Contacts of the strand formed by residues 14 - 23 (chain A) in PDB entry 1UEX


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 14 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  SER*     3.5     2.6    -      -       -      -
     11A  TYR      2.8    34.9    +      -       -      +
     12A  LYS*     3.3    40.4    +      -       +      +
     13A  GLY*     1.3    81.6    +      -       -      +
     15A  CYS*     1.3    64.9    +      -       -      +
     16A  TYR*     3.7    18.8    -      -       +      +
    126A  LYS*     3.3    32.5    +      -       +      -
    127A  SER      3.2    18.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  CYS*     2.0    51.6    -      -       +      -
      8A  TRP*     3.3    16.1    -      -       +      -
      9A  SER      3.6     4.3    -      -       -      +
     10A  SER*     4.3     2.0    -      -       -      -
     13A  GLY      5.8     0.4    -      -       -      -
     14A  HIS*     1.3    79.2    -      -       -      +
     16A  TYR*     1.3    60.7    +      -       -      +
    126A  LYS*     3.1     5.6    -      -       -      -
    127A  SER*     2.9    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TRP*     3.4     7.1    -      -       -      +
      9A  SER*     2.8    39.3    +      -       -      +
     11A  TYR*     3.3    32.4    -      +       +      -
     14A  HIS*     3.7    25.2    -      -       +      +
     15A  CYS*     1.3    73.0    -      -       -      +
     17A  LYS*     1.3    65.5    +      -       -      +
     40A  ALA*     4.5     7.6    -      -       +      -
     47A  GLU*     3.0    32.9    +      -       +      +
     50A  PHE*     3.5    28.5    -      +       -      -
     51A  VAL*     4.3    19.5    -      -       +      -
     54A  LEU*     3.5    17.7    -      -       +      -
    124A  ILE*     4.6     3.4    -      -       +      -
    125A  CYS      3.1     8.7    -      -       -      +
    126A  LYS*     3.9    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASP*     2.8    53.4    +      -       -      +
      8A  TRP*     3.2    30.7    -      -       +      +
      9A  SER*     6.0     0.2    -      -       -      -
     16A  TYR*     1.3    81.7    -      -       -      +
     18A  VAL*     1.3    71.9    +      -       -      +
     19A  PHE*     3.3    41.0    -      -       +      -
     54A  LEU*     4.2     4.9    -      -       -      +
    124A  ILE*     3.6     2.0    -      -       -      +
    125A  CYS      3.3    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LYS*     1.3    87.6    -      -       -      +
     19A  PHE*     1.3    66.0    +      -       -      +
     20A  LYS      4.0     1.2    +      -       -      -
     54A  LEU*     3.7    29.3    -      -       +      +
     55A  ALA*     3.9    11.9    -      -       +      +
     58A  THR*     3.9    26.8    +      -       +      +
     59A  LEU*     3.9    39.7    -      -       +      -
    122A  PRO*     5.2     0.2    -      -       +      -
    123A  PHE      3.5    11.0    -      -       -      +
    124A  ILE*     4.0    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TRP*     3.7    16.6    -      +       -      -
     17A  LYS*     3.3    61.5    -      -       +      -
     18A  VAL*     1.3    74.9    -      -       -      +
     20A  LYS*     1.3    61.7    +      -       -      +
     21A  LYS*     3.4    10.3    +      -       +      +
     31A  PHE*     3.6    28.0    -      +       -      -
     35A  ASN*     5.6     0.4    -      -       -      -
    122A  PRO*     3.1    27.1    -      -       -      +
    123A  PHE*     3.1    45.5    +      +       +      +
    125A  CYS*     3.6    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  VAL*     4.0     1.8    +      -       -      +
     19A  PHE*     1.3    70.0    -      -       -      +
     21A  LYS*     1.3    67.6    +      -       +      +
     22A  VAL*     3.4     8.7    +      -       -      +
     58A  THR*     5.1    10.6    -      -       +      +
     59A  LEU*     3.4    14.3    -      -       +      +
     61A  LYS*     3.1    43.8    -      -       -      +
     64A  TYR*     5.7     5.6    -      -       -      -
    122A  PRO*     3.7    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.2    13.4    -      -       +      +
     20A  LYS*     1.3    79.8    -      -       +      +
     22A  VAL*     1.3    64.2    +      -       -      +
    122A  PRO*     3.7     1.7    -      -       -      +
    123A  PHE*     3.5    21.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS*     4.1     8.7    -      -       -      +
     21A  LYS*     1.3    80.1    -      -       -      +
     23A  GLY*     1.3    58.6    +      -       -      +
     64A  TYR*     4.3    17.9    -      -       +      +
    120A  LYS*     3.4    49.1    -      -       +      +
    121A  ASN      3.4    12.6    -      -       -      -
    122A  PRO*     4.3     2.2    -      -       +      -
    123A  PHE*     4.8     4.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     1.3    81.3    -      -       -      +
     24A  THR*     1.3    70.1    +      -       -      +
     27A  ASP*     4.5    11.2    -      -       -      -
     28A  ALA*     4.5     3.2    -      -       -      +
     67A  TRP*     3.1    17.7    +      -       -      -
    120A  LYS*     3.8    15.1    -      -       -      +
    121A  ASN      3.2    11.5    +      -       -      +
    123A  PHE*     5.0     4.5    -      -       -      -
----------------------------------------------------------
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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