Contacts of the strand formed by residues 3 - 12 (chain G) in PDB entry 5U07


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 PHE 3 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2G  THR*     1.3    97.2    -      -       -      +
      4G  VAL*     1.3    65.3    +      -       -      +
      5G  ASP*     3.4     2.4    +      -       -      +
    187G  GLN*     6.1     3.6    -      -       -      -
    236G  ASN*     5.3     4.9    -      -       +      +
    237G  VAL      3.4     3.6    -      -       -      +
    238G  ASN*     3.3    46.7    -      -       +      -
    288G  VAL*     3.7     1.3    -      -       -      -
    289G  ARG*     2.9    38.8    +      -       +      +
    290G  PHE      4.0     6.7    -      -       -      -
    291G  ASP      3.9    15.3    -      -       -      -
    292G  ARG*     4.1     3.4    -      -       -      -
    293G  PRO*     3.6    45.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 4 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2G  THR      3.9     0.2    -      -       -      -
      3G  PHE*     1.3    71.2    -      -       -      +
      5G  ASP*     1.3    61.9    +      -       -      +
      6G  ILE*     5.2     2.3    -      -       +      +
    235G  ALA      3.9     0.7    -      -       -      +
    236G  ASN*     3.4     2.0    -      -       -      -
    237G  VAL*     2.8    44.5    +      -       +      +
    239G  LEU*     3.8    31.6    -      -       +      -
    256G  VAL*     4.9     8.1    -      -       +      -
    260G  LEU*     4.2    22.7    -      -       +      -
    286G  ILE*     3.9    24.0    -      -       +      -
    287G  ALA      3.7     4.9    -      -       -      +
    288G  VAL*     4.3    17.5    -      -       +      +
    363G  MET*     5.7     2.2    -      -       +      +
    364G  VAL*     5.9     3.8    -      -       +      -
    367G  ALA*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 5 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  PHE      3.9     5.6    -      -       -      +
      4G  VAL*     1.3    74.6    -      -       -      +
      6G  ILE*     1.3    59.8    +      -       -      +
      7G  HIS*     3.5    19.0    +      -       -      -
    234G  TYR*     3.5     7.0    -      -       +      +
    235G  ALA      3.2     4.7    -      -       -      +
    236G  ASN*     3.0    24.9    -      -       -      +
    285G  HIS      3.9     1.4    -      -       -      +
    286G  ILE*     3.6     2.9    -      -       -      +
    287G  ALA*     2.6    61.4    +      -       -      +
    289G  ARG*     4.3     6.6    +      -       -      +
    293G  PRO*     4.3     6.2    -      -       +      +
    294G  ILE*     3.5    23.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 6 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4G  VAL*     5.4     2.0    -      -       +      +
      5G  ASP*     1.3    76.2    -      -       -      +
      7G  HIS*     1.3    72.6    +      -       -      +
    233G  ARG      3.9     0.2    -      -       -      +
    234G  TYR*     3.3     6.1    -      -       -      -
    235G  ALA*     2.9    46.5    +      -       +      +
    237G  VAL*     6.3     0.9    -      -       +      -
    259G  PHE*     5.4     2.9    -      -       +      -
    260G  LEU*     4.4    21.3    -      -       +      -
    263G  PHE*     3.4    41.7    -      -       +      -
    264G  LEU*     4.0    17.3    -      -       +      -
    284G  VAL*     4.2     3.8    -      -       +      -
    285G  HIS      3.7     2.9    -      -       -      -
    286G  ILE*     4.0    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 7 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ASP*     3.5    21.7    +      -       -      -
      6G  ILE*     1.3    80.8    -      -       -      +
      8G  ALA*     1.3    66.2    +      -       -      +
    232G  TYR*     3.0    26.8    +      -       +      -
    233G  ARG      3.4     7.4    -      -       -      +
    234G  TYR*     3.5    16.4    -      +       -      -
    283G  LEU*     5.6     0.4    -      -       -      -
    284G  VAL*     3.5     1.9    -      -       -      -
    285G  HIS*     2.9    66.1    +      +       +      +
    287G  ALA*     5.0     0.2    -      -       -      +
    294G  ILE      3.4    23.2    +      -       -      -
    296G  PHE*     3.5    28.7    -      +       -      -
    318G  LEU*     4.7     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 8 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  HIS*     1.3    78.5    -      -       -      +
      9G  ILE*     1.3    66.0    +      -       -      +
     10G  GLN      4.1     0.2    -      -       -      -
    232G  TYR*     3.6     4.3    -      -       -      -
    233G  ARG*     2.9    56.0    +      -       +      +
    263G  PHE*     4.4    11.2    -      -       +      -
    264G  LEU*     4.7     0.2    -      -       +      -
    281G  PRO*     4.3    14.8    -      -       +      -
    283G  LEU*     3.1    13.5    -      -       -      +
    284G  VAL*     4.4     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 9 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  ALA*     1.3    72.1    -      -       -      +
     10G  GLN*     1.3    57.9    +      -       -      +
     11G  THR*     5.3     0.7    -      -       +      +
    194G  VAL*     4.7     4.7    -      -       +      -
    230G  THR*     4.7    15.0    -      -       -      +
    231G  PHE      3.5     5.2    -      -       -      +
    232G  TYR*     3.6    35.0    -      -       +      -
    281G  PRO*     3.3     3.0    -      -       -      +
    282G  ASP*     2.6    40.7    +      -       +      +
    283G  LEU*     2.9    27.3    +      -       +      +
    300G  PHE*     4.0    18.6    -      -       +      -
    311G  THR*     5.6     4.0    -      -       -      +
    314G  ALA*     4.6    18.8    -      -       +      +
    315G  CYS*     5.0    10.8    -      -       -      -
    318G  LEU*     4.1    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 10 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  ALA      4.1     0.2    -      -       -      -
      9G  ILE*     1.3    75.9    -      -       -      +
     11G  THR*     1.3    69.8    +      -       -      +
     12G  LEU*     3.9    11.2    +      -       +      +
     43G  TRP*     3.6    10.8    -      -       -      -
    230G  THR*     4.3     0.4    -      -       -      -
    231G  PHE*     2.9    39.4    +      -       +      +
    233G  ARG*     2.8    38.6    +      -       -      -
    264G  LEU      4.8     1.6    +      -       -      +
    266G  THR      5.2     0.4    +      -       -      -
    267G  VAL*     3.9    17.0    -      -       -      +
    279G  THR*     2.4    37.2    +      -       +      -
    280G  LEU      4.2     2.5    -      -       -      -
    281G  PRO*     3.4    23.8    -      -       +      +
    282G  ASP      4.1     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 11 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  TYR*     4.0    11.5    +      -       -      -
    298F  PRO*     3.2    29.0    -      -       +      +
    301F  GLU*     4.8     2.0    -      -       +      -
      9G  ILE*     5.4     1.6    -      -       +      -
     10G  GLN*     1.3    74.7    -      -       -      +
     12G  LEU*     1.3    65.5    +      -       -      +
     13G  PRO*     4.3     0.5    -      -       -      +
    229G  GLY      3.5     7.2    -      -       -      -
    230G  THR*     3.5    30.1    -      -       +      +
    279G  THR*     3.2    23.2    -      -       -      +
    282G  ASP*     3.1    26.2    +      -       -      +
    311G  THR*     3.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 12 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  TYR*     4.4     4.5    -      -       -      -
     10G  GLN*     4.1    16.2    -      -       +      +
     11G  THR*     1.3    81.9    -      -       -      +
     13G  PRO*     1.3    64.2    -      -       +      +
     15G  SER*     3.6    15.5    -      -       -      +
     17G  ILE*     3.8    21.3    -      -       +      -
     38G  VAL*     5.2     1.1    -      -       +      -
     43G  TRP*     5.3     9.6    -      -       +      -
    228G  ALA*     3.4     4.5    -      -       -      +
    229G  GLY      2.9    35.9    +      -       -      +
    231G  PHE*     3.3    34.1    -      -       +      -
    267G  VAL*     5.1     5.4    -      -       +      -
    277G  ALA*     3.2    32.1    -      -       +      +
    279G  THR*     4.0     9.0    -      -       -      -
----------------------------------------------------------
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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