Contacts of the strand formed by residues 133 - 137 (chain D) 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 VAL 133 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122D  GLN*     3.7     6.4    -      -       -      +
    123D  LEU*     3.1    44.6    +      -       +      +
    132D  SER*     1.3    80.0    -      -       -      +
    134D  CYS*     1.3    63.6    +      -       -      +
    135D  LEU      4.1     0.2    +      -       -      -
    174D  VAL*     4.3    11.9    -      -       +      -
    175D  ALA      3.8     6.5    -      -       -      +
    176D  TRP*     4.0    14.4    -      -       +      -
    128E  PHE*     3.7    44.2    -      -       +      -
    144E  VAL*     4.0    18.4    -      -       +      -
    146E  LEU*     4.4    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  VAL*     4.7     0.2    -      -       +      -
    121D  TYR      3.5     4.7    -      -       -      -
    122D  GLN*     5.0     4.3    -      -       -      -
    132D  SER*     5.7     1.1    -      -       -      -
    133D  VAL*     1.3    75.3    -      -       -      +
    135D  LEU*     1.3    59.8    +      -       -      +
    136D  PHE      4.1     0.4    -      -       -      -
    173D  ALA      3.9     0.5    -      -       -      +
    174D  VAL*     3.5     5.1    -      -       -      +
    175D  ALA*     2.7    38.1    +      -       +      +
    182D  PHE*     3.5    37.0    -      -       -      -
    183D  ALA      4.7     0.2    -      -       -      -
    184D  CYS*     3.4    31.2    -      -       -      -
    187D  ALA*     4.0     7.9    -      -       +      -
    188D  PHE*     3.9    19.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119D  ALA      3.6     1.9    -      -       -      +
    120D  VAL*     3.3     3.4    -      -       -      +
    121D  TYR*     2.7    45.7    +      -       +      +
    123D  LEU*     3.7    27.6    -      -       +      -
    133D  VAL*     4.1     1.0    +      -       +      -
    134D  CYS*     1.3    72.6    -      -       -      +
    136D  PHE*     1.3    58.3    +      -       -      +
    137D  THR*     3.9    21.4    +      -       +      -
    172D  SER*     3.8    22.7    -      -       -      +
    173D  ALA      3.5    15.5    -      -       -      +
    174D  VAL*     3.9    14.6    -      -       +      -
    188D  PHE*     4.5     1.1    -      -       -      -
    134E  GLU*     4.8     2.7    -      -       -      +
    142E  THR*     3.8    30.5    -      -       +      -
    144E  VAL*     4.1    11.7    -      -       +      -
    193E  ARG*     4.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118D  PRO*     4.3     4.7    -      -       +      -
    119D  ALA      3.3    15.3    -      -       -      -
    120D  VAL*     3.8    10.8    -      -       +      +
    135D  LEU*     1.3    70.3    -      -       -      +
    137D  THR*     1.3    59.3    +      -       -      +
    139D  PHE*     3.2    44.6    -      +       +      -
    143D  THR*     4.3    10.1    -      -       +      -
    145D  VAL*     4.3    17.5    -      -       +      -
    172D  SER*     3.1     4.6    -      -       -      -
    173D  ALA*     2.9    34.5    +      -       +      +
    188D  PHE*     3.5    39.9    -      +       +      -
    191D  SER*     5.3     9.6    -      -       -      -
    193D  ILE*     4.2    15.3    -      -       +      -
    194D  PRO*     3.7    30.7    -      -       +      -
    197D  THR*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  ASP      3.7     0.2    -      -       -      +
    118D  PRO*     3.6     0.3    -      -       -      +
    119D  ALA*     3.0    32.3    +      -       -      +
    121D  TYR*     3.6    35.7    -      -       +      -
    135D  LEU*     3.9    16.8    -      -       +      -
    136D  PHE*     1.3    73.2    -      -       -      +
    138D  ASP*     1.4    75.2    +      -       -      +
    139D  PHE*     3.2    10.9    +      -       -      -
    170D  SER*     4.5     3.3    -      -       -      -
    171D  ASN      3.3    12.1    +      -       -      -
    172D  SER*     3.6    13.3    -      -       -      -
    134E  GLU*     4.8     0.9    -      -       -      +
    142E  THR*     5.2     1.7    +      -       -      +
    195E  ARG*     4.1    20.1    +      -       -      +
----------------------------------------------------------
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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