Contacts of the strand formed by residues 99 - 109 (chain H) in PDB entry 3F5O


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 ASP 99 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41H  GLU*     4.8     7.0    -      -       +      +
     42H  MET      3.5     4.2    -      -       -      -
     43H  LYS*     3.3    34.7    +      -       -      +
     97H  GLY      3.9     1.6    +      -       -      +
     98H  GLU*     1.3    73.4    -      -       -      +
    100H  ILE*     1.3    63.6    +      -       -      +
    122H  ASN*     3.8     6.8    -      -       -      +
    123H  LYS*     2.9    52.1    +      -       +      +
    124H  ALA      4.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 100 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41H  GLU*     3.2     7.7    -      -       -      +
     42H  MET*     2.8    60.9    +      -       +      +
     44H  VAL*     3.9    19.3    -      -       +      -
     55H  LEU*     3.9    24.7    -      -       +      -
     63H  LEU*     4.1     6.1    -      -       +      -
     94H  ALA*     4.0     5.2    -      -       +      -
     98H  GLU*     4.4     4.3    -      -       +      +
     99H  ASP*     1.3    80.7    -      -       -      +
    101H  VAL*     1.3    63.2    +      -       -      +
    102H  ILE*     4.0    11.4    -      -       +      -
    120H  LEU*     4.0    17.7    -      -       +      -
    121H  THR      3.3     8.3    -      -       -      +
    122H  ASN*     5.0     0.2    -      -       -      -
    123H  LYS*     4.7     0.2    -      -       -      -
    129H  ILE*     3.4    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  ILE*     3.7    22.7    -      -       +      -
     40H  CYS      3.4    10.1    -      -       -      +
     41H  GLU*     3.8    15.0    -      -       +      +
    100H  ILE*     1.3    76.8    -      -       -      +
    102H  ILE*     1.3    64.2    +      -       -      +
    103H  THR*     3.7    12.6    -      -       -      +
    119H  ASP      3.6     1.4    -      -       -      +
    120H  LEU*     3.2     6.4    -      -       -      +
    121H  THR*     2.8    45.5    +      -       -      +
    123H  LYS*     3.7    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 102 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28H  ILE*     5.2     0.9    -      -       +      -
     38H  VAL      3.7     1.9    -      -       -      +
     39H  ILE*     3.4     2.4    -      -       -      -
     40H  CYS*     2.8    59.4    +      -       +      +
     41H  GLU      4.1     8.3    -      -       -      +
     42H  MET*     4.3     2.7    -      -       +      -
     63H  LEU*     4.2    25.4    -      -       +      +
     67H  ILE*     4.0    23.5    -      -       +      +
    100H  ILE*     4.0    24.0    -      -       +      +
    101H  VAL*     1.3    77.2    -      -       -      +
    103H  THR*     1.3    59.2    +      -       -      +
    104H  ALA      4.1     0.2    +      -       -      -
    118H  VAL*     3.6    27.4    -      -       +      -
    119H  ASP      3.6     1.8    -      -       -      -
    120H  LEU*     4.0    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 103 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  LYS*     4.0    28.0    -      -       -      +
     38H  VAL      3.5     3.1    -      -       -      +
     39H  ILE*     4.0    14.6    -      -       +      +
    101H  VAL*     3.7    18.2    -      -       -      +
    102H  ILE*     1.3    73.7    +      -       -      +
    104H  ALA*     1.3    63.6    +      -       -      +
    105H  HIS*     4.3     7.2    +      -       +      +
    117H  SER      3.9     0.7    -      -       -      +
    118H  VAL*     3.3     4.6    -      -       -      -
    119H  ASP*     2.9    47.7    +      -       +      +
    121H  THR*     5.3     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 104 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  LYS*     3.3     7.6    -      -       -      +
     38H  VAL*     2.8    32.9    +      -       +      +
     67H  ILE*     3.5    42.0    -      -       +      +
     68H  SER*     3.8     6.1    -      -       -      -
     71H  ALA*     4.1     5.5    -      -       +      +
    102H  ILE      4.1     0.6    +      -       -      -
    103H  THR*     1.3    75.2    -      -       -      +
    105H  HIS*     1.3    61.2    +      -       -      +
    117H  SER      3.4     4.9    -      -       -      -
    118H  VAL*     3.8    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 105 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131E  GLN*     5.6     1.1    +      -       -      -
     36H  GLY      3.2    10.3    -      -       -      +
     37H  LYS*     4.6    10.8    -      -       +      -
     71H  ALA*     4.8     2.0    -      -       -      -
    103H  THR*     5.0     7.4    +      -       +      +
    104H  ALA*     1.3    77.9    -      -       -      +
    106H  VAL*     1.3    70.8    +      -       -      +
    107H  LEU*     3.2    25.1    +      -       +      +
    116H  THR*     3.3     5.0    +      -       -      -
    117H  SER*     2.5    63.3    +      -       -      -
    119H  ASP*     5.8     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 106 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  GLY*     2.9    25.2    +      -       -      +
     71H  ALA*     3.6    33.4    -      -       +      +
     72H  LEU*     3.6    29.6    -      -       +      +
     75H  THR*     4.3     1.8    -      -       +      -
    105H  HIS*     1.3    79.0    -      -       -      +
    107H  LEU*     1.3    63.3    +      -       -      +
    108H  LYS      4.1    15.3    -      -       -      +
    109H  GLN*     4.1    22.4    -      -       +      +
    115H  PHE      3.7     9.6    -      -       -      +
    116H  THR*     4.1     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91E  MET*     3.8    26.0    -      -       +      -
    128E  LEU*     4.0    24.5    -      -       +      +
    131E  GLN*     3.8    29.6    -      -       -      +
    105H  HIS*     3.2    35.4    -      -       +      +
    106H  VAL*     1.3    74.8    -      -       -      +
    108H  LYS*     1.3    60.1    +      -       -      +
    115H  PHE*     2.7    16.2    +      -       +      +
    116H  THR      4.2     6.7    -      -       -      +
    117H  SER*     3.3    20.4    -      -       -      +
    133H  ARG*     4.2    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 108 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91E  MET*     3.3    45.1    -      -       +      +
     92E  SER*     4.8     9.0    -      -       -      -
    127E  LYS*     5.9     7.6    -      -       +      -
    128E  LEU*     5.7     2.7    -      -       +      +
    150F  COA      2.9    30.3    +      -       -      -
    106H  VAL*     3.6     5.8    -      -       -      +
    107H  LEU*     1.3    81.2    -      -       -      +
    109H  GLN*     1.3    79.9    +      -       -      +
    110H  GLY*     3.4     8.7    -      -       -      +
    114H  ALA*     3.5     1.4    -      -       -      -
    115H  PHE*     2.8    43.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 109 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  GLY*     5.9     1.0    -      -       -      -
     72H  LEU*     5.3     2.7    -      -       +      +
     75H  THR*     3.5    39.8    +      -       -      +
     76H  GLU      5.2     0.4    +      -       -      -
     77H  ARG*     4.8    10.1    +      -       -      +
    106H  VAL*     4.1    15.5    -      -       +      +
    108H  LYS*     1.3    88.5    +      -       -      +
    110H  GLY*     1.3    63.2    +      -       -      +
    113H  LEU      3.9     2.5    -      -       -      -
    114H  ALA*     4.4     9.2    -      -       +      +
    138H  LEU*     5.2     4.9    -      -       +      -
----------------------------------------------------------
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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