Contacts of the strand formed by residues 55 - 60 (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 GLN 55 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  PRO*     4.4    13.7    -      -       -      +
     38A  VAL      4.2     0.3    -      -       -      +
     40A  ALA*     3.0    31.0    +      -       -      +
     43A  ALA*     3.9    20.6    -      -       +      +
     44A  ASN      4.4     7.6    +      -       -      +
     45A  THR*     4.1    17.1    -      -       +      +
     54A  GLY*     1.3    78.3    -      -       -      +
     56A  VAL*     1.3    67.9    +      -       -      +
     57A  LEU*     3.8    27.5    -      -       +      +
     69A  PRO*     3.8    24.6    -      -       +      +
     70A  ILE      5.2     6.3    -      -       -      +
     94A  PHE*     3.3    11.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     4.6     4.7    -      -       +      -
     38A  VAL      3.5    15.0    -      -       -      +
     55A  GLN*     1.3    78.9    -      -       -      +
     57A  LEU*     1.3    67.3    +      -       -      +
     69A  PRO*     4.3     0.3    -      -       -      +
     70A  ILE*     3.1    38.9    +      -       +      +
     72A  PHE*     3.7    19.3    -      -       +      -
     94A  PHE*     4.1     7.7    -      -       +      -
     95A  GLY*     3.7    19.3    -      -       -      -
     98A  VAL*     3.9    26.5    -      -       +      -
    105A  ILE*     5.1     0.7    -      -       +      -
    107A  ALA*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  SER      5.6     0.2    -      -       -      +
     13A  GLY*     5.3     1.6    -      -       -      -
     14A  PRO*     4.8    11.4    -      -       +      -
     19A  PHE*     4.1    32.3    -      -       +      -
     36A  LEU      3.5     5.4    -      -       -      +
     37A  LEU*     3.7     4.2    -      -       -      +
     38A  VAL*     3.0    32.8    +      -       +      +
     40A  ALA*     4.3     5.8    -      -       +      -
     55A  GLN*     3.8    39.9    -      -       +      +
     56A  VAL*     1.3    74.5    -      -       -      +
     58A  LYS*     1.3    59.3    +      -       -      +
     59A  CYS*     3.8     7.7    +      -       -      -
     67A  CYS*     4.1    19.3    -      -       +      +
     68A  GLN      3.6     6.1    -      -       -      +
     69A  PRO*     4.3    21.8    -      -       +      -
     70A  ILE*     4.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     4.8    11.0    -      -       +      -
     35A  PHE*     3.9    46.5    -      -       +      -
     36A  LEU      3.8     2.9    -      -       -      -
     37A  LEU*     4.6     5.2    -      -       +      -
     57A  LEU*     1.3    71.1    -      -       -      +
     59A  CYS*     1.3    56.8    +      -       -      +
     60A  ASP      4.2     0.3    +      -       -      -
     66A  ARG      4.2     0.7    -      -       -      +
     67A  CYS*     3.5     0.3    -      -       -      -
     68A  GLN*     2.7    58.8    +      -       -      +
     69A  PRO      6.0     0.4    -      -       -      -
     70A  ILE*     3.6    25.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  TYR*     3.8    18.8    -      -       +      -
     19A  PHE*     4.4    15.9    -      -       -      -
     35A  PHE*     3.5    11.6    -      -       -      -
     36A  LEU*     3.1    39.9    +      -       +      +
     38A  VAL*     4.6     9.9    -      -       -      -
     57A  LEU*     4.5     7.2    -      -       -      -
     58A  LYS*     1.3    74.6    -      -       -      +
     60A  ASP*     1.3    60.6    +      -       -      +
     61A  TRP      4.1     0.2    +      -       -      -
     66A  ARG      3.7     3.6    -      -       -      -
     67A  CYS*     2.0    47.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  TYR*     3.2    14.3    -      -       -      -
     33A  ARG*     3.5    26.6    +      -       -      +
     34A  MET      4.6     2.9    -      -       -      +
     35A  PHE*     4.0    14.1    -      -       +      -
     36A  LEU*     5.0     0.2    -      -       -      -
     58A  LYS      4.2     0.2    +      -       -      -
     59A  CYS*     1.3    74.3    -      -       -      +
     61A  TRP*     1.3    76.9    +      -       -      +
     65A  ARG*     3.1    29.5    +      -       -      -
     66A  ARG*     3.0    24.0    +      -       -      +
----------------------------------------------------------
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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