Contacts of the strand formed by residues 13 - 21 (chain A) in PDB entry 1U0O


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 CYS 13 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  ASP      4.2     3.4    -      -       -      -
      2A  CYS*     2.0    49.1    -      -       -      -
      3A  PRO*     4.1     9.0    -      -       +      -
      6A  TRP*     3.1    33.6    -      -       +      -
      7A  SER      3.0     3.4    -      -       -      -
     12A  ASN*     1.3    74.7    -      -       -      +
     14A  TYR*     1.3    62.9    +      -       -      +
    129A  LYS*     3.5     0.5    -      -       -      -
    130A  SER*     2.8    36.9    +      -       -      +
    131A  PRO      4.5     0.4    -      -       -      -
    132A  PRO*     4.3    16.8    -      -       -      -
    133A  PRO*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TRP*     3.1     3.4    -      -       -      -
      7A  SER*     2.5    46.6    +      -       -      +
      9A  TYR*     3.2    41.3    +      +       +      -
     10A  GLU*     5.8     0.2    -      -       -      +
     12A  ASN*     3.9     8.7    +      -       +      +
     13A  CYS*     1.3    75.5    -      -       -      +
     15A  LYS*     1.3    60.0    +      -       -      +
     40A  VAL*     3.4    27.4    -      -       +      -
     48A  GLU*     2.5    32.4    +      -       +      +
     51A  PHE*     3.4    28.0    -      +       +      -
     52A  VAL*     4.2     7.9    -      -       +      -
     55A  LEU*     4.6     6.7    -      -       +      -
    127A  VAL*     4.4     6.5    -      -       +      -
    128A  CYS      3.3     7.6    -      -       -      +
    129A  LYS*     3.2    41.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER      4.7     2.5    -      -       -      -
      5A  GLY*     4.4    17.3    -      -       -      +
      6A  TRP*     3.3    47.6    -      -       +      +
      7A  SER*     4.8     1.1    -      -       -      +
     14A  TYR*     1.3    77.2    -      -       -      +
     16A  PHE*     1.3    67.9    +      -       -      +
     17A  PHE*     3.4    43.4    -      -       +      -
     33A  GLN*     5.2     1.1    -      -       -      +
     55A  LEU*     4.5     4.5    -      -       -      +
    127A  VAL*     3.1     8.8    -      -       -      +
    128A  CYS      2.9    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LYS*     1.3    88.5    +      -       -      +
     17A  PHE*     1.3    72.8    +      -       -      +
     18A  GLN*     3.4    50.0    +      -       +      -
     55A  LEU*     4.0    17.9    -      -       +      +
     56A  VAL*     4.3    12.1    -      -       +      -
     59A  ASN*     3.3    40.5    +      -       +      +
     60A  ILE*     3.5    34.8    -      -       +      -
     67A  ALA*     5.2     1.1    -      -       +      -
    125A  PRO*     3.9    12.1    -      -       +      -
    126A  PHE*     3.1    23.8    -      -       -      -
    127A  VAL*     4.2     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  TRP*     4.1     7.6    -      +       -      -
     15A  LYS*     3.4    53.6    -      -       +      -
     16A  PHE*     1.3    79.8    -      -       -      +
     18A  GLN*     1.3    64.6    +      -       -      +
     19A  GLN*     3.4     7.1    +      -       +      +
     29A  PHE*     3.2    19.1    -      +       -      -
     33A  GLN*     3.1    32.1    -      -       +      -
    125A  PRO*     3.1     3.1    -      -       -      +
    126A  PHE*     2.7    68.8    +      +       +      +
    128A  CYS*     3.5    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     3.4    23.3    +      -       +      -
     17A  PHE*     1.3    71.2    -      -       -      +
     19A  GLN*     1.3    53.5    +      -       -      +
     20A  LYS*     2.8    27.0    +      -       -      +
     59A  ASN      5.4     0.4    -      -       -      +
     60A  ILE*     3.6     6.2    -      -       -      +
     61A  GLN*     3.3    41.5    +      -       +      +
     64A  ASP*     3.2    23.4    +      -       -      -
    125A  PRO*     3.3    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  PHE*     3.2     5.6    -      -       +      +
     18A  GLN*     1.3    74.1    -      -       -      +
     20A  LYS*     1.3    61.0    +      -       -      +
     21A  MET*     2.9    37.1    -      -       +      +
     29A  PHE*     3.4    31.3    -      -       -      -
    125A  PRO*     4.3     0.2    -      -       -      -
    126A  PHE*     3.0    34.8    -      -       +      -
----------------------------------------------------------
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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  GLN*     2.8    17.2    +      -       -      +
     19A  GLN*     1.3    71.2    -      -       -      +
     21A  MET*     1.3    63.7    +      -       -      +
     64A  ASP*     2.7    44.7    +      -       -      -
    123A  LYS*     3.3    43.7    -      -       +      +
    124A  ASN      3.3     7.6    -      -       -      -
    125A  PRO*     4.0    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLN*     2.9    41.7    +      -       +      +
     20A  LYS*     1.3    78.9    -      -       -      +
     22A  ASN*     1.3    67.5    +      -       -      +
     25A  ASP*     3.0    43.5    -      -       +      +
     26A  ALA*     4.0     2.9    -      -       +      +
     29A  PHE*     3.8    15.5    -      -       +      -
     68A  TRP*     3.1     5.2    +      -       -      -
    122A  GLN      3.7     2.0    -      -       -      -
    123A  LYS*     3.8    13.2    -      -       -      +
    124A  ASN      2.7    30.1    +      -       -      +
    126A  PHE*     3.4    22.0    -      -       +      -
----------------------------------------------------------
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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