Contacts of the strand formed by residues 407 - 412 (chain F) in PDB entry 2HU4


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 SER 407 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350F  LYS*     2.9    25.5    +      -       -      +
    351F  GLY*     3.2    21.8    -      -       -      +
    352F  PHE*     3.7     8.1    -      -       -      -
    363F  GLY      5.1     1.0    -      -       -      -
    374F  PHE*     3.4    40.3    -      -       -      -
    405F  GLY      4.6     0.7    +      -       -      -
    406F  TYR*     1.3    77.6    -      -       -      +
    408F  GLY*     1.3    59.2    +      -       -      +
    423F  TRP*     3.3    20.9    -      -       -      -
    424F  VAL*     4.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 408 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228F  SER*     4.8     0.9    -      -       -      -
    279F  SER*     3.8    10.8    -      -       -      -
    350F  LYS*     4.5     1.6    -      -       -      -
    352F  PHE*     4.0     7.4    -      -       -      -
    407F  SER*     1.3    75.4    -      -       -      +
    409F  SER*     1.3    60.0    +      -       -      -
    422F  PHE*     3.3     2.9    -      -       -      +
    423F  TRP*     2.8    60.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 409 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228F  SER*     4.8     6.1    +      -       -      -
    229F  GLU*     3.9    12.5    +      -       -      +
    279F  SER*     3.8    22.0    +      -       -      -
    280F  CYS      4.3     9.9    +      -       -      +
    281F  TYR*     4.5     6.4    -      -       -      +
    352F  PHE*     3.8    20.3    -      -       -      +
    353F  SER      5.6     0.4    -      -       -      -
    354F  PHE*     3.5    29.1    -      -       -      -
    408F  GLY*     1.3    74.4    -      -       -      -
    410F  PHE*     1.3    64.7    +      -       -      +
    421F  CYS      3.6     5.2    -      -       -      -
    422F  PHE*     4.2     2.5    -      -       -      +
    423F  TRP*     4.3     4.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 410 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  TYR*     4.2    14.6    -      +       -      -
    122F  ILE*     3.2    51.6    -      -       +      +
    123F  SER*     4.8     0.7    -      -       -      -
    124F  CYS*     4.1    15.0    -      -       -      -
    229F  GLU*     3.0    11.4    -      -       -      +
    354F  PHE*     4.6     1.0    -      -       -      -
    409F  SER*     1.3    74.9    -      -       -      +
    411F  VAL*     1.3    72.0    +      -       -      +
    412F  GLN*     4.4     3.8    -      -       -      -
    420F  PRO*     4.2     0.2    -      -       -      +
    421F  CYS*     2.7    67.7    +      -       +      +
    422F  PHE*     3.5    32.3    -      -       -      -
    423F  TRP*     4.0    11.0    -      +       +      -
    445F  SER*     3.8    18.4    -      -       -      -
    447F  CYS*     4.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 411 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91F  LEU*     5.5     1.1    -      -       +      -
    124F  CYS*     4.0    14.4    +      -       -      +
    229F  GLU*     3.0    15.1    +      -       -      +
    281F  TYR*     3.6    18.8    -      -       +      -
    282F  PRO*     3.5    26.9    -      -       +      -
    354F  PHE*     5.4     4.3    -      -       +      -
    410F  PHE*     1.3    85.6    -      -       -      +
    412F  GLN*     1.3   103.5    -      -       -      +
    418F  ILE*     2.9    36.1    -      -       +      -
    419F  ARG      3.4     7.6    -      -       -      +
    420F  PRO*     5.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 412 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  TYR*     4.6    13.1    +      -       -      -
    124F  CYS*     4.8     9.9    -      -       -      -
    129F  CYS*     5.2     2.2    -      -       -      -
    410F  PHE*     4.4     5.2    -      -       +      -
    411F  VAL*     1.3    89.4    -      -       -      +
    412F  HIS*     1.1    74.5    +      -       -      +
    413F  THR*     3.6    19.2    +      -       -      +
    417F  CYS      5.2     0.4    -      -       -      -
    418F  ILE*     3.4     3.3    -      -       -      -
    419F  ARG*     2.3    71.3    +      -       +      +
    421F  CYS*     2.7     7.9    -      -       -      -
    447F  CYS*     2.6    33.7    -      -       -      -
    210H  ILE*     5.2     7.8    -      -       -      +
    211H  ILE*     6.2     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