Contacts of the strand formed by residues 17 - 24 (chain F) 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 LYS 17 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13F  HIS*     3.1    19.6    +      -       -      -
     14F  ALA      3.0    22.2    +      -       -      +
     15F  GLU      3.0     6.5    +      -       -      +
     16F  GLY*     1.3    83.7    -      -       -      +
     18F  PHE*     1.3    66.0    +      -       -      +
     91F  ILE*     4.8     6.1    -      -       +      -
    106F  TRP*     3.3    36.3    +      -       +      +
    107F  VAL      3.2    14.6    -      -       -      +
    108F  SER*     4.1     8.3    -      -       -      +
    111F  GLU*     3.4    26.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11F  VAL*     3.6    32.8    -      -       +      -
     12F  VAL      3.6     7.9    -      -       -      -
     13F  HIS*     3.4    29.4    -      +       +      -
     16F  GLY      4.4     4.3    -      -       -      -
     17F  LYS*     1.3    78.1    -      -       -      +
     19F  LEU*     1.3    66.8    +      -       -      +
     20F  VAL*     3.1     7.3    +      -       -      +
    105F  ARG      3.6     0.3    -      -       -      +
    106F  TRP*     3.5     2.9    -      -       -      -
    107F  VAL*     2.4    36.5    +      -       -      +
    109F  ALA*     3.7    38.1    -      -       +      -
    112F  ILE*     3.8    17.0    -      -       +      -
    127F  ILE*     4.2    17.3    -      -       +      -
    130F  TYR*     3.5    28.0    -      +       -      -
    131F  GLN*     5.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 19 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10F  CYS      4.8     2.6    -      -       -      +
     11F  VAL*     5.9     0.2    -      -       -      -
     12F  VAL*     3.1    25.9    +      -       +      +
     18F  PHE*     1.3    70.2    -      -       -      +
     20F  VAL*     1.3    76.2    +      -       -      +
     33F  GLN*     4.5     4.2    -      -       -      +
     34F  PRO*     3.6    22.8    -      -       +      +
     52F  LEU*     4.2    10.5    -      -       +      -
     56F  THR*     4.0    11.4    -      -       +      -
     58F  ILE*     3.8    29.6    -      -       +      -
     94F  THR*     5.0     1.6    -      -       +      -
    104F  CYS*     3.7    23.1    -      -       +      -
    105F  ARG      3.8     5.4    -      -       -      +
    106F  TRP*     3.2    42.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 20 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18F  PHE      3.8     8.5    -      -       -      +
     19F  LEU*     1.3    75.6    -      -       -      +
     21F  VAL*     1.3    62.0    +      -       -      +
     31F  TRP*     3.4    39.0    -      -       +      -
     32F  ASN      2.7    26.2    -      -       -      +
     33F  GLN*     5.0     1.1    -      -       -      +
     34F  PRO*     4.6     0.7    -      -       -      -
    104F  CYS*     3.3     7.1    -      -       -      +
    105F  ARG*     3.0    46.8    +      -       +      +
    107F  VAL*     4.1    20.9    -      -       +      -
    112F  ILE*     4.8    12.3    -      -       +      -
    123F  VAL*     5.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 21 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20F  VAL*     1.3    76.7    -      -       -      +
     22F  GLU*     1.3    60.7    +      -       -      +
     23F  GLU*     4.9     2.6    -      -       +      +
     30F  LEU      3.8     0.5    -      -       -      +
     31F  TRP*     3.3     8.4    -      -       -      -
     32F  ASN*     3.1    40.1    +      -       +      +
     33F  GLN      4.0    14.8    -      -       -      +
     34F  PRO*     4.2    13.0    -      -       +      +
     55F  GLU*     3.7    22.4    -      -       +      +
     56F  THR*     3.6    29.8    -      -       +      -
    101F  ILE*     3.8    25.1    -      -       +      -
    103F  CYS      3.6     5.6    -      -       -      +
    104F  CYS*     3.8     5.2    -      -       -      -
    105F  ARG*     6.5     0.2    -      -       -      -
    157F  SO4      4.4     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  VAL*     1.3    71.8    -      -       -      +
     23F  GLU*     1.3    67.4    +      -       -      +
     29F  ALA*     4.3    22.1    -      -       +      +
     30F  LEU      4.0     2.0    -      -       -      -
     31F  TRP*     3.7    17.5    +      -       +      +
    101F  ILE*     3.6     7.3    -      -       -      +
    102F  ASP*     3.1    35.0    +      -       +      +
    103F  CYS*     2.8    42.4    +      -       -      +
    104F  CYS*     4.7     0.2    -      -       -      +
    105F  ARG*     3.0    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 23 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  VAL*     4.9     4.0    -      -       +      +
     22F  GLU*     1.3    79.1    -      -       -      +
     24F  THR*     1.3    67.3    +      -       -      +
     28F  LYS      3.5     0.3    -      -       -      +
     29F  ALA*     4.4     0.7    -      -       -      -
     30F  LEU*     2.5    50.0    +      -       -      +
     32F  ASN*     5.4     1.1    -      -       +      +
    100F  ASP*     3.4    36.0    -      -       +      +
    101F  ILE*     3.9    11.5    -      -       +      +
    102F  ASP*     4.0     6.0    +      -       -      -
    119F  ARG*     2.8    39.4    +      -       -      +
    157F  SO4      3.1    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  GLU*     1.3    82.0    -      -       -      +
     25F  ILE*     1.3    62.7    +      -       -      +
     27F  GLY*     3.4    17.7    -      -       -      +
     28F  LYS*     3.0    34.1    +      -       -      +
     29F  ALA*     4.4     5.1    -      -       -      +
     30F  LEU*     5.8     0.2    -      -       -      -
    100F  ASP      4.8     0.8    +      -       -      -
    102F  ASP*     3.0    22.6    +      -       -      -
    119F  ARG*     6.6     0.4    -      -       -      -
----------------------------------------------------------
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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