Contacts of the strand formed by residues 633 - 639 (chain N) 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 VAL 633 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401N  PHE*     3.8    22.7    -      -       +      -
    404N  LYS      5.3     3.1    +      -       -      +
    406N  LEU*     3.4    37.7    -      -       +      +
    521N  LEU*     3.1    43.6    -      -       +      +
    539N  LEU*     4.6     4.9    -      -       +      -
    543N  SER*     4.0    12.3    -      -       -      +
    544N  CYS      3.5    12.3    -      -       -      +
    545N  ILE*     4.1     9.4    -      -       +      -
    631N  GLY      5.5     0.4    -      -       -      +
    632N  ARG*     1.3    73.3    -      -       -      +
    634N  TYR*     1.3    61.3    +      -       -      +
    694N  ASP*     3.9     0.9    -      -       -      +
    695N  ALA*     3.6    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 634 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41N  LYS*     4.3     6.2    +      -       -      -
    521N  LEU*     3.6     7.0    -      -       -      -
    543N  SER*     3.4     2.3    -      -       -      -
    544N  CYS*     3.0    53.2    +      -       +      +
    545N  ILE*     3.3    10.5    +      -       -      -
    546N  SER*     3.2    30.5    -      -       -      -
    547N  VAL*     5.7     1.2    -      -       -      +
    612N  GLU*     3.8    21.1    +      -       +      +
    632N  ARG*     3.2    20.9    -      -       -      -
    633N  VAL*     1.3    73.4    -      -       -      +
    635N  ARG*     1.3    64.2    +      -       -      +
    692N  TYR*     3.1    54.5    -      +       +      +
    693N  ILE      3.7     4.9    -      -       -      +
    694N  ASP*     3.4    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 635 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519N  TRP*     2.9    32.3    +      -       -      +
    520N  GLY*     3.7    34.4    -      -       -      +
    521N  LEU*     3.9     8.7    -      -       -      +
    542N  MET*     4.5     2.7    -      -       +      -
    543N  SER*     4.4     5.8    -      -       -      +
    634N  TYR*     1.3    79.0    -      -       -      +
    636N  PRO*     1.3    77.5    +      -       +      +
    637N  LEU*     4.3    12.0    -      -       +      +
    692N  TYR*     3.3     6.5    -      -       -      +
    693N  ILE*     2.9    36.4    +      -       +      +
    698N  GLU*     3.1    29.5    +      -       -      -
    703N  ILE*     4.1     9.5    -      -       -      +
    742N  GLU*     2.4    36.7    +      -       -      +
    748N  ILE*     5.7     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 636 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37N  PHE*     4.7     3.4    -      -       +      -
    542N  MET*     3.6    44.2    -      -       +      +
    635N  ARG*     1.3    94.9    +      -       +      +
    637N  LEU*     1.3    74.7    +      -       -      +
    681N  TRP*     3.7    36.1    -      -       +      -
    690N  VAL*     5.6     0.4    -      -       +      -
    691N  GLU      3.3     5.4    -      -       -      +
    692N  TYR*     3.9    12.8    -      -       +      -
    743N  ILE*     3.5    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 637 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635N  ARG*     4.3     9.6    -      -       +      +
    636N  PRO*     1.3    83.6    -      -       -      +
    638N  PHE*     1.3    64.5    +      -       -      +
    639N  ILE*     4.3     0.9    -      -       -      +
    690N  VAL*     3.1     6.3    -      -       -      +
    691N  GLU*     2.7    40.0    +      -       -      +
    693N  ILE*     3.4    34.3    -      -       +      -
    703N  ILE*     3.5    39.0    -      -       +      -
    740N  HIS*     3.7     7.6    -      -       +      -
    741N  CYS      3.0    16.8    -      -       -      +
    742N  GLU*     3.3    30.1    -      -       +      +
    743N  ILE*     3.7    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 638 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25N  ILE*     5.2     5.2    -      -       +      -
     30N  SER*     4.6     9.2    -      -       -      -
     33N  VAL*     3.6    37.5    -      -       +      -
    637N  LEU*     1.3    72.7    -      -       -      +
    639N  ILE*     1.3    60.8    +      -       -      +
    651N  LEU*     3.4    37.2    -      -       +      -
    653N  VAL*     4.0    26.5    -      -       +      -
    658N  ILE*     5.9     0.7    -      -       +      -
    690N  VAL*     3.2    27.4    -      -       +      -
    707N  PRO*     5.3     4.5    -      -       +      -
    740N  HIS*     3.0    11.4    -      -       -      +
    741N  CYS*     2.8    42.9    +      -       +      +
    742N  GLU      4.4     3.4    -      -       -      -
    743N  ILE*     3.7    30.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 639 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    605N  ARG*     3.2    50.7    -      -       +      +
    638N  PHE*     1.3    75.5    -      -       -      +
    640N  VAL*     1.3    58.8    +      -       -      +
    641N  GLU*     3.5    20.6    -      -       +      +
    651N  LEU*     3.4     4.5    -      -       -      +
    652N  LYS*     2.8    41.3    +      -       +      +
    688N  GLY      4.2    11.0    -      -       -      +
    689N  LEU      3.2    16.3    +      -       -      +
    690N  VAL      4.3     4.3    -      -       -      +
    691N  GLU*     3.4    34.5    -      -       +      +
    739N  THR      3.8     7.0    -      -       -      +
    740N  HIS*     4.1     6.3    -      -       +      -
----------------------------------------------------------
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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