Contacts of the strand formed by residues 853 - 862 (chain B) in PDB entry 3HOU


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 853 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778B  MET*     3.6    26.9    -      -       -      -
    794B  ASN*     5.2     0.7    +      -       -      -
    795B  ILE      3.3    12.1    -      -       -      -
    796B  LEU*     4.2     2.5    -      -       -      -
    797B  TYR*     3.9     9.4    -      -       -      +
    852B  ARG*     1.3    78.0    -      -       -      +
    854B  LEU*     1.3    62.9    +      -       -      +
    855B  PHE*     6.0     0.2    -      -       -      +
    971B  THR*     3.4     8.1    -      -       -      +
    972B  LYS*     3.0    34.6    +      -       -      +
   1094B  ARG*     2.5    28.6    +      -       -      -
   1098B  MET*     5.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 854 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    785B  TYR*     4.4    16.6    -      -       +      +
    794B  ASN*     3.5     8.5    -      -       -      +
    795B  ILE*     2.7    40.5    +      -       +      +
    797B  TYR*     3.0    36.1    -      -       +      +
    853B  SER*     1.3    79.1    +      -       -      +
    855B  PHE*     1.3    64.0    +      -       -      +
    856B  PHE*     3.6    31.4    -      -       +      -
    969B  ARG*     4.4    13.2    -      -       +      -
    970B  THR      3.5     4.9    -      -       -      +
    971B  THR*     3.3    15.0    -      -       -      +
     59C  ALA*     4.7    17.9    -      -       +      +
     61C  GLU*     4.5     0.9    -      -       -      +
     62C  PHE*     5.0     8.3    -      -       +      -
      1J  MET*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 855 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    792B  MET*     3.5    17.9    -      -       +      -
    793B  ALA      3.2    12.8    -      -       -      -
    794B  ASN*     3.7    19.7    -      -       -      +
    853B  SER*     6.0     0.2    -      -       -      +
    854B  LEU*     1.3    78.9    -      -       -      +
    856B  PHE*     1.3    77.8    +      -       -      +
    857B  ARG*     3.2    33.4    -      -       +      -
    945B  GLU*     4.0    23.1    -      -       +      -
    968B  VAL      3.9     1.1    -      -       -      +
    969B  ARG*     3.5     1.4    -      -       -      -
    970B  THR*     2.8    51.7    +      -       -      +
    972B  LYS*     3.6    43.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 856 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    785B  TYR*     4.3    21.1    -      +       -      -
    790B  ASP*     5.1     3.1    -      -       -      +
    792B  MET*     3.0     5.4    -      -       -      -
    793B  ALA*     2.9    52.5    +      -       +      +
    795B  ILE*     4.6     9.4    -      -       +      -
    854B  LEU*     3.6    40.6    -      -       +      -
    855B  PHE*     1.3    83.0    -      -       -      +
    857B  ARG*     1.3    61.1    +      -       -      +
    858B  SER*     5.4     1.1    -      -       -      +
    950B  ASP*     3.5    19.5    -      -       -      -
    967B  ARG*     3.4    37.9    -      -       +      -
    968B  VAL      3.5     4.0    -      -       -      +
    969B  ARG*     3.6    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 857 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     231  BRU      5.5     0.2    +      -       -      -
     241    G      3.8     1.8    +      -       -      -
    791B  THR*     5.3     1.8    -      -       -      -
    792B  MET*     2.8    42.2    -      -       -      +
    855B  PHE*     3.2    28.6    -      -       +      -
    856B  PHE*     1.3    74.7    -      -       -      +
    858B  SER*     1.3    70.1    +      -       -      +
    859B  TYR*     3.5    30.6    +      -       +      -
    942B  ARG*     2.7    46.1    -      -       -      +
    945B  GLU*     2.7    42.7    +      -       -      +
    966B  VAL      3.8     0.2    -      -       -      +
    967B  ARG*     3.3     3.6    -      -       -      -
    968B  VAL*     3.1    33.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 858 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    789B  MET*     3.4    32.0    +      -       -      -
    790B  ASP      2.9    18.7    +      -       -      -
    791B  THR*     3.4    23.7    -      -       -      +
    792B  MET      3.8     5.9    -      -       -      +
    857B  ARG*     1.3    81.5    +      -       -      +
    859B  TYR*     1.3    65.2    +      -       -      +
    860B  MET*     4.0     1.9    +      -       -      +
    965B  LYS*     5.4     2.7    -      -       -      -
    966B  VAL      3.2    11.2    -      -       -      -
    967B  ARG*     3.9    14.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 859 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    857B  ARG*     3.5    37.4    -      -       +      -
    858B  SER*     1.3    76.4    -      -       -      +
    860B  MET*     1.3    63.8    +      -       -      +
    911B  ILE*     4.1    13.9    -      -       +      -
    912B  ILE*     5.2     4.9    -      -       +      -
    939B  THR*     4.8    18.8    -      -       +      -
    940B  PRO      4.0     8.7    -      -       -      -
    941B  LEU*     2.8    41.7    -      -       +      +
    942B  ARG*     3.0    37.7    +      -       +      +
    945B  GLU*     3.7     2.8    +      -       -      -
    965B  LYS*     3.4     3.6    -      -       -      +
    966B  VAL*     3.0    37.1    +      -       +      +
    968B  VAL*     4.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 860 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  ASN*     3.0    26.7    -      -       -      +
    858B  SER      4.8     2.2    -      -       -      +
    859B  TYR*     1.3    78.7    -      -       -      +
    861B  ASP*     1.3    86.7    +      -       -      +
    862B  GLN*     4.8     3.6    -      -       -      +
    912B  ILE*     4.6     4.9    -      -       -      +
    939B  THR*     4.9     8.2    -      -       -      +
    963B  PHE*     3.4    19.7    -      -       +      -
    964B  VAL      3.2    16.2    -      -       -      +
    965B  LYS*     3.4    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 861 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    860B  MET*     1.3    87.8    -      -       -      +
    862B  GLN*     1.3    84.2    +      -       -      +
    874B  PHE*     3.8    13.3    -      -       +      -
    912B  ILE*     4.2    14.4    -      -       +      -
    914B  LYS*     2.6    41.6    +      -       -      +
    937B  ALA      4.0     3.8    -      -       -      +
    938B  SER      4.8     0.5    -      -       -      +
    939B  THR*     3.7    17.1    +      -       -      +
    963B  PHE*     3.7     0.7    -      -       -      -
    964B  VAL*     2.9    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 862 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ARG      5.5     0.3    -      -       -      +
    121B  ASN*     5.4     3.1    -      -       -      +
    860B  MET*     4.8     3.5    -      -       -      +
    861B  ASP*     1.3    80.8    +      -       -      +
    863B  GLU*     1.3    65.2    +      -       -      +
    864B  LYS*     3.9     0.8    -      -       -      +
    872B  GLU*     3.5     0.7    -      -       -      +
    874B  PHE*     4.2     3.1    -      -       -      -
    914B  LYS*     2.6    34.5    +      -       -      -
    957B  ASN*     3.6    30.3    +      -       -      +
    959B  ASP*     5.4     0.2    +      -       -      -
    961B  LEU*     5.0     5.7    -      -       -      +
    962B  LYS      3.1    12.1    -      -       -      +
    963B  PHE*     3.1    42.0    -      -       +      -
----------------------------------------------------------
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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