Contacts of the strand formed by residues 209 - 215 (chain L) in PDB entry 1FSK


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 THR 209 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123L  PRO*     3.8    14.7    -      -       +      +
    124L  PRO*     4.8     9.6    -      -       +      +
    202L  VAL      5.0     0.2    -      -       -      -
    203L  ALA*     3.8     1.4    -      -       -      +
    204L  HIS*     3.0    30.9    +      -       -      +
    205L  PRO*     4.9     0.7    -      -       -      +
    207L  SER*     2.8    31.2    +      -       -      -
    208L  SER*     1.3    76.9    +      -       -      +
    210L  LYS*     1.3    67.7    +      -       -      +
    211L  VAL*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 210 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201L  ASN*     5.9     5.6    -      -       +      -
    202L  VAL      3.5    13.9    -      -       -      +
    203L  ALA*     3.6    23.9    -      -       +      +
    209L  THR*     1.3    77.6    -      -       -      +
    211L  VAL*     1.3    68.4    +      -       -      +
    212L  ASP*     5.2     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 211 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124L  PRO*     5.3     7.6    -      -       +      +
    126L  VAL*     3.3    35.4    -      -       +      -
    200L  CYS      3.7     0.2    -      -       -      +
    202L  VAL*     2.8    47.9    +      -       +      +
    209L  THR*     4.0    17.3    -      -       +      -
    210L  LYS*     1.3    80.6    -      -       -      +
    212L  ASP*     1.3    81.0    +      -       -      +
    213L  LYS*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 212 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199L  THR*     4.2     8.7    -      -       -      +
    200L  CYS      3.3     4.9    -      -       -      +
    201L  ASN*     3.2    35.9    -      -       -      +
    210L  LYS*     5.2     7.4    -      -       -      +
    211L  VAL*     1.3    82.6    +      -       -      +
    213L  LYS*     1.3    65.8    +      -       -      +
    214L  LYS      4.2     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 213 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123K  GLU*     3.0    36.1    +      -       -      +
    126L  VAL*     3.3    40.4    -      -       +      +
    127L  PHE*     5.8     0.2    -      -       -      -
    128L  PRO*     3.9    27.4    -      -       +      -
    199L  THR*     2.9    13.1    +      -       -      -
    200L  CYS*     3.0    36.5    +      -       -      -
    211L  VAL*     4.2     8.0    -      -       +      -
    212L  ASP*     1.3    77.0    -      -       -      +
    214L  LYS*     1.3    64.9    +      -       -      +
    215L  ILE*     3.5     2.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 214 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128L  PRO*     4.6     7.6    -      -       -      +
    197L  THR*     3.6    30.6    +      -       -      +
    198L  VAL      3.6    12.8    -      -       -      +
    199L  THR*     3.7     8.3    +      -       -      -
    212L  ASP      4.1     1.2    +      -       -      -
    213L  LYS*     1.3    74.3    -      -       -      +
    215L  ILE*     1.3    67.0    +      -       -      +
    216L  VAL*     3.2    35.5    +      -       +      +
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Residues in contact with ILE 215 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128L  PRO*     3.2    32.3    -      -       +      -
    129L  LEU      3.6    13.5    -      -       -      +
    130L  ALA*     3.9    23.3    -      -       +      -
    143L  LEU*     3.8    32.1    -      -       +      -
    144L  GLY      3.8     7.6    -      -       -      +
    145L  CYS*     4.2     7.6    -      -       +      -
    159L  TRP*     3.7    26.2    -      -       +      -
    193L  TRP*     3.2    22.8    +      -       +      -
    198L  VAL*     3.0    15.8    +      -       +      +
    200L  CYS*     5.1     0.2    -      -       -      -
    213L  LYS      3.5     6.5    +      -       -      +
    214L  LYS*     1.3    73.4    -      -       -      +
    216L  VAL*     1.3    63.3    +      -       -      +
    217L  PRO*     4.4     0.2    -      -       -      +
----------------------------------------------------------
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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