Contacts of the strand formed by residues 5 - 14 (chain E) in PDB entry 3SHD


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 HIS 5 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET*     3.8    25.3    -      -       +      +
      3D  LYS*     3.9    30.4    +      -       +      -
      3E  LYS      5.0     0.9    -      -       -      -
      4E  PRO*     1.3    74.8    -      -       -      +
      6E  VAL*     1.3    58.8    +      -       -      +
      7E  THR      4.0     0.4    -      -       -      -
     37E  HIS*     3.1    28.8    +      +       +      -
     77E  THR*     3.5    31.2    +      -       +      +
     78E  PRO*     3.3    20.5    +      -       +      +
     79E  PHE*     3.3    16.1    -      +       +      -
     80E  LEU      2.9    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 6 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  PHE      5.8     0.4    +      -       -      -
      3D  LYS*     5.1     1.6    -      -       -      +
      4D  PRO*     3.4    35.0    -      -       +      -
     80D  LEU*     4.0    13.7    -      -       +      -
      4E  PRO*     3.5    14.3    +      -       +      +
      5E  HIS*     1.3    75.2    -      -       -      +
      7E  THR*     1.3    61.9    +      -       -      +
     37E  HIS*     3.5     4.6    -      -       -      +
     38E  LEU*     2.8    44.0    +      -       +      +
     44E  LEU*     4.6     2.2    -      -       +      -
     80E  LEU*     3.3     8.3    -      -       +      +
     82E  PHE*     3.2    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 7 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  HIS      4.0     0.4    -      -       -      -
      6E  VAL*     1.3    76.6    -      -       -      +
      8E  VAL*     1.3    62.3    +      -       -      +
     36E  GLY      3.1    22.0    -      -       -      +
     37E  HIS*     3.8    16.4    -      -       +      +
     79E  PHE*     3.7    31.5    -      -       +      -
     80E  LEU      2.8    10.5    +      -       -      +
     81E  ARG*     3.2    15.3    -      -       -      +
     82E  PHE*     3.0    30.1    +      -       -      -
    158E  SO4      2.9    30.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 8 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  THR*     1.3    80.3    -      -       -      +
      9E  ALA*     1.3    54.9    +      -       -      +
     35E  ALA*     2.8    29.4    -      -       -      +
     36E  GLY      2.7    29.8    +      -       -      +
     37E  HIS      5.0     0.9    -      -       -      -
     38E  LEU      5.7     1.6    -      -       -      +
     44E  LEU*     3.7    40.8    -      -       +      +
     47E  ALA*     3.7    16.4    -      -       +      +
     48E  ALA*     3.5    33.4    -      -       +      +
     51E  GLU*     4.9     2.7    -      -       +      -
     81E  ARG*     5.1     0.2    -      -       -      -
     82E  PHE*     3.4     7.9    -      -       +      +
     84E  PHE*     4.0    11.7    -      -       +      -
    158E  SO4      5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 9 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  VAL*     1.3    76.1    -      -       -      +
     10E  CYS*     1.3    58.8    +      -       -      +
     33E  GLN*     4.1     3.4    -      -       +      -
     34E  PRO      3.6     0.9    -      -       -      -
     35E  ALA*     3.4    19.7    -      -       +      -
     81E  ARG*     3.6    36.3    -      -       -      +
     82E  PHE      2.8    11.5    +      -       -      +
     83E  LEU*     3.4    10.8    -      -       +      -
     84E  PHE*     2.7    35.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 10 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  ALA*     1.3    79.1    -      -       -      +
     11E  VAL*     1.3    64.1    +      -       -      +
     12E  VAL*     3.4    19.5    +      -       +      -
     33E  GLN*     3.4     7.8    -      -       -      +
     34E  PRO*     3.1    36.2    +      -       +      +
     48E  ALA*     4.0    35.0    -      -       -      -
     49E  ALA*     5.7     0.2    -      -       -      -
     52E  LEU*     4.6     9.4    -      -       +      -
     62E  PRO*     4.6     2.2    -      -       -      -
     84E  PHE*     3.4    11.9    -      -       -      +
     86E  ILE*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 11 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  ALA      4.2     0.4    -      -       -      -
     10E  CYS*     1.3    70.9    -      -       -      +
     12E  VAL*     1.3    59.0    +      -       -      +
     13E  HIS      4.2     0.2    +      -       -      -
     18E  PHE*     3.8    18.4    -      -       +      -
     19E  LEU      6.0     0.2    -      -       -      -
     33E  GLN*     4.0    21.3    -      -       +      +
     66E  ILE*     4.3     4.7    -      -       +      -
     83E  LEU*     4.0    17.5    -      -       +      -
     84E  PHE      2.6    14.8    +      -       -      +
     85E  ALA*     3.5     0.5    -      -       -      -
     86E  ILE      2.8    28.1    +      -       -      +
    126E  SER*     4.2    21.5    -      -       -      +
    127E  ILE*     4.9     3.6    -      -       +      -
    130E  TYR*     3.2    39.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 12 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  CYS*     3.4    27.0    +      -       +      +
     11E  VAL*     1.3    77.6    -      -       -      +
     13E  HIS*     1.3    63.8    +      -       -      +
     18E  PHE*     3.2     6.9    -      -       -      -
     19E  LEU*     2.8    48.9    +      -       +      +
     34E  PRO*     4.7     2.9    -      -       +      -
     52E  LEU*     4.5    21.3    -      -       +      -
     58E  ILE*     5.5     0.7    -      -       +      -
     86E  ILE*     3.4    23.1    -      -       +      +
     88E  LEU*     3.6    32.3    -      -       +      -
    106E  TRP*     3.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 13 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  VAL*     1.3    76.3    -      -       -      +
     14E  ALA*     1.3    60.6    +      -       -      +
     15E  GLU      4.7     1.4    +      -       -      -
     16E  GLY*     3.6    35.6    +      -       -      -
     17E  LYS      3.1    17.6    +      -       -      -
     18E  PHE*     3.3    30.4    -      +       +      -
     86E  ILE      3.0     6.7    +      -       -      +
     87E  GLU*     3.0    28.5    -      -       -      +
     88E  LEU*     2.8    30.5    +      -       -      +
    106E  TRP*     4.0     1.8    -      -       -      -
    130E  TYR*     3.0    28.3    +      +       +      +
    137F  PRO*     6.2     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 14 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13E  HIS*     1.3    81.0    -      -       -      +
     15E  GLU*     1.3    71.1    +      -       -      +
     16E  GLY      3.4     1.3    -      -       -      -
     17E  LYS*     3.1    14.8    +      -       -      +
     88E  LEU*     3.6    23.6    -      -       +      +
     90E  GLN*     3.9     4.9    -      -       -      -
     91E  ILE*     3.3    40.0    -      -       +      +
    106E  TRP*     3.7     9.2    -      -       +      -
----------------------------------------------------------
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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