A  TYR*     3.7    29.7    +      -       +      -
    476A  VAL*     4.4     2.1    -      -       -      -
    477A  ARG*     3.1    60.0    +      -       +      +
    479A  CYS*     5.3     2.8    -      -       -      -
    589A  ARG*     3.5     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     4.6     7.6    -      -       +      -
    449A  GLU*     1.3    77.8    -      -       -      +
    451A  TYR*     1.3    61.6    +      -       -      +
    452A  PRO      3.7    20.3    -      -       -      +
    453A  SER*     3.8     6.6    +      -       -      -
    474A  PHE*     4.8    15.3    -      -       +      -
    475A  ASN      4.5     3.4    -      -       -      +
    476A  VAL*     5.6     4.7    -      -       +      -
    558A  ILE*     4.3    28.5    -      -       +      -
    589A  ARG*     2.9    51.3    +      -       +      +
    590A  GLN      5.0     4.3    -      -       -      +
    591A  ALA*     4.1    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449A  GLU*     3.7    33.2    -      -       +      -
    450A  VAL*     1.3    78.0    -      -       -      +
    452A  PRO*     1.3    66.0    -      -       +      +
    474A  PHE*     4.8     1.1    -      -       -      -
    475A  ASN*     3.4    45.7    +      -       +      +
    477A  ARG*     3.2    42.7    -      -       +      +
    538A  GLU*     3.9    13.6    +      -       -      -
----------------------------------------------------------
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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