Contacts of the strand formed by residues 166 - 173 (chain D) in PDB entry 5FLZ


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 ILE 166 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    605B  LEU*     4.9    18.6    -      -       +      -
    134D  GLU*     3.5    38.8    +      -       +      +
    135D  GLY*     3.2     5.6    -      -       -      -
    136D  PHE*     3.0    29.5    +      -       -      +
    165D  LYS*     1.4    75.8    -      -       -      +
    167D  LEU*     1.4    62.5    -      -       -      +
    168D  THR*     3.7    21.3    -      -       -      +
    199D  ASP*     3.9     5.8    -      -       +      +
    253D  SER      5.6     1.3    -      -       -      +
    256D  TYR*     3.8    45.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  PHE*     4.0    22.4    -      -       +      -
    155D  LEU*     3.6    41.7    -      -       +      +
    158D  LEU*     3.9    15.7    -      -       +      +
    159D  CYS*     4.1    12.3    -      -       +      +
    162D  TYR      4.6    12.8    -      -       -      +
    165D  LYS      3.7    17.5    -      -       -      +
    166D  ILE*     1.4    71.5    -      -       -      +
    168D  THR*     1.4    61.9    +      -       -      +
    197D  ASP      3.6    25.1    -      -       -      +
    198D  SER*     3.2     5.6    +      -       -      +
    199D  ASP*     3.1    39.4    +      -       -      +
    200D  ALA      3.4     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 168 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  PHE*     3.0    15.9    +      -       -      +
    137D  GLN*     3.3     8.9    -      -       -      -
    138D  LEU*     3.0    21.6    +      -       -      +
    155D  LEU*     5.3     1.6    -      -       -      +
    166D  ILE*     3.7     8.8    -      -       -      +
    167D  LEU*     1.4    73.6    -      -       -      +
    169D  THR*     1.4    69.8    +      -       -      +
    170D  TYR*     3.5    32.5    -      -       +      +
    198D  SER*     3.8     1.3    -      -       -      -
    200D  ALA*     3.4    17.5    -      -       +      +
    202D  VAL*     4.5     4.9    -      -       +      -
    256D  TYR*     3.5    26.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  LEU*     3.1    28.7    +      -       -      +
    140D  HIS*     3.2    26.8    +      -       -      +
    155D  LEU*     5.1     3.8    -      -       +      -
    168D  THR*     1.4    80.2    -      -       -      +
    170D  TYR*     1.3    58.8    +      -       -      +
    171D  SER*     3.3    16.4    -      -       -      +
    194D  LEU*     4.9     9.4    -      -       +      -
    198D  SER*     3.6    15.3    -      -       -      +
    200D  ALA      3.0     7.1    +      -       -      -
    201D  THR*     3.3    19.9    -      -       -      +
    202D  VAL      2.9    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 170 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137D  GLN*     3.4    36.2    +      -       +      -
    138D  LEU      2.8     8.1    +      -       -      +
    139D  LEU*     3.6    21.2    -      -       +      -
    140D  HIS*     3.2    27.2    +      -       -      +
    168D  THR*     3.5    22.5    -      -       +      +
    169D  THR*     1.3    73.4    -      -       -      +
    171D  SER*     1.3    59.0    +      -       -      +
    172D  VAL*     5.8     0.4    -      -       -      -
    202D  VAL*     3.5    26.2    -      -       +      +
    204D  PHE*     3.7    32.3    -      +       +      -
    235D  ILE*     3.8    23.3    -      -       +      -
    238D  VAL*     3.8    33.7    -      -       +      +
    239D  THR*     5.8     1.4    -      -       +      +
    252D  MET*     5.5     4.5    -      -       -      +
    377D  LEU*     5.5     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 171 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  HIS*     3.0    28.2    +      -       -      -
    142D  VAL*     4.3     6.3    -      -       -      -
    169D  THR*     3.3    19.5    -      -       -      +
    170D  TYR*     1.3    71.6    -      -       -      +
    172D  VAL*     1.4    62.5    +      -       -      +
    173D  PHE*     3.6    20.6    +      -       -      -
    194D  LEU*     4.2     5.6    -      -       -      +
    201D  THR*     3.3    11.9    +      -       -      -
    202D  VAL      2.8    11.9    +      -       -      +
    203D  VAL*     3.6     2.1    -      -       -      -
    204D  PHE*     2.9    25.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13D  CYS*     5.8     6.1    -      -       +      -
    140D  HIS      3.1    17.1    +      -       -      +
    141D  SER*     4.0    19.2    -      -       -      +
    142D  VAL*     3.0    28.2    +      -       -      +
    170D  TYR      5.6     0.4    -      -       -      +
    171D  SER*     1.4    71.1    -      -       -      +
    173D  PHE*     1.4    67.8    -      -       -      +
    174D  PRO*     5.6     0.2    -      -       +      -
    204D  PHE*     3.3    21.1    -      -       +      +
    206D  ASN*     3.5    31.0    -      -       +      +
    209D  LEU*     5.1     2.7    -      -       +      -
    231D  ILE*     4.1    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 173 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  VAL*     4.8     9.2    -      -       +      -
    171D  SER*     3.8    22.7    -      -       -      -
    172D  VAL*     1.4    78.3    -      -       -      +
    174D  PRO*     1.4    69.1    -      -       +      +
    176D  ARG*     3.7    28.3    -      -       -      +
    187D  THR*     4.5    15.9    -      -       +      -
    191D  LEU*     4.1    20.6    -      -       +      -
    194D  LEU*     5.2     6.1    -      -       +      -
    201D  THR*     5.1     1.6    -      -       -      -
    203D  VAL*     3.3    44.0    -      -       +      -
    204D  PHE      2.9     6.6    +      -       -      +
    205D  ASP*     3.9     5.4    -      -       -      +
    206D  ASN*     3.0    29.6    +      -       -      +
    267D  PHE*     3.9    23.1    -      +       -      -
    386D  VAL*     4.4    13.2    -      -       +      -
----------------------------------------------------------
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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