Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 1U3H


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 72 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  CYS      3.6     7.2    -      -       -      +
     23A  SER*     4.6     4.3    -      -       -      +
     24A  TYR*     4.4     0.6    -      -       -      -
     66A  PHE*     4.2     5.9    -      -       -      -
     67A  ASN*     3.3    44.4    +      -       +      +
     70A  GLU*     3.4    43.9    +      -       +      +
     71A  LYS*     1.3    78.1    -      -       -      +
     73A  LEU*     1.3    66.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ASN*     3.6     1.7    -      -       -      +
     22A  CYS*     2.7    37.6    +      -       +      +
     24A  TYR*     5.0     4.0    -      -       +      -
     32A  PHE*     3.8    33.4    -      -       +      -
     34A  TRP*     3.9    11.9    -      -       +      +
     49A  ILE*     4.5     2.5    -      -       +      -
     64A  ILE*     3.2    33.4    -      -       +      -
     65A  PHE      3.4    11.2    -      -       -      +
     66A  PHE*     3.5    22.9    -      -       +      -
     72A  LYS*     1.3    80.1    -      -       -      +
     74A  SER*     1.3    65.1    +      -       -      +
     90A  CYS*     3.7    28.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     4.6     0.4    -      -       -      -
     20A  LEU      2.9    19.3    -      -       -      -
     21A  ASN*     3.8    12.3    -      -       -      +
     34A  TRP*     4.3     6.1    -      -       -      -
     63A  THR      3.7     1.2    -      -       -      +
     64A  ILE*     3.3     3.5    -      -       -      +
     65A  PHE*     2.7    49.1    +      -       -      +
     73A  LEU*     1.3    78.1    -      -       -      +
     75A  LEU*     1.3    57.6    -      -       -      +
     76A  HIS*     3.0    25.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ALA      3.4     4.3    -      -       -      +
     20A  LEU*     3.0    43.9    +      -       +      +
     34A  TRP*     3.6    51.6    -      -       +      -
     46A  LEU*     4.6    15.9    -      -       +      -
     47A  ILE*     5.4     2.9    -      -       +      -
     62A  PHE*     4.3    13.2    -      -       +      -
     63A  THR      3.6    24.5    -      -       -      +
     64A  ILE*     4.4    10.1    -      -       +      +
     74A  SER*     1.3    72.3    -      -       -      +
     76A  HIS*     1.3    66.5    +      -       -      +
     77A  ILE*     3.9    13.6    +      -       +      +
     88A  TYR*     4.8     6.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  THR*     4.6    11.0    -      -       +      +
     18A  ALA      3.4     4.3    -      -       -      +
     19A  ILE*     3.5    40.7    -      -       +      +
     61A  ARG      3.1    14.9    -      -       -      +
     62A  PHE*     3.6     1.4    -      -       -      -
     63A  THR*     2.8    30.0    +      -       -      +
     65A  PHE*     3.7    38.5    -      +       +      -
     74A  SER*     3.0    29.1    +      -       -      -
     75A  LEU*     1.3    75.7    -      -       -      +
     77A  ILE*     1.3    61.3    +      -       -      +
     78A  ALA*     3.7     2.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLU      3.8     1.7    -      -       -      +
     17A  THR*     3.5     2.1    -      -       -      -
     18A  ALA*     2.7    41.3    +      -       +      +
     20A  LEU*     5.3     2.5    -      -       +      -
     61A  ARG*     3.7     7.2    -      -       +      +
     62A  PHE*     3.5    40.4    -      -       +      -
     75A  LEU*     4.4    14.8    -      -       +      +
     76A  HIS*     1.3    73.0    -      -       -      +
     78A  ALA*     1.3    67.5    +      -       -      +
     79A  ASP      3.7     0.2    +      -       -      -
     80A  SER*     4.0     9.0    +      -       -      -
     84A  ASP*     3.9    17.7    -      -       +      +
     88A  TYR*     3.6    34.3    -      -       +      +
    112A  LEU*     4.2    12.8    -      -       +      -
----------------------------------------------------------
 Back to top of page


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