Contacts of the strand formed by residues 117 - 123 (chain A) in PDB entry 1EUB


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 117 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  LYS*     3.1    10.3    -      -       -      +
    116A  MET*     1.3    93.5    +      -       +      +
    118A  LEU*     1.3    71.3    +      -       -      +
    151A  LEU*     4.5     0.4    -      -       -      -
    152A  ASN*     3.2    29.6    -      -       +      +
    271A  GLU*     5.1     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  LYS*     3.8    30.1    -      -       +      +
    117A  ASN*     1.3    80.7    -      -       -      +
    119A  THR*     1.3    67.8    +      -       -      +
    120A  TYR*     4.7     0.2    -      -       -      -
    151A  LEU*     4.9     0.9    -      -       +      +
    152A  ASN      2.8     7.5    +      -       -      +
    153A  PHE*     3.1     9.2    -      -       -      -
    154A  THR*     3.0    19.5    +      -       -      -
    162A  ASP*     3.2    51.6    -      -       +      +
    163A  ILE*     4.6     2.9    -      -       +      -
    191A  PRO*     4.2     4.9    -      -       +      -
    228A  LEU*     3.4    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  LEU*     1.3    80.4    -      -       -      +
    120A  TYR*     1.3    64.0    +      -       -      +
    154A  THR*     2.6    40.8    -      -       +      +
    156A  LEU*     4.2     8.3    -      -       +      +
    160A  ILE*     2.6    43.0    +      -       +      +
    161A  ALA*     3.5     2.8    -      -       -      -
    162A  ASP*     2.8    23.2    +      -       -      +
    163A  ILE*     3.2    10.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  THR*     1.3    76.2    -      -       -      +
    121A  ARG*     1.3    66.0    +      -       -      +
    122A  ILE*     3.4    20.9    -      -       +      -
    138A  PHE*     3.6    12.5    -      +       -      -
    139A  LYS*     5.6     0.7    -      -       -      +
    142A  PHE*     2.9    41.2    -      +       +      +
    153A  PHE*     3.4    39.7    -      +       +      -
    154A  THR      2.9    16.2    +      -       -      -
    155A  ARG*     2.9    65.2    -      -       +      +
    161A  ALA*     3.9     8.7    -      -       -      +
    163A  ILE*     2.6    34.5    -      -       +      +
    224A  PHE*     4.0     3.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with ARG 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TYR*     1.3    78.5    -      -       -      +
    122A  ILE*     1.3    66.9    +      -       +      +
    123A  VAL*     3.9    25.4    +      -       +      +
    155A  ARG*     4.8     3.8    -      -       +      -
    156A  LEU      6.0     0.4    -      -       -      -
    157A  HIS*     4.7    26.3    +      -       -      +
    159A  GLY*     6.5     0.7    -      -       -      -
    161A  ALA*     4.1    15.9    -      -       +      +
    163A  ILE      2.9     6.7    +      -       -      -
    164A  MET*     3.1    22.1    -      -       +      +
    165A  ILE*     3.1    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TYR*     3.4    17.9    -      -       +      -
    121A  ARG*     1.3    76.2    -      -       +      +
    123A  VAL*     1.3    74.3    +      -       -      +
    131A  HIS*     6.4     2.0    -      -       +      -
    134A  VAL*     5.2     5.6    -      -       +      +
    135A  GLU*     5.6     2.0    -      -       +      -
    138A  PHE*     2.8    61.7    -      -       +      -
    155A  ARG*     3.2    33.4    -      -       +      +
    165A  ILE*     3.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ARG*     4.3    36.6    -      -       +      +
    122A  ILE*     1.3    86.9    -      -       -      +
    124A  ASN*     1.3    75.0    +      -       -      +
    125A  TYR*     3.5     2.4    -      -       -      -
    134A  VAL*     4.9     5.2    -      -       -      -
    164A  MET*     4.8     8.7    -      -       +      -
    165A  ILE*     2.7    19.3    +      -       -      +
    166A  SER*     3.2    20.8    -      -       -      +
    167A  PHE*     4.7     2.3    -      -       -      -
----------------------------------------------------------
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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