Contacts of the strand formed by residues 99 - 109 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  GLU*     6.1     1.8    -      -       +      -
     42G  MET      3.5     4.3    -      -       -      +
     43G  LYS*     3.4    31.0    +      -       -      +
     97G  GLY      3.7     3.6    +      -       -      +
     98G  GLU*     1.3    73.0    -      -       -      +
    100G  ILE*     1.3    63.1    +      -       -      +
    122G  ASN*     3.8     7.5    +      -       -      +
    123G  LYS*     2.9    47.2    +      -       +      +
    124G  ALA      4.6     0.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 100 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  GLU*     3.2     8.5    -      -       -      +
     42G  MET*     2.8    62.2    +      -       +      +
     44G  VAL*     4.1     9.9    -      -       +      -
     55G  LEU*     3.8    24.7    -      -       +      -
     63G  LEU*     4.1     6.7    -      -       +      -
     94G  ALA*     3.9    13.0    -      -       +      -
     98G  GLU*     4.2     4.3    -      -       +      +
     99G  ASP*     1.3    78.6    -      -       -      +
    101G  VAL*     1.3    64.7    +      -       -      +
    102G  ILE*     4.1    20.0    -      -       +      -
    120G  LEU*     4.1     8.3    -      -       +      -
    121G  THR      3.3     7.6    -      -       -      +
    122G  ASN*     4.8     0.4    -      -       -      -
    123G  LYS      4.2     0.2    -      -       -      +
    129G  ILE*     3.4    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39G  ILE*     3.6    28.3    -      -       +      -
     40G  CYS      3.4     5.2    -      -       -      +
     41G  GLU*     3.8    18.6    -      -       +      +
    100G  ILE*     1.3    77.4    -      -       -      +
    102G  ILE*     1.3    64.5    +      -       -      +
    103G  THR*     3.8    10.5    -      -       -      +
    119G  ASP      3.5     1.6    -      -       -      +
    120G  LEU*     3.3     4.5    -      -       -      -
    121G  THR*     2.8    45.7    +      -       -      +
    123G  LYS*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 102 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28G  ILE*     5.2     0.7    -      -       +      -
     38G  VAL      3.7     1.9    -      -       -      +
     39G  ILE*     3.4     3.1    -      -       -      -
     40G  CYS*     2.8    55.4    +      -       +      +
     41G  GLU      4.3    10.5    -      -       -      +
     42G  MET*     4.3     2.2    -      -       +      +
     63G  LEU*     4.0    27.1    -      -       +      +
     67G  ILE*     3.8    27.5    -      -       +      +
    100G  ILE*     4.1    22.4    -      -       +      -
    101G  VAL*     1.3    75.3    -      -       -      +
    103G  THR*     1.3    59.5    +      -       -      +
    104G  ALA      4.1     0.2    -      -       -      -
    118G  VAL*     3.4    28.7    -      -       +      -
    119G  ASP      3.4     3.1    -      -       -      +
    120G  LEU*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 103 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37G  LYS*     3.8    18.4    -      -       -      +
     38G  VAL      3.6     2.9    -      -       -      +
     39G  ILE*     3.9    14.7    -      -       +      +
    101G  VAL*     3.8    17.0    -      -       -      +
    102G  ILE*     1.3    75.3    -      -       -      +
    104G  ALA*     1.3    60.3    +      -       -      +
    105G  HIS*     3.7    28.8    +      -       +      -
    117G  SER      3.9     0.5    -      -       -      +
    118G  VAL*     3.2     5.4    -      -       -      -
    119G  ASP*     2.9    43.3    +      -       -      +
    121G  THR*     5.2     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 104 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37G  LYS*     3.3     9.7    -      -       -      +
     38G  VAL      2.8    31.9    +      -       -      +
     67G  ILE*     3.4    42.0    -      -       +      +
     68G  SER*     3.8     5.2    -      -       -      -
     71G  ALA*     4.1     6.0    -      -       +      +
    102G  ILE      4.1     0.4    -      -       -      -
    103G  THR*     1.3    73.4    -      -       -      +
    105G  HIS*     1.3    60.8    +      -       -      +
    117G  SER      3.3     5.2    -      -       -      -
    118G  VAL*     3.8    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 105 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36G  GLY      3.3     5.2    -      -       -      -
     37G  LYS*     3.2    39.6    +      -       +      +
     71G  ALA*     4.8     0.4    -      -       -      -
    103G  THR*     3.7    26.7    +      -       +      +
    104G  ALA*     1.3    74.0    -      -       -      +
    106G  VAL*     1.3    67.8    +      -       -      +
    107G  LEU*     3.5    11.2    +      -       +      +
    116G  THR*     3.2     6.0    -      -       -      -
    117G  SER*     2.9    39.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 106 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36G  GLY*     2.8    26.5    +      -       -      +
     71G  ALA*     3.6    36.6    -      -       +      +
     72G  LEU*     3.8    17.0    -      -       +      -
     75G  THR*     4.2     6.1    -      -       +      -
    105G  HIS*     1.3    75.4    -      -       -      +
    107G  LEU*     1.3    62.2    +      -       -      +
    108G  LYS      4.0     7.6    -      -       -      +
    109G  GLN*     3.9    28.3    -      -       +      -
    115G  PHE      3.7     9.9    -      -       -      +
    116G  THR*     4.1     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 107 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91F  MET*     3.8    26.2    -      -       -      -
    127F  LYS*     5.6     3.8    +      -       -      -
    128F  LEU*     4.0    26.1    -      -       +      +
    131F  GLN*     3.8    27.8    -      -       -      +
    105G  HIS*     3.5     8.5    +      -       +      +
    106G  VAL*     1.3    75.6    -      -       -      +
    108G  LYS*     1.3    59.5    +      -       -      +
    115G  PHE*     2.7    16.1    +      -       +      +
    116G  THR      4.1     9.6    -      -       -      +
    117G  SER*     4.1    27.4    -      -       -      +
    133G  ARG*     4.1    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 108 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  COA      3.2    31.3    +      -       -      -
     91F  MET*     3.3    45.8    -      -       +      +
     92F  SER*     5.0     6.7    -      -       -      -
    128F  LEU*     5.7     2.2    -      -       +      +
    106G  VAL*     3.6     3.3    -      -       -      +
    107G  LEU*     1.3    81.4    -      -       -      +
    109G  GLN*     1.3    89.0    +      -       -      +
    110G  GLY*     3.5     4.6    -      -       -      +
    114G  ALA*     3.5     2.3    -      -       -      +
    115G  PHE*     2.9    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 109 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72G  LEU*     4.2     9.3    -      -       -      +
     75G  THR*     3.2    39.4    +      -       -      +
     77G  ARG*     4.3    19.6    -      -       -      +
     79G  ALA*     5.1     3.3    +      -       -      +
    106G  VAL*     3.9    17.7    -      -       +      +
    108G  LYS*     1.3    91.1    +      -       -      +
    110G  GLY*     1.3    58.3    +      -       -      +
    113G  LEU      3.9     2.0    -      -       -      -
    114G  ALA*     4.1     9.2    -      -       +      -
    138G  LEU*     3.5    23.4    -      -       -      +
----------------------------------------------------------
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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