Contacts of the strand formed by residues 17 - 25 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL      3.8     0.2    -      -       -      +
     13A  HIS*     3.3     7.2    +      -       -      -
     14A  ALA      2.9    31.7    +      -       -      +
     15A  GLU*     3.2    15.7    -      -       +      +
     16A  GLY*     1.3    86.6    -      -       -      +
     18A  PHE*     1.3    67.5    +      -       -      +
     91A  ILE*     4.3    14.1    -      -       +      -
    106A  TRP*     4.1    20.5    +      -       +      +
    107A  VAL      3.4    16.6    -      -       -      +
    108A  SER*     3.9    26.6    -      -       -      +
    111A  GLU*     4.9     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.6    24.7    -      -       +      -
     12A  VAL      3.3     9.9    -      -       -      +
     13A  HIS*     3.4    29.4    -      +       +      -
     16A  GLY      4.8     2.5    -      -       -      -
     17A  LYS*     1.3    78.7    -      -       -      +
     19A  LEU*     1.3    64.5    +      -       -      +
     20A  VAL*     3.8     0.7    +      -       -      +
     33A  GLN*     6.0     1.1    -      -       -      +
    105A  ARG      3.7     0.5    -      -       -      +
    106A  TRP*     3.3     4.4    -      -       -      -
    107A  VAL*     2.6    47.7    +      -       -      +
    109A  ALA*     3.6    35.2    -      -       +      -
    112A  ILE*     3.8    15.4    -      -       +      +
    127A  ILE*     4.1    16.4    -      -       +      -
    130A  TYR*     3.4    37.7    -      +       -      -
    131A  GLN*     4.6     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  CYS      5.1     0.5    -      -       -      +
     12A  VAL*     3.0    28.4    +      -       +      +
     18A  PHE*     1.3    71.6    -      -       -      +
     20A  VAL*     1.3    68.8    +      -       -      +
     32A  ASN      4.4     0.3    -      -       -      +
     33A  GLN*     4.5     5.4    +      -       -      +
     34A  PRO*     3.7    26.3    -      -       +      +
     52A  LEU*     4.4     4.3    -      -       +      -
     56A  THR*     3.5    30.5    -      -       +      -
     58A  ILE*     4.3    13.9    -      -       +      -
     94A  THR*     4.2     2.9    -      -       +      -
    104A  CYS*     3.7    22.7    -      -       +      -
    105A  ARG      3.5    13.0    -      -       -      +
    106A  TRP*     3.6    44.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE      4.5     2.2    -      -       -      +
     19A  LEU*     1.3    83.2    -      -       -      +
     21A  VAL*     1.3    63.3    +      -       -      +
     31A  TRP*     3.6    45.5    -      -       +      -
     32A  ASN      3.4    14.6    -      -       -      +
     33A  GLN*     5.0     4.5    -      -       -      +
    104A  CYS*     3.3     6.9    -      -       -      +
    105A  ARG*     2.8    49.5    +      -       +      +
    107A  VAL*     5.0     2.7    -      -       +      -
    112A  ILE*     3.9    33.2    -      -       +      -
    123A  VAL*     5.1     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     1.3    78.6    -      -       -      +
     22A  GLU*     1.3    59.0    +      -       -      +
     23A  GLU*     3.8    17.0    +      -       -      +
     30A  LEU      3.3     5.4    -      -       -      +
     31A  TRP*     3.4     1.9    -      -       -      -
     32A  ASN*     2.8    45.7    +      -       -      +
     33A  GLN      3.6     8.1    -      -       -      +
     34A  PRO*     4.2     5.8    -      -       +      -
     55A  GLU*     3.5    50.0    -      -       +      +
     56A  THR*     4.0    16.8    -      -       +      -
    101A  ILE*     3.9    12.3    -      -       +      -
    103A  CYS      3.6     2.2    -      -       -      -
    104A  CYS*     4.1     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     4.2     1.0    +      -       -      +
     21A  VAL*     1.3    69.4    -      -       -      +
     23A  GLU*     1.3    58.1    +      -       -      +
     29A  ALA*     3.8    28.0    -      -       +      +
     30A  LEU      3.3     7.0    -      -       -      +
     31A  TRP*     3.0    29.4    +      -       +      -
    101A  ILE*     3.5     3.3    -      -       -      -
    102A  ASP*     2.7    43.3    +      -       +      +
    103A  CYS*     2.9    34.1    +      -       -      +
    105A  ARG*     3.2    29.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     3.8    15.3    +      -       -      +
     22A  GLU*     1.3    72.1    -      -       -      +
     24A  THR*     1.3    62.4    +      -       -      +
     25A  ILE*     3.2    17.1    +      -       +      +
     29A  ALA*     4.3     1.1    -      -       -      -
     30A  LEU      2.8    32.8    +      -       -      +
     32A  ASN*     3.9     6.2    -      -       -      +
    100A  ASP*     3.2    28.9    -      -       +      +
    101A  ILE*     3.5    19.0    -      -       +      +
    102A  ASP*     3.6     0.9    -      -       -      -
    119A  ARG*     2.8    31.4    +      -       -      +
    157A  SO4      2.7    32.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLU*     1.3    70.7    -      -       -      +
     25A  ILE*     1.3    61.9    +      -       -      +
     26A  ASN      4.1     1.0    +      -       -      -
     27A  GLY*     3.8    28.3    -      -       -      +
     28A  LYS      3.2    13.2    -      -       -      +
     29A  ALA*     4.1     7.6    -      -       -      +
    100A  ASP      4.4     3.3    +      -       -      +
    102A  ASP*     2.5    30.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLU*     3.4    22.7    -      -       +      +
     24A  THR*     1.3    75.2    -      -       -      +
     26A  ASN*     1.3    90.2    +      -       -      +
     27A  GLY      3.5     0.2    -      -       -      -
     28A  LYS*     2.6    22.8    +      -       -      +
     30A  LEU*     3.5    29.0    -      -       +      +
    119A  ARG*     3.8    29.6    -      -       -      +
----------------------------------------------------------
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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