Contacts of the strand formed by residues 124 - 128 (chain A) in PDB entry 5UHF


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 HIS 124 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  GLU*     3.7     6.7    +      -       -      -
     79A  ASN*     4.0    17.4    -      -       -      +
    104A  GLU*     3.3    28.7    +      -       +      +
    105A  VAL      4.3     3.4    -      -       -      -
    106A  THR*     4.3     4.5    -      -       -      +
    122A  GLY      3.6     4.9    +      -       -      -
    123A  MET*     1.3    79.1    -      -       -      +
    125A  ILE*     1.3    80.4    +      -       -      +
    126A  ALA*     3.1    32.3    +      -       -      -
    127A  THR*     3.2    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  GLU*     4.6     1.6    -      -       -      -
     76A  ILE*     4.3    25.3    -      -       +      +
     79A  ASN*     2.7    28.6    +      -       +      +
     80A  LEU*     4.1    25.6    -      -       +      -
     97A  LEU*     3.9    19.1    -      -       +      -
    105A  VAL*     3.3    21.4    +      -       +      +
    106A  THR      3.7    21.3    -      -       -      +
    107A  ALA*     4.1     7.0    -      -       -      +
    110A  ILE*     4.7     2.5    -      -       +      -
    123A  MET*     3.3    22.6    +      -       +      +
    124A  HIS*     1.3    80.2    -      -       -      +
    126A  ALA*     1.3    67.3    +      -       +      +
    134A  LEU*     5.2     5.2    -      -       +      -
    136A  VAL*     6.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  VAL*     3.9    19.1    -      -       +      -
     71A  GLU*     3.6    12.6    -      -       -      +
     76A  ILE*     4.6     6.1    -      -       +      -
    104A  GLU*     3.5     2.1    -      -       -      +
    105A  VAL*     3.4    35.4    +      -       +      +
    124A  HIS*     3.1    18.7    +      -       -      -
    125A  ILE*     1.3    85.7    -      -       +      +
    127A  THR*     1.3    59.9    +      -       -      +
    128A  LEU*     3.7     5.4    -      -       +      -
    134A  LEU*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  VAL*     4.7     0.2    -      -       -      -
     70A  LYS*     3.4    37.4    +      -       +      +
     71A  GLU*     2.9    24.7    +      -       -      -
    103A  GLY      6.3     0.4    -      -       -      -
    104A  GLU*     4.9     9.9    -      -       +      +
    124A  HIS*     3.2    18.6    +      -       -      -
    126A  ALA*     1.3    71.7    -      -       -      +
    128A  LEU*     1.3    66.2    +      -       -      +
    129A  ASN*     3.1     6.2    +      -       +      +
    653C  VAL*     6.0     2.5    -      -       +      -
    691C  ASP*     3.7    22.4    +      -       -      +
    692C  ALA*     6.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY      4.4     3.1    -      -       -      -
     69A  VAL*     4.6     8.7    -      -       +      +
     99A  LYS*     3.2    35.4    -      -       +      +
    100A  GLN*     4.3     0.7    -      -       -      +
    101A  GLY      3.8     8.1    -      -       -      +
    102A  PRO*     3.7     0.5    -      -       -      +
    103A  GLY      3.3    37.6    +      -       -      +
    105A  VAL*     3.8    32.3    -      -       +      -
    126A  ALA*     3.7     6.0    -      -       +      -
    127A  THR*     1.3    73.4    -      -       -      +
    129A  ASN*     1.3    62.7    +      -       -      +
    132A  GLY*     3.3    27.4    -      -       -      +
    134A  LEU*     4.0    28.3    -      -       +      +
----------------------------------------------------------
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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