Contacts of the strand formed by residues 17 - 24 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  VAL      3.7     0.2    -      -       -      +
     13H  HIS*     3.4     6.5    +      -       -      -
     14H  ALA      2.9    31.0    +      -       -      +
     15H  GLU      3.4    12.6    -      -       -      +
     16H  GLY*     1.3    87.5    -      -       -      +
     18H  PHE*     1.3    67.2    +      -       -      +
     91H  ILE*     4.4    13.7    -      -       +      -
    106H  TRP*     3.9    25.0    +      -       +      +
    107H  VAL      3.1    17.5    -      -       -      +
    108H  SER*     4.1    23.7    -      -       -      +
    111H  GLU*     4.6     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11H  VAL*     3.7    26.0    -      -       +      -
     12H  VAL      3.3    14.8    -      -       -      +
     13H  HIS*     3.1    37.9    -      +       +      -
     16H  GLY      5.1     2.2    -      -       -      -
     17H  LYS*     1.3    77.8    -      -       -      +
     19H  LEU*     1.3    62.3    +      -       -      +
     20H  VAL*     3.5     2.1    +      -       +      +
    105H  ARG      3.3     4.9    -      -       -      +
    106H  TRP*     3.4     3.3    -      -       -      -
    107H  VAL*     2.6    47.7    +      -       -      +
    108H  SER      4.3     0.4    -      -       -      -
    109H  ALA*     3.7    36.3    -      -       +      -
    112H  ILE*     3.9    14.4    -      -       +      -
    127H  ILE*     4.3    20.6    -      -       +      -
    130H  TYR*     3.6    23.8    -      +       -      -
    131H  GLN*     5.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 19 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  CYS      4.8     1.7    -      -       -      +
     12H  VAL*     3.2    25.9    +      -       +      +
     18H  PHE*     1.3    72.0    -      -       -      +
     20H  VAL*     1.3    68.4    +      -       -      +
     33H  GLN*     4.4     3.1    -      -       -      +
     34H  PRO*     3.3    31.3    -      -       +      +
     52H  LEU*     4.5     2.9    -      -       +      -
     56H  THR*     3.7    15.5    -      -       +      +
     58H  ILE*     3.4    33.2    -      -       +      -
     94H  THR*     5.0     1.3    -      -       +      -
    104H  CYS*     3.5    31.2    -      -       +      -
    105H  ARG      4.0     6.5    -      -       -      +
    106H  TRP*     3.9    36.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 20 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18H  PHE*     4.5     1.1    -      -       +      +
     19H  LEU*     1.3    79.4    -      -       -      +
     21H  VAL*     1.3    65.7    +      -       -      +
     22H  GLU      3.9     0.2    +      -       -      -
     31H  TRP*     3.5    45.8    -      -       +      -
     32H  ASN      3.7    13.0    -      -       -      +
     33H  GLN*     4.8     4.7    -      -       +      +
    104H  CYS*     3.3     2.3    -      -       -      -
    105H  ARG*     2.9    46.8    +      -       +      +
    107H  VAL*     5.0     3.1    -      -       +      -
    112H  ILE*     3.6    37.0    -      -       +      -
    123H  VAL*     5.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 21 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  LEU      4.3     0.4    -      -       -      -
     20H  VAL*     1.3    74.9    -      -       -      +
     22H  GLU*     1.3    60.9    +      -       -      +
     23H  GLU*     4.2     2.7    -      -       -      +
     30H  LEU      3.5     1.9    -      -       -      +
     31H  TRP*     3.5     1.4    -      -       -      -
     32H  ASN*     2.8    49.0    +      -       +      +
     33H  GLN      3.8     9.1    -      -       -      +
     34H  PRO*     4.1     4.3    -      -       +      -
     55H  GLU*     3.4    50.3    -      -       +      +
     56H  THR*     3.6    14.8    -      -       +      -
    101H  ILE*     4.3    17.9    -      -       +      -
    103H  CYS      3.8     3.1    -      -       -      +
    104H  CYS*     3.6    15.9    -      -       -      -
    157H  SO4      4.5     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20H  VAL      3.9     0.4    +      -       -      -
     21H  VAL*     1.3    71.2    -      -       -      +
     23H  GLU*     1.3    62.3    +      -       -      +
     29H  ALA*     3.6    30.7    -      -       +      +
     30H  LEU      3.4     4.7    -      -       -      +
     31H  TRP*     2.6    37.6    +      -       +      -
    101H  ILE*     3.8     3.2    -      -       -      +
    102H  ASP*     2.9    33.7    +      -       +      +
    103H  CYS*     2.8    30.3    +      -       -      +
    105H  ARG*     3.5    32.1    +      -       +      -
    117H  ASN*     4.8     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 23 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21H  VAL*     4.6     3.8    -      -       -      +
     22H  GLU*     1.3    75.4    -      -       -      +
     24H  THR*     1.3    61.6    +      -       -      +
     29H  ALA*     4.2     0.7    -      -       -      -
     30H  LEU*     2.6    48.4    +      -       -      +
     32H  ASN*     3.8    22.3    +      -       -      +
    100H  ASP*     3.4    25.1    -      -       +      +
    101H  ILE*     3.1    22.8    -      -       +      +
    102H  ASP*     4.1     5.8    -      -       -      -
    119H  ARG*     3.4    29.5    +      -       -      +
    157H  SO4      3.1    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23H  GLU*     1.3    74.9    -      -       -      +
     25H  ILE*     1.3    61.1    -      -       -      +
     26H  ASN*     4.5     0.4    -      -       -      -
     27H  GLY*     3.5    14.8    -      -       -      +
     28H  LYS      3.3    36.8    -      -       -      +
     29H  ALA*     3.6     7.0    -      -       +      +
     30H  LEU*     5.6     0.2    -      -       -      -
    100H  ASP      4.2     4.3    +      -       -      +
    102H  ASP*     3.0    24.7    +      -       -      +
----------------------------------------------------------
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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