Contacts of the strand formed by residues 64 - 71 (chain K) 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 64 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  ARG*     4.7     6.1    +      -       -      -
    125A  GLU*     4.2     3.4    -      -       -      -
    134A  GLN*     5.8     0.4    +      -       -      -
    139I  GLU*     2.8    28.6    +      -       -      -
     62K  PRO      3.8     0.2    -      -       -      -
     63K  GLN*     1.3   104.0    +      -       +      +
     65K  PHE*     1.3    58.5    -      -       -      +
     84K  PHE*     3.3     8.8    -      -       -      -
     85K  ALA*     2.8    39.2    +      -       +      +
     87K  GLU*     6.2     0.4    -      -       -      +
    135K  ARG*     3.1    71.8    +      -       +      +
    136K  TYR      3.4    18.4    -      -       -      +
    137K  PRO*     4.9     1.6    -      -       +      -
    138K  LEU*     3.8     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 65 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65F  PHE*     5.4     0.7    -      +       -      -
    140F  MET*     3.6    34.5    -      -       +      -
    141F  ILE*     4.7     3.4    -      -       +      -
     64K  HIS*     1.3    73.4    -      -       -      +
     66K  ILE*     1.3    60.9    +      -       -      +
     67K  ARG      3.4    32.1    -      -       -      -
     68K  MET*     3.7    11.9    -      -       +      -
     82K  PHE*     3.7    24.2    -      +       +      -
     83K  LEU      3.7     9.0    -      -       -      -
     84K  PHE*     3.7    26.5    -      +       +      -
    135K  ARG*     3.5     0.3    -      -       -      -
    136K  TYR*     2.6    45.5    +      -       +      +
    137K  PRO      4.1    10.8    -      -       -      +
    138K  LEU*     4.0     1.7    -      -       +      +
    140K  MET*     3.8    22.2    -      -       +      -
    141K  ILE*     4.0    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 66 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140F  MET*     4.5     1.0    -      -       -      +
     11K  VAL*     4.5     9.0    -      -       +      -
     64K  HIS      4.7     0.2    -      -       -      -
     65K  PHE*     1.3    79.9    -      -       -      +
     67K  ARG*     1.3    63.3    +      -       +      +
     83K  LEU*     2.9    25.8    +      -       +      +
     84K  PHE      3.3    31.4    -      -       -      +
     85K  ALA*     3.4    21.8    -      -       +      +
    129K  CYS*     3.9    27.8    -      -       +      -
    130K  TYR*     4.4    14.1    -      -       +      +
    134K  GLN*     2.7    46.5    -      -       -      +
    135K  ARG*     4.9     3.6    -      -       +      -
    136K  TYR*     3.7    15.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 67 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139F  GLU*     3.0    34.2    +      -       -      +
    140F  MET*     3.4    17.0    -      -       -      +
    142F  GLY*     3.0    29.9    +      -       -      +
    143F  ASP      3.7     7.5    +      -       -      -
    144F  PHE*     4.7     3.0    -      -       -      +
     65K  PHE*     3.4    12.9    -      -       -      -
     66K  ILE*     1.3    92.0    -      -       +      +
     68K  MET*     1.3    77.0    +      -       -      +
     69K  HIS*     3.4    44.2    +      -       +      +
     83K  LEU*     2.9    31.6    +      -       +      +
    125K  GLU*     5.9     0.2    +      -       -      -
    129K  CYS*     4.2    15.3    -      -       -      -
    134K  GLN*     4.3     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 68 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44F  LEU*     4.3     3.8    -      -       +      -
     82F  PHE*     3.9    13.2    -      -       -      -
    140F  MET      2.9     5.9    +      -       -      -
    141F  ILE*     3.4    49.4    -      -       +      +
     65K  PHE*     4.0     1.3    -      -       +      -
     67K  ARG*     1.3    93.7    +      -       -      +
     69K  HIS*     1.3    86.6    +      -       -      +
     70K  GLN*     3.6     7.0    -      -       +      +
     80K  LEU*     3.7    28.7    -      -       +      -
     81K  ARG      3.2    14.8    -      -       -      +
     82K  PHE*     3.3    47.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 69 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142F  GLY      3.8     0.7    -      -       -      -
    144F  PHE*     3.8    23.0    -      +       +      -
     67K  ARG*     3.4    50.8    +      -       +      +
     68K  MET*     1.3    76.2    -      -       -      +
     70K  GLN*     1.3    61.0    -      -       -      +
     71K  TRP*     3.8     1.3    +      -       -      +
     79K  PHE      3.6     2.4    -      -       -      +
     81K  ARG*     2.8    44.6    +      -       +      +
     83K  LEU*     4.7    13.4    -      -       +      +
    122K  LEU*     4.2    26.8    -      -       +      +
    125K  GLU*     4.2    21.9    +      -       +      +
    126K  SER*     4.9     3.9    +      -       -      -
    129K  CYS*     3.7    19.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 70 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38F  LEU*     4.1    15.2    -      -       -      +
     42F  GLU      3.2    21.3    +      -       -      -
     43F  THR*     3.5     7.8    +      -       -      -
     44F  LEU*     3.2    29.9    +      -       -      +
    141F  ILE      4.5     1.5    -      -       -      +
    142F  GLY      3.1    10.7    +      -       -      +
    143F  ASP*     3.0    16.3    +      -       -      +
    144F  PHE      2.7    31.9    +      -       -      -
    146F  TRP*     3.9    24.5    -      -       +      -
      2K  PHE*     5.8     3.6    -      -       -      -
      4K  PRO*     6.0     1.0    -      -       -      +
     68K  MET*     3.6     9.2    -      -       +      +
     69K  HIS*     1.3    72.9    -      -       -      +
     71K  TRP*     1.3    59.9    +      -       -      +
     78K  PRO*     6.3     1.2    -      -       -      +
     79K  PHE      3.4     4.0    -      -       -      +
     80K  LEU*     3.4    28.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 71 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144F  PHE*     3.5    32.4    -      +       +      -
    145F  ASN*     4.7     7.2    -      -       +      +
    146F  TRP*     4.5     4.3    -      -       -      -
     69K  HIS*     3.8     2.9    +      -       +      +
     70K  GLN*     1.3    77.9    -      -       -      +
     72K  ILE*     1.3    74.3    +      -       -      +
     73K  ALA*     3.6    36.8    -      -       +      +
     74K  PRO*     3.9    12.8    -      -       +      -
     78K  PRO*     3.6     0.5    -      -       -      +
     79K  PHE*     2.6    66.3    +      +       +      +
    120K  SER*     3.9    28.0    -      -       -      -
    121K  PRO*     4.2    20.3    -      -       +      +
    122K  LEU*     3.7    33.6    -      -       +      +
    158K  SO4      5.9     2.0    -      -       -      -
----------------------------------------------------------
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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