Contacts of the strand formed by residues 208 - 213 (chain A) in PDB entry 5FL6


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 208 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  LEU*     3.5    26.0    -      -       +      +
    142A  VAL*     3.9    24.2    -      -       +      -
    196A  GLU*     3.4     3.6    -      -       -      -
    197A  GLY      2.8    35.2    +      -       -      +
    198A  SER      4.5     0.4    -      -       -      +
    199A  LEU*     3.7    24.2    -      -       +      +
    205A  ALA*     3.6    23.6    -      -       +      +
    206A  GLN      4.2     2.2    -      -       -      +
    207A  GLY*     1.3    78.8    -      -       -      +
    209A  ILE*     1.3    66.4    +      -       -      +
    210A  TRP*     3.5    25.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  LEU*     3.9    21.3    -      -       +      +
     86A  ARG*     4.1     8.3    -      -       -      +
     88A  TYR*     4.3     8.3    -      -       -      +
    138A  GLY*     3.8    27.4    -      -       -      +
    140A  LEU      3.1     9.8    +      -       -      +
    141A  ALA*     3.3     4.1    -      -       +      +
    142A  VAL      2.9    27.4    +      -       -      +
    194A  GLN*     3.8    33.2    -      -       +      +
    195A  TYR      3.7     3.6    -      -       -      +
    196A  GLU*     4.1    26.9    -      -       +      +
    208A  VAL*     1.3    73.2    -      -       -      +
    210A  TRP*     1.3    61.5    +      -       -      +
    211A  THR*     4.0     1.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  SER*     3.0    17.7    +      -       -      -
    107A  HIS*     3.6    19.1    -      +       -      +
    119A  HIS*     3.6    31.4    -      +       -      -
    142A  VAL*     3.3    42.2    -      -       +      -
    144A  ALA*     4.2     8.5    -      -       +      -
    193A  PHE      3.9     0.2    -      -       -      +
    194A  GLN*     3.2     8.4    -      -       -      +
    195A  TYR*     2.8    59.0    +      +       +      +
    197A  GLY      4.1     3.8    -      -       -      -
    198A  SER      2.8    27.0    +      -       -      +
    200A  THR*     3.7    12.1    -      -       +      -
    208A  VAL*     3.6    25.5    -      -       +      +
    209A  ILE*     1.3    72.3    -      -       -      +
    211A  THR*     1.3    59.7    +      -       -      +
    212A  VAL*     4.2     2.2    -      -       +      -
    268A  Y0R      3.4    27.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.9    19.1    -      -       +      -
     82A  LEU*     3.8    10.6    -      -       -      +
    142A  VAL      3.0     7.1    +      -       -      -
    143A  LEU*     3.5    14.8    -      -       +      +
    144A  ALA*     2.8    33.3    +      -       -      +
    192A  TYR*     3.5    37.0    -      -       +      -
    193A  PHE      3.3     3.4    -      -       -      -
    194A  GLN*     2.9    24.1    +      -       -      +
    209A  ILE*     4.6     2.3    +      -       -      +
    210A  TRP*     1.3    73.0    -      -       -      +
    212A  VAL*     1.3    59.9    +      -       -      +
    213A  PHE*     4.1     6.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ILE*     3.8    31.2    -      -       +      -
    107A  HIS*     4.1    24.2    -      -       +      +
    117A  GLU*     6.1     0.2    -      -       -      -
    144A  ALA*     3.3    20.0    -      -       +      +
    145A  ALA      6.1     0.2    -      -       -      -
    146A  PHE*     3.9    28.9    -      -       +      -
    192A  TYR*     3.3     2.2    -      -       -      -
    193A  PHE*     2.8    47.3    +      -       +      +
    195A  TYR*     4.6    10.5    -      -       +      -
    210A  TRP*     4.9     0.9    -      -       +      -
    211A  THR*     1.3    77.8    -      -       -      +
    213A  PHE*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.9    27.1    -      -       +      -
    143A  LEU*     4.1    25.8    -      -       +      -
    144A  ALA      3.0    27.7    +      -       -      +
    145A  ALA*     4.0     5.5    -      -       +      -
    146A  PHE*     4.5    11.4    +      -       -      -
    185A  LEU*     4.3    13.9    -      -       +      -
    186A  PRO*     3.8    23.1    -      -       +      -
    188A  ASP      3.7    15.0    -      -       -      +
    189A  PHE*     3.6    40.4    -      +       -      -
    191A  ARG      3.9     3.6    -      -       -      +
    192A  TYR*     4.0    11.2    -      +       +      -
    193A  PHE*     5.1     2.1    -      -       -      -
    211A  THR*     4.6     5.6    -      -       +      -
    212A  VAL*     1.3    83.1    -      -       -      +
    214A  ASN*     1.3    63.7    +      -       -      +
    215A  GLN      3.6    18.6    -      -       -      +
----------------------------------------------------------
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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