Contacts of the strand formed by residues 29 - 35 (chain G) 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 ASP 29 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25G  GLU*     3.2     5.8    -      -       -      -
     26G  PHE      3.0    30.7    +      -       -      +
     27G  ASP      3.3     2.0    -      -       -      +
     28G  GLY*     1.3    78.2    -      -       -      +
     30G  GLU*     1.3    61.5    +      -       -      +
     31G  LEU      3.5     0.2    +      -       -      -
    138G  PHE*     3.9     3.7    -      -       -      -
    123H  TYR*     3.8    23.0    +      -       -      -
    149H  ARG*     3.1    27.1    +      -       -      +
    151H  GLY*     4.0    16.5    -      -       -      -
    153H  TRP*     3.4    51.1    +      -       +      +
    154H  THR      5.2     0.2    +      -       -      -
    155H  PHE*     4.5     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 30 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23G  THR*     5.1     4.3    -      -       +      -
     24G  PHE      3.8     5.2    -      -       -      +
     25G  GLU*     4.6     2.7    -      -       +      -
     29G  ASP*     1.3    72.5    +      -       -      +
     31G  LEU*     1.3    62.8    +      -       -      +
     32G  PHE*     3.7    21.0    -      -       -      +
     33G  TYR*     3.2    30.2    -      -       -      -
     42G  ILE      4.7     1.0    -      -       -      +
     44G  MET*     3.5    36.4    -      -       +      +
    133G  TYR*     4.9     0.9    +      -       -      -
    135G  THR*     4.1     0.4    -      -       -      -
    136G  SER*     3.1    36.6    +      -       -      -
    138G  PHE*     3.4    26.2    -      -       +      -
    151H  GLY      5.4     0.4    +      -       -      -
    153H  TRP*     2.9    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  TYR*     4.4     2.0    -      -       +      -
     24G  PHE*     2.9    30.1    +      -       +      +
     25G  GLU      3.9     9.9    -      -       -      +
     26G  PHE*     3.9    24.0    -      -       +      +
     29G  ASP      3.5     0.4    +      -       -      -
     30G  GLU*     1.3    71.9    -      -       -      +
     32G  PHE*     1.3    77.9    +      -       +      +
     43G  TRP*     3.5    12.4    -      -       +      -
     44G  MET*     3.1    21.1    +      -       -      +
     45G  LEU      4.7     0.7    +      -       -      -
     48G  PHE*     4.0    14.7    -      -       +      -
     52G  ARG*     3.3    42.0    -      -       -      +
     86H  GLU*     4.0     4.0    -      -       -      +
    153H  TRP*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 32 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  TYR*     4.9     2.0    -      +       -      -
     23G  THR*     3.4     5.2    -      -       -      -
     24G  PHE*     3.1    73.9    +      +       +      +
     30G  GLU*     3.4    11.8    -      -       -      +
     31G  LEU*     1.3    85.7    -      -       +      +
     33G  TYR*     1.3    69.6    +      -       -      +
     34G  VAL*     4.1     7.4    -      -       +      -
     41G  THR*     3.5    14.1    -      -       +      -
     42G  ILE      3.1    25.1    -      -       -      +
     43G  TRP*     3.4    47.1    -      +       -      -
     44G  MET      4.6     0.4    -      -       -      +
     52G  ARG*     5.4     0.7    -      -       -      -
     54G  PHE*     3.5    36.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21G  GLN*     5.4     3.6    -      -       +      -
     22G  TYR      3.1    14.1    -      -       -      +
     23G  THR*     3.6    14.6    -      -       +      -
     30G  GLU*     3.2    20.0    -      -       -      -
     32G  PHE*     1.3    76.0    -      -       -      +
     34G  VAL*     1.3    71.2    +      -       -      +
     35G  ASP*     4.1    18.4    +      -       +      -
     41G  THR*     3.9     0.3    -      -       -      -
     42G  ILE*     2.9    66.5    +      -       +      +
    133G  TYR*     5.3     9.4    -      +       -      -
    134G  GLU      6.0     1.6    -      -       -      -
    135G  THR      6.5     0.4    -      -       -      -
    136G  SER*     3.5    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 34 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21G  GLN*     5.8     0.3    -      -       -      -
     22G  TYR*     2.9    44.3    +      -       +      +
     32G  PHE*     4.1    15.0    -      -       +      -
     33G  TYR*     1.3    80.5    -      -       -      +
     35G  ASP*     1.3    64.8    +      -       -      +
     36G  LEU*     3.1    33.0    +      -       +      +
     39G  LYS*     5.1     1.3    -      -       -      -
     40G  GLU      3.5     4.9    -      -       -      +
     41G  THR*     4.5     5.4    -      -       -      +
     54G  PHE*     4.2    13.7    -      -       +      -
     56G  PRO*     3.9    37.5    -      -       +      +
     59G  GLY*     4.5     1.6    -      -       -      -
     60G  LEU*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 35 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33G  TYR*     3.7    18.0    +      -       +      -
     34G  VAL*     1.3    67.8    -      -       -      +
     36G  LEU*     1.3    52.3    +      -       -      +
     37G  ASP*     3.1    12.4    +      -       -      +
     38G  LYS*     2.7    59.7    +      -       +      +
     39G  LYS*     2.6    37.6    +      -       -      -
     40G  GLU      2.8    17.2    +      -       -      +
     42G  ILE*     4.0    15.4    -      -       +      +
----------------------------------------------------------
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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