Contacts of the strand formed by residues 251 - 258 (chain D) 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 251 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  TRP*     2.9    33.9    +      -       -      -
    219D  ARG*     3.8    15.8    +      -       -      -
    242D  THR*     3.4     5.0    -      -       -      -
    243D  ASP      2.9    40.2    +      -       -      -
    250D  ALA*     1.3    73.1    -      -       -      +
    252D  TYR*     1.3    60.8    +      -       -      +
    267D  GLU*     2.6    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 252 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240D  VAL*     5.1     3.6    -      -       +      -
    241D  MET      3.5     5.8    -      -       -      +
    242D  THR*     4.0     5.8    -      -       +      +
    249D  GLN*     3.9     1.7    +      -       -      -
    250D  ALA*     3.2    48.1    +      -       +      -
    251D  SER*     1.3    78.3    +      -       -      +
    253D  LYS*     1.3    62.0    +      -       -      +
    267D  GLU*     3.2    10.1    +      -       -      +
    268D  LEU*     2.9    47.4    +      -       +      -
    270D  ALA*     4.1    24.0    -      -       +      -
    273D  TYR      2.6    29.0    +      -       -      -
    274D  HIS*     3.1     9.2    -      +       -      -
    275D  TYR*     3.2    58.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 253 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  TRP*     3.6    53.8    -      -       +      +
    240D  VAL*     3.4     6.8    -      -       -      +
    241D  MET      3.1    31.8    +      -       -      -
    251D  SER      4.4     0.2    +      -       -      -
    252D  TYR*     1.3    79.6    -      -       -      +
    254D  ILE*     1.3    66.1    +      -       -      +
    255D  PHE*     3.6    26.4    -      -       +      -
    265D  SER*     5.3     7.5    +      -       -      +
    266D  VAL      3.1    16.4    -      -       -      +
    267D  GLU*     3.7    29.6    -      -       +      +
    268D  LEU*     4.6     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 254 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239D  THR      3.6     8.1    -      -       -      +
    240D  VAL*     4.6     9.2    -      -       +      -
    253D  LYS*     1.3    75.2    -      -       -      +
    255D  PHE*     1.3    68.3    +      -       -      +
    265D  SER*     3.4     3.3    -      -       -      -
    266D  VAL*     2.9    33.4    +      -       +      +
    268D  LEU*     3.4    34.1    -      -       +      -
    303D  VAL*     4.2     7.2    -      -       +      -
    305D  PHE*     3.2    63.7    -      -       +      -
    310D  LEU*     3.7    21.3    -      -       +      +
    312D  TYR*     4.4     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 255 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215D  ILE*     3.8    35.0    -      -       +      -
    218D  TRP*     3.8    23.8    -      +       -      -
    238D  PHE*     3.3    28.8    -      -       -      +
    239D  THR*     3.2    24.8    +      -       +      +
    241D  MET*     3.8    28.5    -      -       +      -
    253D  LYS*     3.6    33.2    -      -       +      -
    254D  ILE*     1.3    79.6    -      -       -      +
    256D  LYS*     1.3    61.7    +      -       -      +
    257D  MET*     4.4     9.9    -      -       -      -
    262D  VAL*     4.2    13.0    -      -       +      -
    264D  LYS      3.7     2.9    -      -       -      +
    265D  SER*     3.6    23.1    -      -       -      -
    310D  LEU*     4.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 256 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236D  SER*     3.7    15.8    +      -       -      -
    237D  CYS      3.6     3.8    -      -       -      -
    238D  PHE*     3.7    14.6    -      -       +      -
    255D  PHE*     1.3    73.8    -      -       -      +
    257D  MET*     1.3    64.2    +      -       -      +
    258D  GLU*     3.5    23.8    +      -       -      -
    262D  VAL*     3.6     2.9    -      -       -      -
    263D  VAL*     3.0    38.7    +      -       +      +
    264D  LYS*     2.9    27.3    +      -       +      +
    308D  GLN*     2.7    33.7    +      -       -      +
    309D  ASN*     4.2     8.5    +      -       -      -
    310D  LEU*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 257 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190D  LEU*     3.6    22.2    -      -       +      -
    192D  ILE*     3.4    19.3    -      -       +      -
    205D  LEU*     3.7    22.0    -      -       -      -
    215D  ILE*     5.8     0.9    -      -       -      -
    230D  CYS*     4.8     1.8    -      -       -      -
    235D  GLY      4.4     0.2    -      -       -      +
    236D  SER*     3.5     0.9    -      -       -      -
    237D  CYS*     2.9    44.3    +      -       +      +
    238D  PHE      4.3     2.2    -      -       -      -
    239D  THR*     3.3    42.8    -      -       +      +
    255D  PHE*     4.4    12.6    -      -       -      -
    256D  LYS*     1.3    74.9    -      -       -      +
    258D  GLU*     1.3    70.1    +      -       -      +
    259D  LYS      4.2     0.2    -      -       -      -
    260D  GLY*     4.4     7.0    -      -       -      -
    261D  LYS      3.2    21.8    -      -       -      +
    262D  VAL*     4.3     3.6    -      -       -      -
    263D  VAL*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235D  GLY      4.1    11.2    -      -       -      +
    236D  SER*     3.0    25.5    +      -       -      +
    256D  LYS*     3.5    14.0    +      -       -      -
    257D  MET*     1.3    79.9    -      -       -      +
    259D  LYS*     1.3    75.5    +      -       +      +
    260D  GLY      3.1     0.2    -      -       -      -
    261D  LYS*     2.9    24.9    +      -       -      +
    263D  VAL*     3.7    29.5    -      -       +      +
----------------------------------------------------------
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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