Contacts of the strand formed by residues 276 - 282 (chain F) in PDB entry 5JLH


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 ILE 276 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215F  LEU*     3.7    18.8    -      -       +      +
    216F  ALA*     5.6     4.7    -      -       -      -
    219F  ALA*     4.8    12.6    -      -       +      +
    221F  SER      5.0     3.0    +      -       -      +
    234F  LEU*     5.8     8.5    -      -       +      -
    235F  GLU*     5.7     7.6    -      -       +      +
    268F  ILE*     3.9     8.5    -      -       +      -
    269F  ASN      3.5     3.8    -      -       -      -
    270F  PHE*     3.6    25.8    -      -       +      -
    275F  TYR*     1.3    75.3    -      -       -      +
    277F  VAL*     1.3    58.8    +      -       -      +
    278F  GLY*     3.3    30.3    -      -       -      +
    279F  ALA*     6.0     0.4    -      -       +      -
    466F  SER*     5.3     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 277 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269F  ASN*     3.0    38.8    +      -       +      +
    271F  ASP*     3.7    28.7    -      -       +      +
    276F  ILE*     1.3    75.7    -      -       -      +
    278F  GLY*     1.3    56.5    +      -       -      +
    465F  ARG*     3.4     5.3    -      -       +      +
    466F  SER*     2.8    36.4    +      -       -      -
    467F  PRO      3.9    19.5    -      -       -      +
    468F  ARG*     5.5     3.6    -      -       -      -
    469F  GLN      5.6     0.9    -      -       -      +
    470F  GLY*     2.9    32.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 278 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235F  GLU*     6.0     4.0    -      -       -      -
    268F  ILE*     4.0     1.0    -      -       -      +
    269F  ASN*     3.0    27.5    +      -       -      +
    276F  ILE*     3.3    17.0    -      -       -      +
    277F  VAL*     1.3    81.4    -      -       -      +
    279F  ALA*     1.3    61.6    +      -       -      +
    464F  ASP      4.4     5.2    -      -       -      -
    465F  ARG*     4.1    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 279 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235F  GLU*     5.4    13.2    -      -       +      +
    238F  LEU*     5.5    11.0    -      -       +      -
    266F  ILE*     5.2     4.9    -      -       +      -
    267F  ARG      3.2    17.3    -      -       -      +
    268F  ILE*     4.3    11.2    -      -       +      -
    269F  ASN*     3.9     5.8    +      -       -      -
    276F  ILE*     6.0     0.2    -      -       +      -
    278F  GLY*     1.3    74.9    -      -       -      +
    280F  ASN*     1.3    64.5    +      -       -      +
    281F  ILE*     6.2     0.4    -      -       +      -
    460F  ASN      5.1     0.9    -      -       -      +
    463F  LEU*     3.6    27.3    -      -       +      +
    464F  ASP      5.0     3.3    +      -       -      +
    465F  ARG*     5.2     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 280 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266F  ILE*     3.8     1.6    -      -       -      +
    267F  ARG*     2.9    65.0    +      -       -      +
    269F  ASN*     3.7    16.6    +      -       -      +
    279F  ALA*     1.3    74.5    -      -       -      +
    281F  ILE*     1.3    69.6    +      -       -      +
    282F  GLU*     3.7    14.7    +      -       -      +
    460F  ASN*     3.8    24.9    -      -       +      +
    463F  LEU*     4.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 281 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238F  LEU*     4.5    16.2    -      -       +      -
    241F  ALA*     5.7     6.1    -      -       +      -
    245F  LEU*     4.3    17.3    -      -       +      -
    264F  LYS*     4.1    16.8    -      -       +      -
    265F  PHE      3.5     4.7    -      -       -      +
    266F  ILE*     3.6    37.7    -      -       +      -
    279F  ALA*     6.2     0.4    -      -       +      -
    280F  ASN*     1.3    77.1    -      -       -      +
    282F  GLU*     1.3    80.0    +      -       -      +
    283F  THR*     4.3     1.8    -      -       +      -
    456F  VAL*     3.7    19.4    -      -       +      +
    459F  LEU*     5.2     9.2    -      -       +      -
    460F  ASN*     2.9    35.3    +      -       -      +
    463F  LEU*     4.4     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 282 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264F  LYS*     3.8     0.2    -      -       -      -
    265F  PHE*     2.6    47.3    +      -       +      +
    267F  ARG*     2.8    36.2    +      -       -      +
    280F  ASN*     3.7    10.6    +      -       -      +
    281F  ILE*     1.3    80.0    -      -       -      +
    283F  THR*     1.3    65.7    +      -       -      +
    284F  TYR*     2.1    47.6    +      -       +      -
    456F  VAL*     4.6     2.7    -      -       -      -
    460F  ASN*     5.4     0.4    -      -       -      +
----------------------------------------------------------
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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