Contacts of the strand formed by residues 183 - 190 (chain D) in PDB entry 1FBA


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 VAL 183 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  LEU*     3.3    39.9    -      -       +      +
     18D  ILE*     3.6    23.3    -      -       +      -
     19D  ALA*     4.2    12.3    -      -       +      +
     22D  ILE*     4.8     1.1    -      -       +      -
    143D  ASP      3.1    11.7    +      -       -      +
    144D  PHE*     3.1    12.5    -      -       +      +
    145D  ALA      2.8    25.9    +      -       -      -
    182D  ILE*     1.3    69.4    -      -       -      +
    184D  PRO*     1.3    73.5    -      -       -      +
    185D  ILE      3.6     0.9    +      -       -      +
    225D  GLY      3.7    15.0    -      -       -      +
    226D  THR*     4.2     6.3    -      -       -      -
    227D  LEU*     4.5    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 184 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145D  ALA      4.2     0.4    -      -       -      +
    173D  TYR*     3.3    29.4    -      -       +      +
    174D  ALA*     3.7    35.0    -      -       +      +
    177D  CYS*     3.9     8.7    -      -       +      -
    178D  GLN*     3.8     8.3    -      -       +      -
    182D  ILE      3.2    10.5    -      -       -      +
    183D  VAL*     1.3    84.6    -      -       -      +
    185D  ILE*     1.3    63.7    +      -       -      +
    186D  VAL*     3.6     1.8    +      -       +      +
    225D  GLY      3.4    14.6    -      -       -      +
    226D  THR*     3.7    14.9    -      -       +      -
    227D  LEU      3.3    22.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 185 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  ILE*     3.7    26.9    -      -       +      -
     77D  ILE*     4.8     9.4    -      -       +      -
    144D  PHE*     3.6    31.2    -      -       +      -
    145D  ALA      3.0    21.0    +      -       -      +
    146D  LYS*     4.8     4.9    -      -       +      -
    147D  TRP      3.9     9.0    +      -       -      -
    173D  TYR*     3.0    17.4    +      -       -      -
    183D  VAL*     4.7     2.0    -      -       +      +
    184D  PRO*     1.3    71.9    -      -       -      +
    186D  VAL*     1.3    62.6    -      -       -      +
    187D  GLU*     3.5     4.9    +      -       +      +
    227D  LEU*     3.6    25.1    -      -       +      +
    228D  LEU      4.5     0.9    -      -       -      -
    229D  LYS*     3.5    39.5    -      -       +      +
    268D  THR*     4.2     6.7    -      -       -      +
    300D  SER*     5.4     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170D  LEU*     4.0    26.7    -      -       +      +
    173D  TYR*     4.5     3.8    -      -       +      -
    174D  ALA*     4.4    23.8    -      -       +      -
    184D  PRO      4.4     5.2    -      -       -      +
    185D  ILE*     1.3    70.9    -      -       -      +
    187D  GLU*     1.3    59.3    +      -       -      +
    188D  PRO*     3.3     9.5    -      -       +      +
    212D  VAL*     3.9    27.6    -      -       +      -
    213D  TYR*     5.3     2.2    -      -       -      +
    216D  LEU*     4.5    16.8    -      -       +      -
    226D  THR*     4.8     6.5    -      -       -      +
    227D  LEU      2.9    17.8    +      -       -      +
    228D  LEU*     3.5     8.5    -      -       +      +
    229D  LYS      2.8    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 187 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146D  LYS*     3.3    29.0    +      -       -      +
    147D  TRP      3.3    15.0    +      -       -      +
    148D  ARG*     3.6    31.4    +      -       +      +
    149D  CYS*     2.9    28.1    +      -       -      +
    170D  LEU*     4.0     6.3    -      -       -      +
    185D  ILE*     3.5     5.3    +      -       +      +
    186D  VAL*     1.3    72.5    -      -       -      +
    188D  PRO*     1.3    60.3    -      -       -      +
    189D  GLU*     4.3     3.3    -      -       +      +
    229D  LYS*     3.3    48.2    +      -       +      +
    270D  LEU*     4.0    14.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 188 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  CYS*     4.0     6.1    -      -       +      +
    151D  LEU*     5.1     5.8    -      -       +      -
    166D  ASN*     6.5     0.4    -      -       +      -
    170D  LEU*     3.8    17.9    -      -       +      -
    186D  VAL*     3.3    13.0    -      -       +      +
    187D  GLU*     1.3    82.8    -      -       -      +
    189D  GLU*     1.3    62.8    +      -       -      +
    190D  VAL*     3.4     8.1    +      -       -      +
    208D  VAL*     4.2    13.2    -      -       +      +
    209D  LEU*     4.0    25.6    -      -       +      +
    212D  VAL*     4.1    17.7    -      -       +      -
    228D  LEU*     3.8    10.5    -      -       +      -
    229D  LYS      3.6    10.3    -      -       -      +
    230D  PRO*     4.5     4.7    -      -       +      +
    231D  ASN*     3.5     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148D  ARG*     2.8    44.9    +      -       -      +
    149D  CYS      2.9    17.4    +      -       -      +
    150D  VAL*     3.5     3.9    -      -       -      +
    151D  LEU*     2.9    27.6    +      -       -      +
    187D  GLU*     3.5     6.6    +      -       +      +
    188D  PRO*     1.3    70.8    -      -       -      +
    190D  VAL*     1.3    72.1    +      -       -      +
    191D  LEU*     3.5    14.0    +      -       +      +
    192D  PRO*     4.3    10.9    -      -       -      +
    231D  ASN*     4.0     2.9    -      -       +      -
    270D  LEU*     3.7    44.0    -      -       +      +
    272D  GLY*     4.5     6.2    -      -       -      -
    361D  HIS*     5.1     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  LEU*     3.5    14.6    -      -       +      +
    153D  ILE*     3.6    38.4    -      -       +      -
    188D  PRO      4.4     3.8    -      -       -      +
    189D  GLU*     1.3    73.2    -      -       -      +
    191D  LEU*     1.3    69.0    +      -       -      +
    192D  PRO*     3.6     4.0    -      -       -      +
    201D  ALA*     5.3     1.6    -      -       +      +
    204D  VAL*     4.0    10.1    -      -       +      -
    205D  THR*     4.2    15.0    -      -       +      +
    208D  VAL*     4.2    28.9    -      -       +      -
    231D  ASN*     3.0    42.9    +      -       -      +
----------------------------------------------------------
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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