Contacts of the strand formed by residues 192 - 198 (chain D) in PDB entry 5FL6


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 TYR 192 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  LEU*     3.4    34.5    -      -       +      +
     46D  ARG      2.6    30.9    +      -       -      -
     48D  LEU*     3.8    19.5    -      -       +      +
     82D  LEU      4.3     4.7    +      -       -      -
    189D  PHE      3.6    22.7    -      -       -      -
    190D  SER      3.8     3.8    -      -       -      -
    191D  ARG*     1.3    77.2    -      -       -      +
    193D  PHE*     1.3    69.7    +      -       -      +
    194D  GLN*     3.8    19.3    +      -       -      -
    211D  THR*     3.6    24.0    -      -       +      -
    212D  VAL      3.4    15.0    -      -       -      +
    213D  PHE*     4.2     5.4    -      +       +      -
    214D  ASN      4.1     2.9    -      -       -      +
    256D  ALA*     3.4     2.8    -      -       -      -
    257D  SER*     2.8    48.7    +      -       -      -
    258D  PHE*     3.6     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  ILE*     3.8    40.4    -      -       +      -
     36D  PRO*     4.1    31.0    -      -       +      -
     39D  ALA*     4.3     4.3    -      -       +      -
    109D  VAL*     5.5     6.5    -      -       +      -
    146D  PHE*     6.3     0.9    -      +       -      -
    192D  TYR*     1.3    77.9    -      -       -      +
    194D  GLN*     1.3    61.7    +      -       -      +
    195D  TYR*     5.7     1.3    -      -       +      -
    211D  THR*     3.3     5.0    -      -       -      -
    212D  VAL*     2.8    51.6    +      -       +      +
    213D  PHE      4.9     2.5    -      -       -      -
    214D  ASN*     4.3    18.2    -      -       -      -
    254D  ILE*     3.9    13.9    -      -       +      -
    255D  GLU      3.2    13.9    -      -       -      +
    256D  ALA*     4.1    12.8    -      -       +      -
    258D  PHE*     3.7    27.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 194 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  LEU*     3.5    31.4    -      -       +      +
     48D  LEU*     5.0     0.2    -      -       -      +
     82D  LEU*     4.1    11.3    -      -       -      +
     86D  ARG*     2.8    31.8    +      -       -      +
    192D  TYR*     3.8    17.0    +      -       +      -
    193D  PHE*     1.3    75.2    -      -       -      +
    195D  TYR*     1.3    64.2    -      -       -      +
    209D  ILE*     3.8    14.4    -      -       +      +
    210D  TRP      3.2    12.3    -      -       -      +
    211D  THR*     2.8    21.8    +      -       -      -
    253D  VAL      4.5     0.3    -      -       -      +
    254D  ILE*     4.3     0.9    -      -       -      -
    255D  GLU*     2.8    42.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  SER*     2.9    32.3    +      -       -      -
     32D  VAL*     3.6    29.5    +      -       +      +
     34D  ILE*     5.6     1.8    -      -       +      -
    107D  HIS*     2.6    34.4    +      +       -      -
    193D  PHE*     5.7     0.7    -      -       +      -
    194D  GLN*     1.3    79.8    -      -       -      +
    196D  GLU*     1.3    73.8    +      -       -      +
    197D  GLY*     4.1     0.9    -      -       -      -
    209D  ILE*     3.8     4.5    -      -       -      +
    210D  TRP*     2.9    52.3    +      +       +      +
    212D  VAL*     4.6     6.7    -      -       +      -
    249D  LEU*     4.9     4.0    -      -       +      -
    252D  ARG*     3.8    19.7    -      -       +      -
    253D  VAL      4.4     6.5    -      -       -      +
    254D  ILE*     4.1    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  PHE*     4.7     1.4    -      -       -      +
    137D  PRO*     4.8     8.2    -      -       -      +
    138D  GLY      5.2     3.1    +      -       -      -
    195D  TYR*     1.3    78.0    -      -       -      +
    197D  GLY*     1.3    61.6    +      -       -      +
    207D  GLY*     3.4    30.2    +      -       -      +
    208D  VAL      3.4    11.2    -      -       -      +
    209D  ILE*     3.9    20.3    -      -       +      +
    252D  ARG*     2.8    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 197 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  PHE*     3.5     7.2    -      -       -      -
     30D  SER*     3.4    13.7    -      -       -      -
    195D  TYR*     3.9     3.2    +      -       -      -
    196D  GLU*     1.3    74.6    -      -       -      +
    198D  SER*     1.3    61.0    +      -       -      -
    206D  GLN*     3.3     2.3    -      -       -      +
    207D  GLY      3.1    12.1    +      -       -      -
    208D  VAL      2.8    32.2    +      -       -      -
    210D  TRP*     4.1     1.4    -      -       -      -
    252D  ARG*     3.4    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 198 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  GLN*     3.4    34.3    +      -       -      -
     30D  SER*     2.9    32.1    +      -       -      -
    197D  GLY*     1.3    74.6    -      -       -      -
    199D  LEU*     1.3    81.3    +      -       -      +
    204D  CYS      3.5     1.8    -      -       -      -
    205D  ALA      3.1    13.7    -      -       -      -
    206D  GLN*     3.9     3.6    -      -       -      -
    208D  VAL*     3.7     7.6    -      -       -      -
    210D  TRP*     2.9    21.8    +      -       -      +
    244D  ARG*     3.8     0.3    +      -       -      -
----------------------------------------------------------
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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