Contacts of the strand formed by residues 31 - 34 (chain B) 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 ASN 31 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  HIS*     4.0     1.4    -      -       -      +
     30B  ASN*     1.3    81.8    -      -       -      +
     32B  MET*     1.3    65.0    +      -       -      +
     33B  TYR*     2.8    36.6    +      -       +      +
     48B  TYR*     5.1     2.4    -      -       -      -
     49B  SER      3.2    10.6    +      -       -      +
     50B  TYR*     4.1    10.6    -      -       -      -
     94B  SER*     3.2     6.6    -      -       -      -
     95B  GLY      3.0    33.4    +      -       -      +
     96B  ASP      3.5     9.2    -      -       -      +
     97B  ALA*     3.1    18.5    -      -       -      +
     98B  GLY      3.5     6.3    +      -       -      -
     61C  GLN*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  CYS*     5.1     1.6    -      -       -      -
     25B  GLN*     3.4    27.1    -      -       +      -
     31B  ASN*     1.3    76.7    -      -       -      +
     33B  TYR*     1.3    64.3    +      -       -      +
     48B  TYR*     3.0     6.2    -      -       -      +
     49B  SER      2.8    30.7    +      -       -      -
     69B  ARG*     2.9    48.7    -      -       -      +
     72B  GLN      3.1    14.1    -      -       -      +
     73B  GLU      3.4     4.3    -      -       -      +
     74B  ASN      3.4    29.6    -      -       -      +
     75B  PHE*     3.4    28.7    -      -       +      -
     92B  CYS*     5.1     7.2    -      -       -      -
     93B  ALA      3.2    12.1    -      -       -      +
     94B  SER*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  TYR*     4.4    17.3    -      -       +      -
     31B  ASN*     2.8    49.7    +      -       +      +
     32B  MET*     1.3    77.9    -      -       -      +
     34B  TRP*     1.3    62.5    +      -       -      +
     35B  TYR*     3.4    23.1    -      -       +      -
     45B  LEU*     3.7    14.8    -      -       +      -
     47B  TYR      3.6     4.7    -      -       -      -
     48B  TYR*     3.6    21.8    -      +       +      -
     75B  PHE*     3.8     3.5    -      -       -      -
     92B  CYS*     3.3     8.7    -      -       -      -
     93B  ALA*     2.8    42.3    +      -       +      +
     95B  GLY*     4.2     5.9    -      -       -      -
     96B  ASP      4.3     2.8    +      -       -      -
     98B  GLY      3.6    10.7    +      -       -      -
     99B  GLY*     5.1     1.7    -      -       -      -
    106B  GLN*     3.3    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLN*     4.4     9.4    -      -       +      -
     21B  LEU*     3.8    25.6    -      -       +      -
     22B  SER      3.8    16.4    -      -       -      -
     23B  CYS*     3.6    21.1    -      -       +      -
     33B  TYR*     1.3    73.1    -      -       -      +
     35B  TYR*     1.3    59.3    +      -       -      +
     45B  LEU*     3.4     2.6    -      -       -      +
     46B  ILE*     2.7    34.0    +      -       +      +
     47B  TYR      2.9    14.1    +      -       -      +
     75B  PHE*     3.2    50.2    +      +       -      -
     76B  SER      3.4    12.1    -      -       -      -
     77B  LEU*     3.8    43.3    -      -       +      -
     90B  TYR*     4.0    24.9    -      -       +      -
     91B  PHE      3.7     4.9    -      -       -      -
     92B  CYS*     3.7    28.9    -      -       +      -
    112B  THR*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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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