Contacts of the strand formed by residues 142 - 151 (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 CYS 142 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     3.8    33.7    -      -       -      -
    104D  LEU*     3.4    17.0    -      -       -      +
    105D  GLY      4.4     4.3    -      -       -      -
    106D  ILE*     3.8    36.6    -      -       +      -
    137D  TYR*     2.9    21.8    +      -       +      +
    138D  LYS*     3.4    12.7    +      -       -      +
    140D  ASP      5.0     0.2    -      -       -      -
    141D  GLY*     1.3    78.8    -      -       -      +
    143D  ASP*     1.3    66.6    +      -       -      +
    144D  PHE      4.5     2.0    -      -       -      +
    182D  ILE*     3.3    14.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 143 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ILE*     3.8    30.0    -      -       +      +
     98D  LYS*     4.7     9.7    +      -       -      -
    103D  ILE*     3.8    26.2    -      -       +      +
    104D  LEU      2.9     6.7    +      -       -      -
    138D  LYS*     2.9    31.1    +      -       -      +
    141D  GLY      4.3     8.3    -      -       -      +
    142D  CYS*     1.3    77.2    -      -       -      +
    144D  PHE*     1.3    62.4    +      -       -      +
    182D  ILE*     3.7    11.6    -      -       -      -
    183D  VAL*     3.1    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 144 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  ILE*     3.7    24.7    -      -       +      -
     29D  ILE*     4.4     9.9    -      -       +      -
     75D  GLY*     4.2     8.7    -      -       -      -
     76D  VAL      3.9    17.7    -      -       -      -
     77D  ILE*     3.8    16.4    -      -       +      -
    103D  ILE*     3.6    27.1    -      -       +      -
    104D  LEU      3.4    11.3    -      -       -      +
    105D  GLY*     3.2    30.3    -      -       -      -
    106D  ILE*     3.1    26.9    +      -       -      +
    142D  CYS*     3.7     0.7    -      -       -      +
    143D  ASP*     1.3    79.2    +      -       -      +
    145D  ALA*     1.3    65.2    +      -       -      +
    182D  ILE*     3.6     5.7    -      -       -      +
    183D  VAL*     3.1    17.9    -      -       +      +
    185D  ILE*     3.6    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 145 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106D  ILE*     3.3    14.1    -      -       +      +
    108D  VAL*     4.3    12.1    -      -       +      -
    134D  CYS*     5.5     0.4    -      -       -      -
    144D  PHE*     1.3    80.2    -      -       -      +
    146D  LYS*     1.3    61.3    +      -       -      +
    173D  TYR*     3.4     9.0    -      -       +      +
    177D  CYS*     3.8    20.2    -      -       -      -
    182D  ILE*     3.7    17.0    -      -       +      -
    183D  VAL      2.8     6.8    +      -       -      +
    185D  ILE*     3.0    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 146 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  ASP*     2.7    29.0    +      -       -      +
     77D  ILE*     3.9    35.4    -      -       +      +
    106D  ILE      3.0     7.1    +      -       -      +
    107D  LYS*     3.5    24.2    -      -       +      +
    108D  VAL*     3.0    27.0    +      -       -      +
    109D  ASP*     3.8     3.0    +      -       -      +
    145D  ALA*     1.3    76.3    -      -       -      +
    147D  TRP*     1.3    64.8    +      -       -      +
    148D  ARG*     4.0    21.0    -      -       -      +
    173D  TYR*     3.8     2.0    -      -       -      -
    185D  ILE*     4.4     8.3    -      -       +      +
    187D  GLU*     3.3    27.7    +      -       -      +
    229D  LYS*     5.1     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 147 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108D  VAL*     4.2     4.5    -      -       +      -
    109D  ASP*     3.6    23.6    -      -       +      -
    124D  THR*     3.4    41.3    -      -       +      +
    125D  GLN      3.6    14.4    -      -       -      -
    126D  GLY*     3.6    28.9    -      -       -      -
    127D  LEU*     3.5    26.7    -      -       +      -
    130D  LEU*     4.5     4.0    -      -       +      -
    146D  LYS*     1.3    76.6    -      -       -      +
    148D  ARG*     1.3    62.1    +      -       -      +
    149D  CYS*     3.7    12.4    -      -       -      -
    169D  VAL*     4.0    15.5    +      -       +      +
    170D  LEU*     3.5    20.4    -      -       +      +
    173D  TYR*     3.5    47.7    +      +       +      -
    185D  ILE      3.9     3.0    +      -       -      +
    187D  GLU*     3.3    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 148 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  ASP*     3.1    17.3    +      -       -      +
    112D  VAL*     4.6     6.6    -      -       -      +
    124D  THR*     2.8    29.7    +      -       -      +
    146D  LYS*     4.0    12.8    -      -       -      +
    147D  TRP*     1.3    75.0    -      -       -      +
    149D  CYS*     1.3    63.8    +      -       -      +
    150D  VAL*     3.6    18.0    -      -       +      +
    187D  GLU*     3.6    27.3    +      -       +      +
    189D  GLU*     2.8    31.8    +      -       -      +
    191D  LEU*     3.8     0.4    -      -       -      +
    361D  HIS*     2.4    56.8    +      -       -      +
    362D  ALA      5.4     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 149 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  THR*     3.6     7.9    -      -       -      -
    147D  TRP*     3.7    11.4    +      -       -      -
    148D  ARG*     1.3    75.3    -      -       -      +
    150D  VAL*     1.3    64.3    +      -       -      +
    151D  LEU*     5.5     1.3    -      -       +      -
    166D  ASN*     3.3    29.8    -      -       +      +
    169D  VAL*     3.6    19.3    -      -       -      -
    170D  LEU*     3.6    32.1    -      -       +      -
    187D  GLU      2.9    14.2    +      -       -      +
    188D  PRO*     4.5     3.8    -      -       +      -
    189D  GLU*     2.9    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 150 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112D  VAL*     4.3    14.8    -      -       +      +
    122D  VAL*     3.6    27.4    +      -       +      +
    124D  THR*     4.6     1.8    +      -       -      -
    148D  ARG*     3.6    37.5    -      -       +      +
    149D  CYS*     1.3    81.2    -      -       -      +
    151D  LEU*     1.3    71.7    +      -       -      +
    152D  LYS*     5.1     0.9    -      -       -      +
    162D  SER*     4.9     0.9    +      -       -      -
    166D  ASN*     4.3     2.6    +      -       -      -
    189D  GLU*     3.5     2.9    -      -       +      +
    191D  LEU*     3.4    34.3    -      -       +      -
    362D  ALA*     3.3    34.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 151 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  CYS*     5.5     2.2    -      -       +      -
    150D  VAL*     1.3    77.4    -      -       -      +
    152D  LYS*     1.3    62.2    +      -       -      +
    153D  ILE      4.3     0.3    +      -       -      -
    158D  PRO*     4.5    14.1    -      -       +      -
    162D  SER*     3.5    34.5    -      -       -      +
    163D  ILE*     4.8     4.0    -      -       +      +
    166D  ASN*     3.6    26.0    -      -       +      +
    188D  PRO*     5.1     6.7    -      -       +      -
    189D  GLU      2.9    11.5    +      -       -      +
    190D  VAL*     3.5    14.1    -      -       +      +
    191D  LEU*     2.9    31.8    +      -       -      +
    208D  VAL*     3.1    49.4    -      -       +      -
----------------------------------------------------------
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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