Contacts of the strand formed by residues 89 - 100 (chain D) in PDB entry 4FPR


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 LEU 89 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  MET*     3.9    34.5    -      -       +      +
    136A  LYS*     3.9     6.8    -      -       +      +
     30D  GLU*     3.8    20.4    -      -       +      +
     31D  ILE      3.7     3.4    -      -       -      -
     32D  ARG*     3.4    29.2    -      -       +      +
     76D  CYS*     3.5     1.2    -      -       -      -
     77D  ALA*     2.9    35.8    +      -       +      +
     87D  VAL*     3.6    21.7    +      -       +      +
     88D  VAL*     1.3    72.9    -      -       -      +
     90D  CYS*     1.3    62.4    +      -       -      +
    123D  THR*     4.1    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  GLU*     3.4     6.7    -      -       -      +
     31D  ILE*     2.7    49.3    +      -       +      +
     33D  TYR*     3.8    25.1    -      -       +      +
     39D  PRO*     4.9     0.7    -      -       -      -
     44D  ALA*     4.2     2.9    -      -       +      -
     74D  VAL*     4.0    10.8    -      -       +      -
     75D  GLN      3.3     4.0    -      -       -      +
     76D  CYS*     2.0    47.6    -      -       -      -
     88D  VAL*     3.9     7.2    -      -       -      -
     89D  LEU*     1.3    76.9    -      -       -      +
     91D  THR*     1.3    63.1    +      -       -      +
     92D  CYS*     3.7     1.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  LYS*     2.7    34.2    +      -       -      +
     28D  SER*     4.2    14.4    -      -       -      +
     29D  GLY      3.6     8.7    -      -       -      +
     30D  GLU*     4.8     4.0    +      -       -      +
     74D  VAL*     3.2     8.4    -      -       -      -
     75D  GLN*     2.8    35.7    +      -       -      +
     90D  CYS*     1.3    72.4    -      -       -      +
     92D  CYS*     1.3    63.4    +      -       -      +
     93D  LYS*     3.8     5.0    +      -       +      +
    122D  GLU*     3.9    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  ILE      3.7     2.1    -      -       -      +
     28D  SER*     3.3     3.3    -      -       -      -
     29D  GLY      2.8    37.8    +      -       -      +
     31D  ILE*     4.3    13.9    -      -       +      -
     48D  CYS*     2.1    62.1    -      -       +      -
     51D  VAL*     3.9    10.3    -      -       -      -
     73D  LYS      3.8     0.2    -      -       -      -
     74D  VAL*     4.6     0.9    -      -       +      -
     90D  CYS*     3.7     1.2    +      -       +      +
     91D  THR*     1.3    72.9    -      -       -      +
     93D  LYS*     1.3    56.6    +      -       -      +
     94D  ILE*     3.1    24.8    -      -       -      +
    119D  PHE*     3.9     5.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  SER*     3.6    31.4    +      -       -      -
     27D  ILE      3.6     4.5    -      -       -      +
     28D  SER*     3.6    20.4    -      -       -      +
     71D  THR      3.8     1.0    -      -       -      +
     72D  ALA*     3.5     1.4    -      -       -      -
     73D  LYS*     2.9    58.9    +      -       +      +
     91D  THR*     3.8     6.5    +      -       +      +
     92D  CYS*     1.3    71.9    -      -       -      +
     94D  ILE*     1.3    64.4    +      -       -      +
     95D  THR*     4.4     8.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  SER*     3.2     3.3    -      -       -      -
     27D  ILE      2.9    39.1    +      -       -      +
     48D  CYS*     3.9     0.2    -      -       -      -
     51D  VAL*     3.4    20.2    -      -       +      -
     52D  THR*     3.7    23.8    -      -       -      +
     55D  LEU*     4.0    20.0    -      -       +      -
     70D  MET*     4.0    29.2    -      -       +      -
     71D  THR      3.4     5.2    -      -       -      +
     72D  ALA*     4.4     2.9    -      -       +      -
     92D  CYS*     3.1    42.2    -      -       -      +
     93D  LYS*     1.3    74.5    -      -       -      +
     95D  THR*     1.3    64.0    +      -       -      +
    119D  PHE*     4.2     4.9    -      -       +      -
    131D  TRP*     3.9     3.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  GLU*     3.7    23.6    -      -       +      +
     25D  ALA      3.4    10.8    -      -       -      +
     26D  SER*     3.1    14.1    +      -       -      +
     70D  MET*     3.1     6.2    -      -       -      -
     71D  THR*     2.8    44.9    +      -       -      -
     73D  LYS*     5.5     7.1    +      -       -      +
     93D  LYS*     4.4    10.6    +      -       -      +
     94D  ILE*     1.3    73.5    -      -       -      +
     96D  ALA*     1.3    60.5    +      -       -      +
     97D  HIS*     3.4    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  ARG      4.1     0.7    -      -       -      +
     24D  GLU*     3.4     4.5    -      -       -      +
     25D  ALA      2.8    34.2    +      -       -      +
     66D  TRP      3.5    23.3    -      -       -      +
     69D  ASP      3.6     5.2    -      -       -      -
     70D  MET*     3.8     8.5    -      -       +      -
     95D  THR*     1.3    72.0    -      -       -      +
     97D  HIS*     1.3    60.9    +      -       -      +
     98D  ARG      3.6     0.8    +      -       -      -
     99D  TYR*     4.2    12.6    -      -       +      +
    131D  TRP*     3.6    29.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  LYS*     3.5    46.1    -      -       +      +
     23D  ARG      3.4     5.0    -      -       -      +
     24D  GLU*     4.3    11.1    +      -       -      +
     66D  TRP      5.1     0.2    +      -       -      -
     69D  ASP*     2.8    39.9    +      -       +      +
     71D  THR*     2.6    31.4    +      -       +      +
     95D  THR*     3.4    31.6    +      -       +      +
     96D  ALA*     1.3    74.1    -      -       -      +
     98D  ARG*     1.3    65.6    +      -       +      +
    140D  ARG*     2.7    36.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  CYS*     5.6     2.0    -      -       -      -
     22D  CYS*     3.5    14.5    -      -       -      -
     23D  ARG      4.0     0.9    -      -       -      -
     64D  ARG      4.7     0.9    -      -       -      +
     66D  TRP      4.2     4.7    +      -       -      -
     67D  GLY*     3.2    27.2    +      -       -      -
     68D  ILE      5.6     0.4    -      -       -      +
     69D  ASP*     4.4    19.0    +      -       +      +
     96D  ALA      3.6     0.2    -      -       -      -
     97D  HIS*     1.3    88.2    -      -       +      +
     99D  TYR*     1.3    58.0    +      -       -      +
    100D  ARG*     3.9     1.2    +      -       -      -
    140D  ARG*     4.3    10.0    -      -       +      +
    141D  GLY*     3.2    41.3    +      -       -      +
    142D  CYS      4.0    13.8    -      -       -      +
    143D  ASP      3.4    32.2    +      -       -      -
    144D  HIS*     3.1    38.5    +      -       -      +
    145D  HIS      5.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  CYS*     3.0     5.7    -      -       -      +
     23D  ARG*     2.8    42.4    +      -       -      +
     25D  ALA*     3.5    25.8    -      -       +      -
     65D  ALA      3.9     2.7    -      -       -      -
     66D  TRP*     3.2    43.4    +      +       +      -
     96D  ALA*     4.2    14.4    -      -       +      +
     98D  ARG*     1.3    69.8    -      -       -      +
    100D  ARG*     1.3    82.1    +      -       -      +
    101D  GLU*     3.3     5.0    +      -       +      +
    103D  VAL      6.0     0.4    -      -       -      -
    105D  LYS*     4.1    19.8    -      -       -      +
    106D  ILE      5.3     0.2    +      -       -      -
    131D  TRP*     3.2    38.2    -      +       +      +
    133D  VAL*     3.8    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  VAL      4.2     0.4    -      -       -      -
     22D  CYS*     3.5     8.4    -      -       -      -
     63D  GLN*     2.9    23.6    +      -       -      +
     64D  ARG*     2.9    36.9    +      -       -      +
     65D  ALA*     3.1    25.7    +      -       -      +
     67D  GLY*     4.6     4.8    -      -       -      -
     98D  ARG      4.8     0.8    +      -       -      -
     99D  TYR*     1.3    82.3    -      -       -      +
    101D  GLU*     1.3    62.0    +      -       -      +
    102D  PHE*     3.2    41.7    -      -       +      -
    103D  VAL*     3.7    21.2    +      -       +      +
    142D  CYS*     3.8    33.9    +      -       -      +
    143D  ASP*     4.7     5.5    +      -       -      -
----------------------------------------------------------
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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