Contacts of the strand formed by residues 18 - 23 (chain H) in PDB entry 1AXS


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 VAL 18 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  GLU*     3.5    38.1    -      -       +      +
     12H  MET*     4.2    15.5    -      -       +      -
     17H  SER*     1.3    80.1    +      -       -      +
     19H  LYS*     1.3    64.4    +      -       -      +
     20H  ILE*     4.8     4.9    -      -       +      -
     80H  MET      3.7     0.2    -      -       -      +
     81H  GLN*     3.1     7.8    -      -       -      +
     82H  LEU*     3.0    65.0    +      -       +      -
    109H  VAL*     4.3    12.6    -      -       +      -
    823H  LEU*     3.8    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 19 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  SER*     4.2     4.2    +      -       -      -
     10H  GLU*     4.4     9.2    -      -       -      +
     18H  VAL*     1.3    80.7    -      -       -      +
     20H  ILE*     1.3    62.2    +      -       -      +
     21H  SER*     4.0     2.4    +      -       -      -
     70H  THR*     4.0     7.0    +      -       -      +
     79H  TYR*     3.0    58.8    -      -       +      +
     80H  MET      3.4     3.6    -      -       -      +
     81H  GLN*     4.2    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 20 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLU*     4.2     3.1    -      -       -      +
      7H  SER*     3.3    13.7    -      -       -      +
     10H  GLU*     4.9     3.4    -      -       -      +
     18H  VAL*     4.8     4.7    -      -       +      -
     19H  LYS*     1.3    73.3    -      -       -      +
     21H  SER*     1.3    71.0    +      -       -      +
     36H  TRP*     3.8    17.4    -      -       +      -
     79H  TYR*     3.1     8.2    -      -       -      +
     80H  MET*     2.9    63.3    +      -       +      +
     82H  LEU*     4.2    10.3    -      -       +      -
     90H  TYR*     3.7    27.6    -      -       +      -
    107H  THR*     3.3    30.3    -      -       +      +
    109H  VAL*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 21 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5H  LEU      4.1     1.1    -      -       -      -
      6H  GLU*     3.1     9.9    -      -       -      +
      7H  SER*     3.0    45.4    +      -       -      -
     19H  LYS      4.0     1.8    +      -       -      -
     20H  ILE*     1.3    76.5    -      -       -      +
     22H  CYS*     1.3    64.1    +      -       -      +
     23H  LYS*     4.1     1.3    -      -       -      -
     77H  THR*     4.0     6.5    -      -       -      -
     78H  ALA      3.3     5.2    -      -       -      -
     79H  TYR*     3.6    23.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 22 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     3.4    24.0    -      -       -      -
      5H  LEU      3.3     5.4    -      -       -      -
     21H  SER*     1.3    77.0    -      -       -      +
     23H  LYS*     1.3    63.1    +      -       -      +
     24H  ALA*     3.4     3.6    +      -       -      -
     29H  PHE*     4.8     1.2    -      -       -      -
     34H  ILE*     4.6     9.6    -      -       -      -
     36H  TRP*     3.6    16.8    -      -       +      -
     77H  THR*     3.5     1.9    -      -       -      +
     78H  ALA*     2.8    34.3    +      -       +      +
     92H  CYS*     2.0    49.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 23 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3H  GLN*     3.2     9.5    -      -       -      +
      4H  LEU*     3.3     2.5    -      -       -      -
      5H  LEU*     2.7    45.7    +      -       +      +
     21H  SER*     5.2     1.0    -      -       -      -
     22H  CYS*     1.3    71.5    -      -       -      +
     24H  ALA*     1.3    75.2    +      -       -      +
     25H  THR*     4.7     5.7    -      -       -      +
     75H  SER*     3.8    22.9    +      -       -      +
     76H  ASN*     3.8     2.0    -      -       +      -
     77H  THR*     3.4    22.6    +      -       +      +
----------------------------------------------------------
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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