Contacts of the strand formed by residues 3 - 12 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2I  THR*     1.3    91.8    -      -       -      +
      4I  VAL*     1.3    64.5    +      -       -      +
      5I  ASP*     3.4     3.0    +      -       +      +
    187I  GLN*     6.6     0.2    -      -       -      -
    236I  ASN*     5.5     4.7    -      -       +      +
    237I  VAL      3.6     3.8    -      -       -      -
    238I  ASN*     3.5    43.1    -      -       +      -
    288I  VAL*     4.6     0.7    -      -       -      -
    289I  ARG*     2.9    41.9    +      -       +      +
    290I  PHE      4.0     7.4    -      -       -      -
    291I  ASP      3.8    15.7    -      -       -      -
    292I  ARG*     4.1     3.4    -      -       -      -
    293I  PRO*     3.7    41.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 4 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2I  THR      3.9     0.2    -      -       -      -
      3I  PHE*     1.3    72.4    -      -       -      +
      5I  ASP*     1.3    61.1    +      -       -      +
      6I  ILE*     4.3     8.5    +      -       +      +
    235I  ALA      4.1     0.5    -      -       -      +
    236I  ASN*     3.6     0.9    -      -       -      -
    237I  VAL*     2.8    47.6    +      -       +      +
    239I  LEU*     4.1    24.5    -      -       +      -
    256I  VAL*     5.1    11.4    -      -       +      -
    260I  LEU*     4.5    14.6    -      -       +      -
    286I  ILE*     3.8    25.4    -      -       +      -
    287I  ALA      3.6     4.5    -      -       -      +
    288I  VAL*     4.2    18.2    -      -       +      +
    363I  MET      6.0     0.4    -      -       -      +
    364I  VAL*     5.5     6.1    -      -       +      -
    367I  ALA*     4.7     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 5 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  PHE      3.4     1.3    +      -       -      -
      4I  VAL*     1.3    73.4    -      -       -      +
      6I  ILE*     1.3    64.7    +      -       -      +
      7I  HIS*     3.5    17.8    +      -       -      -
    234I  TYR*     3.4    16.0    +      -       +      +
    235I  ALA      3.3     3.1    -      -       -      -
    236I  ASN*     3.0    25.4    -      -       -      +
    285I  HIS      4.0     1.0    -      -       -      +
    286I  ILE*     3.5     1.2    -      -       -      +
    287I  ALA*     2.6    53.3    +      -       -      +
    289I  ARG*     3.6    21.5    +      -       -      +
    293I  PRO*     4.7     3.4    -      -       +      -
    294I  ILE      3.6    13.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 6 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4I  VAL*     4.4     6.1    -      -       +      +
      5I  ASP*     1.3    77.6    -      -       -      +
      7I  HIS*     1.3    64.2    +      -       -      +
    234I  TYR*     3.4     4.4    -      -       -      -
    235I  ALA*     2.9    42.1    +      -       +      +
    237I  VAL*     6.1     1.6    -      -       +      -
    259I  PHE*     5.4     3.6    -      -       +      -
    260I  LEU*     4.0    26.9    -      -       +      -
    263I  PHE*     3.2    50.0    -      -       +      -
    264I  LEU*     5.0     3.4    -      -       +      -
    284I  VAL*     5.4     1.6    -      -       +      -
    285I  HIS      3.7     4.0    -      -       -      -
    286I  ILE*     3.4    34.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 7 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  ASP*     3.5    20.7    +      -       -      -
      6I  ILE*     1.3    76.5    -      -       -      +
      8I  ALA*     1.3    66.7    +      -       -      +
    232I  TYR*     2.6    31.2    +      -       +      +
    233I  ARG      3.5     5.4    -      -       -      -
    234I  TYR*     3.2    17.6    -      +       -      -
    283I  LEU*     5.7     0.9    -      -       +      -
    284I  VAL*     3.5     5.2    -      -       -      +
    285I  HIS*     2.8    65.6    +      +       +      +
    287I  ALA*     5.2     0.8    -      -       -      +
    289I  ARG*     5.6     0.8    +      -       -      -
    294I  ILE      3.2    24.1    +      -       -      -
    296I  PHE*     3.6    28.9    -      +       -      -
    318I  LEU*     4.7     7.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 8 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6I  ILE*     5.0     0.2    -      -       +      -
      7I  HIS*     1.3    80.2    -      -       -      +
      9I  ILE*     1.3    61.2    +      -       -      +
     10I  GLN*     5.6     0.2    -      -       +      -
    232I  TYR*     3.7     6.5    -      -       -      -
    233I  ARG*     2.8    39.4    +      -       +      +
    263I  PHE*     4.0    25.4    -      -       +      -
    264I  LEU*     4.5     0.9    -      -       +      -
    281I  PRO*     4.5     9.0    -      -       +      -
    283I  LEU*     3.1    14.8    -      -       -      +
    284I  VAL*     3.9    13.2    -      -       +      -
    318I  LEU*     5.9     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 9 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8I  ALA*     1.3    72.5    -      -       -      +
     10I  GLN*     1.3    67.5    +      -       -      +
     11I  THR*     5.5     2.5    -      -       +      -
    194I  VAL*     3.7    20.9    -      -       +      -
    230I  THR*     4.2    15.3    -      -       +      -
    231I  PHE      3.6    10.8    -      -       -      +
    232I  TYR*     4.6     6.7    -      -       +      +
    281I  PRO*     3.6     1.1    -      -       -      +
    282I  ASP*     2.9    28.5    +      -       +      -
    283I  LEU*     2.9    40.9    +      -       +      +
    300I  PHE*     5.2     4.5    -      -       +      -
    311I  THR*     5.5     3.8    -      -       +      +
    314I  ALA*     3.3    33.2    -      -       +      -
    315I  CYS*     4.7    11.0    -      -       -      +
    318I  LEU*     5.7     5.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 10 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8I  ALA*     4.1     1.3    +      -       +      -
      9I  ILE*     1.3    77.6    -      -       -      +
     11I  THR*     1.3    72.3    +      -       -      +
     12I  LEU*     3.5    24.5    +      -       +      +
    230I  THR*     4.3     0.2    -      -       -      -
    231I  PHE*     2.9    35.3    +      -       -      +
    233I  ARG*     2.2    45.2    +      -       -      +
    264I  LEU      4.6     1.2    -      -       -      +
    266I  THR      4.7     1.4    +      -       -      -
    267I  VAL*     3.7    12.1    -      -       -      +
    279I  THR      3.1    25.9    +      -       -      -
    280I  LEU      4.4     1.8    -      -       -      +
    281I  PRO*     3.1    36.6    -      -       +      +
    282I  ASP      4.1     0.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 11 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9I  ILE*     5.5     2.0    -      -       +      -
     10I  GLN*     1.3    76.7    -      -       -      +
     12I  LEU*     1.3    72.1    +      -       -      +
     13I  PRO*     4.8     3.3    -      -       -      +
    229I  GLY      3.3     8.5    -      -       -      -
    230I  THR*     3.4    30.5    -      -       +      +
    279I  THR*     3.5    19.5    -      -       -      +
    282I  ASP*     3.0    29.7    +      -       +      +
    311I  THR*     3.9    11.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 12 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  GLN*     3.5    31.9    -      -       +      +
     11I  THR*     1.3    84.3    -      -       -      +
     13I  PRO*     1.3    65.2    -      -       +      +
     15I  SER*     2.9    27.0    +      -       -      +
     17I  ILE*     5.0     7.4    -      -       +      -
     38I  VAL*     5.6     2.7    -      -       +      -
    228I  ALA*     3.2     7.5    -      -       -      +
    229I  GLY      2.8    32.7    +      -       -      +
    231I  PHE*     3.5    35.4    -      -       +      -
    233I  ARG*     5.9     3.4    -      -       -      +
    267I  VAL*     4.6    16.2    -      -       +      -
    268I  PRO*     5.6     4.7    -      -       +      -
    279I  THR*     4.2    10.8    -      -       -      +
----------------------------------------------------------
 Back to top of page


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