Contacts of the strand formed by residues 120 - 125 (chain X) in PDB entry 5FLX


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 PHE 120 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40X  PRO*     3.5    18.4    -      -       +      -
     41X  PHE*     3.3    37.2    -      +       -      -
     81X  ILE*     3.4    27.4    -      -       +      -
     82X  THR*     4.0    11.2    -      -       -      +
     83X  ALA*     4.5     2.0    -      -       -      -
     84X  PHE      3.1    19.5    +      -       -      -
    102X  VAL*     4.3    11.9    -      -       +      -
    103X  ALA*     3.1    17.5    -      -       -      +
    104X  GLY*     4.0     3.4    -      -       -      -
    105X  PHE*     3.1    17.4    -      -       -      -
    108X  LYS*     3.5    37.7    -      -       +      -
    118X  VAL*     3.2     4.7    -      -       -      +
    119X  ARG*     1.3    98.6    -      -       +      +
    121X  LYS*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 121 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    6471    U      5.1    18.7    +      -       -      +
    6481    A      6.2     0.7    -      -       -      -
     84X  PHE      3.9     2.0    -      -       -      -
     86X  PRO*     3.6    32.0    -      -       +      +
    102X  VAL*     3.2     4.4    -      -       -      -
    103X  ALA*     2.3    51.6    +      -       +      +
    104X  GLY      4.0     5.8    -      -       -      +
    105X  PHE*     3.5    33.0    -      -       +      -
    120X  PHE*     1.3    68.8    -      -       -      +
    122X  VAL*     1.3    76.1    +      -       -      +
    123X  VAL*     3.5     6.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70X  VAL*     5.2     3.1    -      -       +      -
     83X  ALA*     3.6    25.4    -      -       +      -
     84X  PHE      3.1    24.2    +      -       -      +
     85X  VAL*     4.2    12.1    -      -       +      -
     86X  PRO*     4.2     1.4    -      -       +      +
     94X  ILE*     4.5     7.4    -      -       +      -
    100X  VAL*     3.7    24.7    -      -       +      -
    101X  LEU      3.3     4.9    -      -       -      +
    102X  VAL*     4.3     1.1    -      -       -      -
    121X  LYS*     1.3    84.4    -      -       -      +
    123X  VAL*     1.3    62.2    +      -       -      +
    124X  LYS      4.2     7.2    -      -       -      +
    125X  VAL*     4.2     4.7    -      -       +      -
    130X  LEU*     3.2    39.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 123 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     281    U      4.7     9.9    -      -       -      +
     291    G      5.6     2.5    -      -       -      +
    6471    U      5.9     3.1    -      -       -      +
     46X  HIS*     4.8     6.3    -      -       +      +
    101X  LEU*     2.4    46.3    +      -       +      +
    102X  VAL      4.4     0.7    -      -       -      -
    103X  ALA*     4.4    17.3    -      -       +      -
    121X  LYS*     3.6    14.8    -      -       +      +
    122X  VAL*     1.3    79.2    -      -       -      +
    124X  LYS*     1.3    66.1    +      -       +      +
    129X  SER*     3.5     5.6    -      -       -      -
    130X  LEU*     2.9    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 124 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     281    U      2.6    55.5    +      -       -      -
     291    G      3.5    17.1    +      -       -      -
     48X  LYS*     6.3     2.7    -      -       -      -
     99X  GLU      4.3     0.2    -      -       -      -
    100X  VAL*     3.3     7.3    -      -       -      +
    101X  LEU*     2.9    52.0    +      -       +      +
    122X  VAL*     4.2     0.3    -      -       -      +
    123X  VAL*     1.3    83.1    -      -       +      +
    125X  VAL*     1.3    68.8    +      -       -      +
    126X  ALA      4.3     0.2    -      -       -      -
    127X  ASN*     4.7    24.5    +      -       -      +
    128X  VAL      3.3    10.3    -      -       -      +
    129X  SER*     4.0    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 125 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93X  PHE      4.4    11.2    -      -       -      +
     94X  ILE*     3.6    37.7    -      -       +      -
     98X  ASP*     4.5    13.9    -      -       +      +
     99X  GLU      3.2     9.2    -      -       -      +
    100X  VAL*     4.7     2.7    -      -       +      -
    122X  VAL*     4.2     4.0    -      -       +      -
    124X  LYS*     1.3    79.2    -      -       -      +
    126X  ALA*     1.3    77.9    +      -       +      +
    127X  ASN      3.3     0.2    -      -       -      -
    128X  VAL*     2.5    29.1    +      -       -      +
    130X  LEU*     3.7    22.2    -      -       +      -
    133X  LEU*     4.2    12.3    -      -       +      +
    140X  ARG*     5.0     2.1    -      -       -      +
----------------------------------------------------------
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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