Contacts of the strand formed by residues 296 - 299 (chain C) 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 THR 296 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150C  ILE*     3.2    30.4    -      -       +      +
    152C  MET*     4.9     4.9    -      -       +      -
    277C  THR*     4.9    12.3    -      -       +      +
    281C  ILE*     5.0     0.9    -      -       -      +
    292C  LEU      3.3     7.4    +      -       -      -
    293C  TYR*     4.0     7.1    +      -       -      -
    294C  ALA      3.7     2.2    -      -       -      -
    295C  ASN*     1.3    72.7    -      -       -      +
    297C  VAL*     1.3    64.8    +      -       -      +
    298C  LEU*     4.6    10.5    -      -       +      -
    312C  MET*     5.4     7.0    -      -       +      -
    316C  ILE*     5.2     5.6    -      -       +      +
    326C  ILE*     5.5     0.5    -      -       -      +
    327C  LYS      3.8     3.2    +      -       -      -
    328C  ILE*     3.7    29.9    -      -       +      +
    329C  ILE*     2.8    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 297 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  SER*     4.6    12.1    -      -       -      +
    141C  LEU*     4.8     7.0    -      -       +      -
    144C  SER*     3.8    21.8    -      -       -      +
    146C  ARG*     3.8    17.9    -      -       -      -
    149C  GLY*     5.1     0.2    -      -       -      -
    150C  ILE      3.0     6.7    +      -       -      -
    151C  VAL*     3.3    24.2    -      -       +      +
    152C  MET*     2.8    27.9    +      -       -      +
    295C  ASN      3.2    14.6    +      -       -      +
    296C  THR*     1.3    72.6    -      -       -      +
    298C  LEU*     1.3    75.8    -      -       -      +
    329C  ILE*     3.4    21.8    -      -       +      +
    331C  PRO*     5.0     2.2    -      -       +      -
    337C  SER*     6.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 298 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152C  MET*     3.5    32.8    -      -       +      -
    273C  ILE*     6.4     0.4    -      -       +      -
    296C  THR*     4.6    10.5    -      -       +      -
    297C  VAL*     1.3    83.3    -      -       -      +
    299C  SER*     1.3    61.8    +      -       -      +
    303C  THR*     4.0    22.4    -      -       +      +
    308C  ILE*     4.1    25.1    -      -       +      -
    309C  ALA*     4.4    13.2    -      -       +      +
    312C  MET*     5.0    14.1    -      -       +      -
    328C  ILE*     4.5    10.3    -      -       +      -
    329C  ILE      3.5     5.5    +      -       -      -
    330C  ALA*     3.7    27.4    -      -       +      -
    331C  PRO*     4.0     6.8    -      -       -      +
    334C  ARG*     3.8    18.5    -      -       -      +
    337C  SER*     5.0     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 299 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  ALA*     5.5     0.3    -      -       -      -
    140C  SER*     3.7    32.7    +      -       -      -
    151C  VAL*     4.1     1.9    -      -       -      +
    152C  MET      2.8     9.3    +      -       -      +
    153C  ASP*     3.4    26.7    +      -       -      +
    154C  SER      3.4    16.8    +      -       -      +
    298C  LEU*     1.3    75.2    -      -       -      +
    300C  GLY*     1.3    65.2    +      -       -      +
    303C  THR*     2.9    14.2    +      -       -      +
    334C  ARG*     4.1     6.5    -      -       -      -
    337C  SER*     4.3     7.6    -      -       -      -
    338C  VAL*     4.6     6.9    -      -       -      +
----------------------------------------------------------
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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