Contacts of the strand formed by residues 12 - 16 (chain J) in PDB entry 5HHM


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 TYR 12 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10J  PRO*     3.8    16.4    -      -       -      +
     11J  LYS*     1.3   109.9    +      -       +      +
     13J  LEU*     1.3    60.6    +      -       -      +
    110J  ARG*     3.7    30.3    -      -       +      -
    153J  ASP      4.7     2.2    -      -       -      -
    154J  HIS*     3.6    41.3    -      +       +      +
    155J  VAL      3.6    20.3    +      -       -      -
    156J  GLU*     3.8    16.4    -      -       +      +
    215J  TYR*     3.3    54.2    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 13 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10J  PRO*     3.8    30.3    -      -       +      -
     12J  TYR*     1.3    71.3    -      -       -      +
     14J  PHE*     1.3    60.3    +      -       -      +
     15J  ARG*     3.7    36.3    -      -       -      +
     21J  VAL*     4.1    11.0    -      -       +      -
     22J  THR      4.5     7.6    -      -       -      +
     23J  LEU*     3.8    30.5    -      -       +      -
    109J  THR*     4.1    14.1    -      -       +      -
    110J  ARG      2.9    12.6    +      -       -      +
    111J  LEU*     3.6    12.3    -      -       +      -
    112J  THR      3.1    24.4    +      -       -      -
    154J  HIS*     3.2     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 14 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13J  LEU*     1.3    77.2    -      -       -      +
     15J  ARG*     1.3    89.1    +      -       -      +
    112J  THR*     3.4    25.6    -      -       +      -
    114J  THR*     3.3    31.4    -      -       +      -
    117J  LEU*     3.7    20.4    -      -       +      -
    120J  VAL*     3.4    32.5    -      -       +      -
    151J  TYR*     4.1     4.0    -      +       -      -
    152J  PRO*     3.6    35.2    -      -       +      -
    154J  HIS*     4.7     4.9    -      -       +      +
    215J  TYR      5.4     1.3    -      -       -      +
    216J  GLY      4.3    18.4    -      -       -      +
    217J  LEU*     4.2    13.7    -      -       +      -
    221J  ASP*     5.1     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 15 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13J  LEU*     3.7    24.9    -      -       -      +
     14J  PHE*     1.3   107.1    +      -       -      +
     16J  LYS*     1.3    63.6    +      -       -      +
     19J  GLN*     3.7    30.7    -      -       +      +
     20J  ASN      4.7     3.9    +      -       -      -
     21J  VAL*     3.3    41.9    -      -       +      +
    111J  LEU*     4.6     3.6    -      -       +      +
    112J  THR      3.2     6.4    +      -       -      +
    113J  VAL*     3.3    18.2    -      -       +      -
    114J  THR*     3.0    29.1    +      -       -      +
    117J  LEU*     4.9     0.9    -      -       -      -
    218J  SER*     6.1     3.2    -      -       -      -
    221J  ASP*     5.9     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 16 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15J  ARG*     1.3    75.7    -      -       -      +
     17J  GLU*     1.3    80.2    +      -       -      +
     18J  GLY      3.4     0.2    +      -       -      -
     19J  GLN*     3.1    40.8    +      -       +      +
    113J  VAL*     4.0     2.8    -      -       -      +
    114J  THR*     3.4    15.2    -      -       +      +
    115J  GLU      3.8    17.9    -      -       -      +
    116J  ASP*     4.3     9.6    -      -       -      +
    117J  LEU*     4.2    30.3    -      -       +      +
----------------------------------------------------------
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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