Contacts of the strand formed by residues 120 - 131 (chain C) 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 GLN 120 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     101    G      4.4    13.3    +      -       -      +
    113C  GLN*     3.3    34.3    +      -       +      +
    114C  LYS      3.3     9.6    -      -       -      +
    115C  GLN*     4.2    15.8    +      -       -      +
    119C  GLY*     1.3    74.6    -      -       -      +
    121C  ARG*     1.3    61.4    +      -       -      +
    122C  THR*     5.1     0.7    -      -       -      +
    349z    C      5.3     9.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   13471    U      5.3     5.7    +      -       -      -
   13481    G      3.4    28.7    +      -       -      +
   14851    U      5.2     3.6    +      -       -      -
   14861    A      4.3    28.1    +      -       -      -
    113C  GLN*     3.1     7.0    +      -       -      +
    114C  LYS*     2.2    55.1    +      -       +      +
    116C  THR*     4.6     6.0    +      -       -      +
    119C  GLY      4.2     1.0    -      -       -      -
    120C  GLN*     1.3    75.8    -      -       -      +
    122C  THR*     1.3    77.6    +      -       -      +
    145C  LYS*     6.1     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111C  PRO*     4.3     3.6    -      -       -      +
    112C  VAL      3.7     0.4    -      -       -      -
    113C  GLN*     2.8    33.5    +      -       -      +
    114C  LYS*     5.6     0.7    -      -       -      -
    120C  GLN      5.1     0.7    -      -       -      +
    121C  ARG*     1.3    91.3    -      -       -      +
    123C  ARG*     1.3    75.7    +      -       -      +
    124C  PHE*     4.1    19.8    -      -       +      -
    145C  LYS*     4.0    14.7    -      -       -      +
    349z    C      4.8    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   13481    G      4.0    26.6    +      -       -      -
   13491    G      3.7    23.7    +      -       -      -
   13571    A      5.6     2.0    -      -       -      -
   13581    U      6.0     5.7    -      -       -      -
   13591    U      5.1     8.2    +      -       -      -
   13611    G      6.1     1.2    -      -       -      +
    111C  PRO*     3.5     3.3    -      -       -      +
    112C  VAL*     2.6    63.4    +      -       +      +
    113C  GLN      4.5     7.3    +      -       -      +
    114C  LYS*     5.0    12.9    -      -       -      +
    122C  THR*     1.3    77.2    +      -       -      +
    124C  PHE*     1.3    63.0    +      -       -      +
    142C  LYS*     5.4     4.0    -      -       -      +
    143C  CYS*     3.8    42.8    +      -       +      -
    144C  SER      3.3    15.3    -      -       -      +
    145C  LYS*     3.7     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  ILE*     4.0    17.9    -      -       +      -
    110C  MET      3.8     2.0    -      -       -      -
    111C  PRO*     4.0    23.3    -      -       +      -
    122C  THR*     4.1    18.2    -      -       +      -
    123C  ARG*     1.3    76.5    -      -       -      +
    125C  LYS*     1.3    59.5    +      -       -      +
    126C  ALA      4.1     0.2    -      -       -      -
    143C  CYS*     3.2     2.4    -      -       -      -
    144C  SER      2.4    53.4    +      -       -      +
    145C  LYS      4.0    17.0    -      -       -      -
    146C  GLU      4.8     3.8    -      -       -      +
    147C  VAL*     3.5    35.2    -      -       +      -
    150C  ALA*     3.9     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   13551    C      5.8     0.4    -      -       -      -
   13561    G      3.9    41.7    +      -       -      -
    108C  LYS      3.9     0.7    -      -       -      +
    109C  ILE*     3.2     3.4    -      -       -      -
    110C  MET*     2.7    65.9    +      -       +      +
    112C  VAL*     4.2    15.5    -      -       +      -
    123C  ARG      4.2     0.2    +      -       -      -
    124C  PHE*     1.3    73.3    -      -       -      +
    126C  ALA*     1.3    60.0    +      -       -      +
    127C  PHE*     3.6    29.1    -      -       +      -
    141C  VAL*     3.3    22.4    -      -       +      +
    142C  LYS      3.8     6.9    -      -       -      +
    143C  CYS*     4.0    19.7    -      -       +      +
    234C  GLY*     5.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  VAL*     5.0     0.7    -      -       +      -
    108C  LYS      3.6     3.8    -      -       -      -
    109C  ILE*     3.7    23.8    -      -       +      -
    124C  PHE      4.1     0.6    +      -       -      -
    125C  LYS*     1.3    73.8    -      -       -      +
    127C  PHE*     1.3    74.1    +      -       -      +
    128C  VAL*     4.2     5.4    -      -       +      -
    141C  VAL*     4.0     1.9    -      -       -      -
    142C  LYS      3.2    26.2    +      -       -      +
    150C  ALA*     4.2    28.9    -      -       +      +
    151C  ILE*     4.7     3.4    -      -       +      +
    154C  ALA*     4.2     7.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  VAL*     3.3     8.0    -      -       -      +
    107C  LEU*     2.9    53.5    +      -       +      -
    108C  LYS*     3.1    11.6    +      -       +      +
    110C  MET*     3.6    22.7    -      -       +      -
    125C  LYS*     3.6    25.6    -      -       +      -
    126C  ALA*     1.3    79.7    -      -       -      +
    128C  VAL*     1.3    61.6    +      -       -      +
    129C  ALA      4.4     0.2    -      -       -      -
    139C  LEU*     6.2     3.8    -      -       +      -
    140C  GLY      4.2     3.6    -      -       -      +
    141C  VAL*     3.4    32.3    -      -       +      -
    233C  LEU*     3.5    27.8    -      -       +      -
    234C  GLY*     3.5    37.9    -      -       -      -
    237C  ALA*     5.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  ASP*     4.1    15.3    -      -       +      +
    105C  GLU      4.6     4.9    -      -       -      +
    106C  VAL*     4.2    18.4    -      -       +      -
    107C  LEU*     5.5     0.7    -      -       -      -
    126C  ALA*     4.2     2.6    -      -       +      -
    127C  PHE*     1.3    80.8    -      -       -      +
    129C  ALA*     1.3    64.0    +      -       -      +
    130C  ILE*     4.2     9.6    -      -       +      -
    139C  LEU*     3.9     2.2    -      -       -      +
    140C  GLY*     3.2    31.4    +      -       -      +
    151C  ILE*     4.5    17.3    -      -       +      +
    154C  ALA*     3.7    25.7    -      -       +      +
    155C  ILE*     3.7    25.8    -      -       +      -
    158C  ALA*     3.9     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  ASP*     3.3    19.8    -      -       -      +
    105C  GLU      3.9    12.1    +      -       -      +
    107C  LEU*     4.9    11.6    -      -       +      +
    128C  VAL*     1.3    75.1    -      -       -      +
    130C  ILE*     1.3    63.1    +      -       -      +
    138C  GLY      3.4    11.9    -      -       -      +
    139C  LEU*     4.1    21.1    -      -       +      -
    213C  LEU*     4.2    17.7    -      -       +      -
    216C  MET*     4.1    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  ILE*     4.4     7.4    -      -       +      -
    101C  SER*     4.1    12.8    -      -       -      +
    102C  LEU*     5.4     0.9    -      -       -      +
    103C  LYS      4.0     4.7    -      -       -      -
    104C  ASP*     3.5    26.5    -      -       +      +
    128C  VAL*     4.2     5.6    -      -       +      -
    129C  ALA*     1.3    78.8    -      -       -      +
    131C  GLY*     1.3    59.7    +      -       -      +
    137C  VAL*     3.3     5.7    -      -       -      +
    138C  GLY      2.8    32.4    +      -       -      +
    155C  ILE*     5.1     7.4    -      -       +      -
    158C  ALA*     3.3    45.8    -      -       +      +
    159C  LYS*     3.5    33.7    -      -       +      +
    162C  ILE*     5.4     4.3    -      -       +      -
    213C  LEU*     5.7     0.3    -      -       -      +
    216C  MET*     5.0     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  SER*     3.8    16.4    +      -       -      +
    103C  LYS*     3.3    24.4    +      -       -      +
    130C  ILE*     1.3    80.9    -      -       -      +
    132C  ASP*     1.3    62.6    +      -       -      -
    133C  TYR*     5.5     1.9    -      -       -      -
    136C  HIS      3.1    13.9    -      -       -      -
    137C  VAL*     3.7     8.5    -      -       -      -
    162C  ILE*     5.1     2.0    -      -       -      -
    216C  MET*     4.6     8.5    -      -       -      +
----------------------------------------------------------
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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