Contacts of the strand formed by residues 113 - 122 (chain F) in PDB entry 3F5O


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 LEU 113 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84F  VAL*     4.6     1.6    -      -       +      -
    109F  GLN*     3.7     0.5    -      -       -      -
    110F  GLY*     2.8    32.6    +      -       -      +
    111F  LYS      3.8     0.2    -      -       -      -
    112F  THR*     1.3    93.2    -      -       -      +
    114F  ALA*     1.3    57.2    +      -       -      +
    115F  PHE*     4.0    18.6    -      -       +      -
    135F  THR*     4.2    12.3    -      -       +      -
    136F  LYS      3.3    15.5    -      -       -      +
    137F  HIS*     4.0    13.5    -      -       +      +
    138F  LEU*     4.5     3.4    -      -       -      -
     84H  VAL*     3.8    36.1    -      -       +      -
    113H  LEU*     4.4    17.7    -      -       +      -
    137H  HIS*     4.3     9.4    -      -       -      +
    150H  COA      3.0    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  LEU*     3.6    37.2    -      -       +      -
    108F  LYS      3.5     5.4    -      -       -      +
    109F  GLN*     3.6    14.1    -      -       +      -
    113F  LEU*     1.3    74.1    -      -       -      +
    115F  PHE*     1.3    64.3    -      -       -      +
    116F  THR*     5.0     1.1    -      -       -      -
    134F  HIS      3.9     0.9    -      -       -      +
    135F  THR*     3.4     4.7    -      -       -      +
    136F  LYS*     2.9    35.0    +      -       +      +
    138F  LEU*     4.3    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 115 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106F  VAL*     3.7     1.9    -      -       -      +
    107F  LEU*     2.8    32.7    +      -       +      -
    108F  LYS*     2.8    31.4    +      -       +      +
    110F  GLY      5.3     0.2    -      -       -      -
    113F  LEU*     4.0    29.2    -      -       +      -
    114F  ALA*     1.3    74.4    -      -       -      +
    116F  THR*     1.3    61.4    +      -       -      +
    133F  ARG*     6.0     0.7    -      -       +      -
    134F  HIS      3.7     3.4    -      -       -      -
    135F  THR*     3.5    15.3    -      -       +      -
     89G  THR*     3.2    33.7    -      -       +      -
     90G  TYR      3.9     9.6    -      -       -      -
     91G  MET*     3.5    31.9    -      -       +      -
     84H  VAL*     3.7    24.9    -      -       +      -
    150H  COA      3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 116 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  SER*     3.2    35.5    -      -       -      +
     71F  ALA*     5.3     0.2    -      -       +      -
     72F  LEU*     4.0    32.5    -      -       +      -
    105F  HIS      3.2    13.2    -      -       -      +
    106F  VAL*     4.2     8.7    -      -       +      -
    107F  LEU*     4.2     3.3    -      -       -      +
    114F  ALA      5.0     0.4    -      -       -      -
    115F  PHE*     1.3    81.0    -      -       -      +
    117F  SER*     1.3    60.1    +      -       -      +
    118F  VAL*     5.2     0.2    -      -       -      -
    133F  ARG*     3.1    10.2    -      -       -      +
    134F  HIS*     2.9    47.4    +      -       -      +
    136F  LYS*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 117 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103F  THR      3.9     0.2    -      -       -      +
    104F  ALA*     3.3     2.9    -      -       -      +
    105F  HIS*     2.8    56.7    +      -       -      -
    107F  LEU*     4.0    17.0    -      -       -      +
    116F  THR*     1.3    74.5    -      -       -      +
    118F  VAL*     1.3    65.6    +      -       -      +
    119F  ASP*     4.7     1.7    +      -       -      -
    131F  GLN*     4.4    13.0    +      -       -      +
    132F  GLY      3.4    11.2    +      -       -      -
    133F  ARG*     4.4     0.6    -      -       -      +
    131G  GLN*     3.9    13.5    +      -       -      -
    133G  ARG*     5.5     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63F  LEU      5.0     0.2    -      -       -      +
     64F  VAL*     3.7    45.3    -      -       +      +
     67F  ILE*     5.1     0.2    -      -       +      -
     68F  SER*     3.7    16.8    -      -       -      +
    102F  ILE*     3.5    32.1    -      -       +      -
    103F  THR      3.3     9.2    -      -       -      +
    104F  ALA*     3.8     9.9    -      -       +      -
    116F  THR*     5.0     0.9    -      -       -      +
    117F  SER*     1.3    82.1    +      -       -      +
    119F  ASP*     1.3    68.3    +      -       -      +
    120F  LEU*     4.1    10.6    -      -       +      +
    130F  ALA      4.2     0.2    -      -       -      +
    131F  GLN*     3.3     4.9    -      -       -      +
    132F  GLY      2.8    32.2    +      -       -      +
    134F  HIS*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  VAL      3.6     1.4    -      -       -      +
    102F  ILE*     3.5     2.6    -      -       -      -
    103F  THR*     2.9    43.0    +      -       -      +
    105F  HIS*     6.5     0.9    -      -       -      -
    117F  SER*     4.7     2.8    +      -       -      -
    118F  VAL*     1.3    73.8    -      -       -      +
    120F  LEU*     1.3    63.2    +      -       -      +
    121F  THR*     4.8     5.9    -      -       -      +
    128F  LEU*     3.9    19.3    -      -       +      +
    130F  ALA      3.6     3.6    -      -       -      -
    131F  GLN*     2.9    34.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55F  LEU*     4.1     9.6    -      -       +      -
     60F  THR*     4.0    24.7    -      -       +      +
     63F  LEU*     4.1    14.4    -      -       +      -
     64F  VAL*     4.0    26.7    -      -       +      -
    100F  ILE*     4.0    24.7    -      -       +      -
    101F  VAL      3.2     4.9    -      -       -      +
    102F  ILE*     3.9    14.1    -      -       +      -
    118F  VAL*     4.1     9.2    -      -       +      +
    119F  ASP*     1.3    75.3    -      -       -      +
    121F  THR*     1.3    58.7    +      -       -      +
    128F  LEU*     3.5     4.7    -      -       -      +
    129F  ILE*     2.7    44.5    +      -       +      -
    130F  ALA*     2.9    22.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 121 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  ILE*     3.3     5.7    -      -       -      +
    101F  VAL*     2.8    59.9    +      -       +      +
    103F  THR*     5.4     2.5    -      -       -      +
    119F  ASP*     4.8     6.7    -      -       -      +
    120F  LEU*     1.3    77.5    +      -       -      +
    122F  ASN*     1.3    64.3    +      -       -      +
    123F  LYS*     5.3     0.2    -      -       -      -
    126F  GLY*     3.5    20.1    +      -       -      +
    127F  LYS      3.3     7.2    +      -       -      -
    128F  LEU*     4.1    12.3    -      -       -      +
    129F  ILE*     3.6     4.7    -      -       -      +
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Residues in contact with ASN 122 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98F  GLU*     3.5    37.6    +      -       -      +
     99F  ASP      3.8     6.4    +      -       -      +
    100F  ILE*     6.1     0.2    -      -       -      +
    121F  THR*     1.3    73.6    -      -       -      +
    123F  LYS*     1.3    58.2    +      -       -      +
    124F  ALA*     2.7    35.5    +      -       -      +
    125F  THR*     3.0    31.5    +      -       -      +
    126F  GLY*     2.8    31.0    +      -       -      -
    127F  LYS*     2.8    15.6    +      -       +      +
    129F  ILE*     3.7    13.3    -      -       +      +
----------------------------------------------------------
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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