Contacts of the strand formed by residues 173 - 182 (chain D) in PDB entry 1FYT


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 173 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119D  GLN*     6.5     1.6    -      -       +      -
    120D  ASN*     5.4    19.3    -      -       +      -
    143D  ASP*     3.8    17.5    -      -       -      -
    166D  LEU      4.0     0.2    -      -       -      +
    167D  ASP*     3.7     0.9    -      -       -      +
    168D  MET*     2.7    55.2    +      -       +      +
    171D  MET*     4.4     8.7    -      -       +      +
    172D  ASP*     1.3    78.9    -      -       -      +
    174D  LYS*     1.3    83.4    +      -       -      +
    175D  SER*     3.8     3.6    -      -       -      -
    143E  LYS*     3.3    39.9    -      -       -      +
    198E  ARG*     3.1    26.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 174 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  GLU*     3.2    24.7    -      -       -      +
     82D  MET*     3.8    23.3    -      -       +      +
    116D  PRO*     3.8    29.8    -      -       +      -
    117D  ASN*     4.9     3.1    -      -       -      +
    118D  ILE*     3.7    15.9    -      -       +      +
    165D  VAL*     4.6     3.1    -      -       +      -
    166D  LEU      3.4     8.3    -      -       -      +
    167D  ASP*     3.8    25.9    +      -       +      +
    172D  ASP*     4.4    20.7    +      -       -      +
    173D  PHE*     1.3    95.1    -      -       -      +
    175D  SER*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 175 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118D  ILE*     4.2     5.8    -      -       -      -
    142D  THR*     4.3     4.9    +      -       -      -
    143D  ASP*     3.2    27.8    -      -       -      +
    164D  THR      3.7     0.3    -      -       -      +
    165D  VAL*     3.3     5.7    -      -       -      +
    166D  LEU*     3.0    55.3    +      -       -      +
    173D  PHE*     3.8     2.0    -      -       -      -
    174D  LYS*     1.3    78.3    -      -       -      +
    176D  ASN*     1.3    65.7    +      -       -      +
    177D  SER*     5.3     1.3    +      -       -      -
    198E  ARG*     3.3    15.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 176 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  PRO*     4.7     2.6    -      -       -      +
    118D  ILE*     3.7    20.5    -      -       -      +
    142D  THR*     3.1     6.1    +      -       -      -
    143D  ASP*     3.0    27.5    +      -       -      +
    144D  PHE*     3.3    46.4    +      -       +      +
    145D  ASP      3.8     2.4    +      -       -      -
    146D  SER*     3.7    22.7    +      -       -      +
    163D  LYS*     5.3     5.5    -      -       +      +
    164D  THR      3.3     5.3    -      -       -      +
    165D  VAL*     3.2    29.1    -      -       -      +
    175D  SER*     1.3    76.3    -      -       -      +
    177D  SER*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 177 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  LEU*     4.0    11.2    -      -       -      -
    141D  PHE      3.1    12.6    -      -       -      -
    142D  THR*     4.0     7.2    -      -       -      -
    144D  PHE*     3.9     4.5    -      -       -      -
    163D  LYS*     3.0     6.1    -      -       -      -
    164D  THR      2.9    33.6    +      -       -      -
    166D  LEU*     5.1     6.8    -      -       -      +
    175D  SER*     5.3     1.3    +      -       -      -
    176D  ASN*     1.3    77.5    -      -       -      +
    178D  ALA*     1.3    61.6    +      -       -      +
    145E  THR*     6.2     0.2    -      -       -      -
    174E  SER*     4.1     2.4    +      -       -      -
    196E  ARG*     2.9    40.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 178 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  LEU*     3.9     1.0    -      -       -      +
    141D  PHE*     2.9    31.9    +      -       +      +
    150D  VAL*     3.8    39.7    -      -       +      -
    161D  THR*     3.7    10.8    -      -       -      +
    162D  ASP      4.0     8.1    -      -       -      +
    163D  LYS*     4.3     0.2    -      -       -      -
    177D  SER*     1.3    77.2    -      -       -      +
    179D  VAL*     1.3    67.2    +      -       -      +
    193D  PHE*     3.7    11.2    -      -       +      -
    196E  ARG*     4.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 179 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  VAL*     4.6     6.5    -      -       +      -
    139D  CYS      3.6     7.2    -      -       -      +
    140D  LEU*     3.8    17.7    -      -       +      -
    159D  TYR      3.7     0.3    -      -       -      +
    160D  ILE*     3.3     2.6    -      -       -      +
    161D  THR*     2.8    48.7    +      -       +      +
    178D  ALA*     1.3    79.3    -      -       -      +
    180D  ALA*     1.3    68.9    +      -       -      +
    181D  TRP*     3.4    23.8    -      -       +      -
    193D  PHE*     4.1     1.8    -      -       -      -
    147E  VAL*     4.2    26.7    -      -       +      -
    149E  LEU*     5.1     0.4    -      -       +      -
    194E  SER*     4.2     3.1    -      -       -      +
    196E  ARG*     3.8    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 180 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  VAL*     3.3     3.1    -      -       -      +
    139D  CYS*     2.9    30.6    +      -       +      +
    158D  VAL*     5.0     0.2    -      -       +      -
    159D  TYR      3.0     9.6    -      -       -      +
    160D  ILE*     4.0    14.8    -      -       +      -
    179D  VAL*     1.3    75.5    -      -       -      +
    181D  TRP*     1.3    66.3    +      -       -      +
    187D  PHE*     4.3     4.5    -      -       +      -
    192D  ALA*     4.2    15.9    -      -       +      -
    193D  PHE*     3.4    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 181 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  LYS*     3.3    36.8    -      -       +      +
    137D  SER      3.0    20.0    -      -       -      +
    138D  VAL*     3.7     9.9    -      -       +      -
    158D  VAL*     3.7     0.9    -      -       -      -
    159D  TYR*     2.9    70.0    +      +       +      +
    161D  THR*     3.4    32.8    -      -       +      -
    179D  VAL*     3.4    22.7    -      -       +      -
    180D  ALA*     1.3    78.9    -      -       -      +
    182D  SER*     1.3    62.7    +      -       -      +
    187D  PHE*     4.0     8.3    -      -       -      -
    149E  LEU*     3.5    34.0    -      -       +      +
    151E  THR*     4.9     2.6    -      -       +      +
    176E  ASP*     5.5     0.2    -      -       -      -
    180E  LEU*     4.6     7.0    -      -       +      -
    192E  SER*     3.9    26.8    +      -       -      -
    193E  LEU*     5.1     0.4    -      -       -      -
    194E  SER*     4.1     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 182 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  LYS*     3.2     5.6    -      -       -      -
    137D  SER*     3.0    30.8    +      -       -      +
    157D  ASP      2.9    22.8    +      -       -      -
    158D  VAL*     4.0     3.7    -      -       -      +
    159D  TYR*     5.1     1.3    -      -       -      -
    181D  TRP*     1.3    83.2    -      -       -      +
    183D  ASN*     1.3    69.5    +      -       -      +
    184D  LYS*     2.9    24.7    +      -       -      +
    187D  PHE*     3.7    30.5    -      -       -      -
----------------------------------------------------------
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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