Contacts of the strand formed by residues 52 - 63 (chain A) in PDB entry 1I09


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 GLN 52 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL      3.4     1.2    -      -       -      +
     41A  VAL*     3.1    10.4    -      -       -      -
     42A  ALA      3.1    31.8    +      -       -      +
     44A  PRO*     3.8    19.2    -      -       +      +
     50A  ARG*     2.8    22.9    +      -       -      +
     51A  PRO*     1.3    75.9    +      -       +      +
     53A  GLU*     1.3    66.9    +      -       -      +
     54A  VAL*     3.5     5.8    +      -       +      +
    114A  TYR*     3.6    29.3    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  THR*     3.9    23.8    -      -       +      +
     40A  VAL      3.6     5.4    -      -       -      -
     41A  VAL*     4.5    14.7    -      -       +      +
     52A  GLN*     1.3    74.2    -      -       -      +
     54A  VAL*     1.3    63.0    +      -       -      +
     55A  SER*     4.1     1.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  THR      3.5     1.9    -      -       -      +
     39A  THR*     3.4     2.8    -      -       -      +
     40A  VAL*     2.9    43.4    +      -       +      +
     42A  ALA*     4.6     7.2    -      -       +      -
     52A  GLN*     4.1    13.0    -      -       +      +
     53A  GLU*     1.3    77.3    -      -       -      +
     55A  SER*     1.3    62.6    +      -       -      +
     56A  TYR*     4.7     8.2    -      -       +      -
     75A  LEU*     3.9    26.0    -      -       +      -
    114A  TYR*     3.8    48.5    -      -       +      +
    116A  PHE*     6.4     0.9    -      -       +      -
    131A  VAL*     5.7     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  VAL*     4.2     5.4    -      -       -      -
     38A  THR      3.2     8.7    -      -       -      -
     39A  THR*     3.8    16.2    -      -       -      -
     53A  GLU      4.1     2.0    +      -       -      -
     54A  VAL*     1.3    76.0    -      -       -      +
     56A  TYR*     1.3    54.5    +      -       -      +
     75A  LEU*     3.5     5.2    -      -       -      +
     76A  CYS*     2.7    50.1    +      -       -      +
     77A  ASP*     4.5     8.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  MET*     5.2     3.1    -      -       -      -
     37A  VAL*     3.9     1.4    -      -       -      -
     38A  THR*     3.0    63.1    +      -       +      +
     40A  VAL*     5.0     4.7    -      -       +      -
     54A  VAL*     4.7    12.6    -      -       +      -
     55A  SER*     1.3    77.0    -      -       -      +
     57A  THR*     1.3    59.8    +      -       -      +
     59A  THR*     2.7    39.7    -      -       +      +
     73A  ALA*     3.4    15.7    -      -       +      -
     74A  LYS      2.8    20.4    -      -       -      +
     75A  LEU*     4.1    11.0    -      -       +      -
     76A  CYS*     3.8     3.4    -      -       -      -
     82A  VAL*     5.1     0.7    -      -       +      -
     84A  ILE*     3.8    28.1    -      -       +      +
    116A  PHE*     4.5    20.5    -      +       -      -
    131A  VAL*     6.4     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  SER*     4.7     3.5    -      -       -      -
     36A  LYS      2.9    28.6    +      -       -      -
     37A  VAL*     4.8     3.6    -      -       -      -
     56A  TYR*     1.3    76.7    -      -       -      +
     58A  ASP*     1.3    92.6    +      -       -      +
     59A  THR*     3.4     5.8    +      -       -      +
     73A  ALA*     3.7     1.9    -      -       -      +
     74A  LYS*     2.6    51.1    +      -       +      +
     76A  CYS*     4.4    16.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LYS*     4.5     1.6    +      -       -      +
     57A  THR*     1.3   100.1    +      -       -      +
     59A  THR*     1.3    64.8    +      -       -      +
     60A  LYS*     3.3    22.4    +      -       -      +
     72A  GLN*     3.2    12.9    -      -       -      +
     73A  ALA*     3.9     1.6    -      -       -      -
     74A  LYS*     3.5    28.4    -      -       +      +
     81A  LEU*     6.2     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LYS*     5.6     8.4    +      -       +      +
     38A  THR*     4.6     7.0    -      -       -      +
     56A  TYR*     2.7    46.9    -      -       +      +
     57A  THR*     4.4     3.1    -      -       -      -
     58A  ASP*     1.3    75.9    -      -       -      +
     60A  LYS*     1.3    58.7    +      -       -      +
     61A  VAL*     5.8     0.7    -      -       -      +
     71A  TYR*     5.1    15.5    -      -       -      -
     72A  GLN      3.5     7.2    -      -       -      -
     73A  ALA*     4.1     2.5    -      -       +      -
     84A  ILE*     5.7     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ASP*     3.6    24.6    +      -       -      +
     59A  THR*     1.3    73.8    -      -       -      +
     61A  VAL*     1.3    52.8    +      -       -      +
     62A  ILE*     2.5    38.0    +      -       +      +
     71A  TYR*     4.5     2.9    -      -       -      -
     72A  GLN*     3.1    40.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR      5.8     0.4    -      -       -      +
     60A  LYS*     1.3    66.0    -      -       -      +
     62A  ILE*     1.3    64.2    +      -       -      +
     63A  GLY*     3.2    18.8    +      -       -      +
     64A  ASN*     4.9     7.0    -      -       +      +
     69A  VAL*     4.3    17.9    -      -       +      -
     70A  VAL      3.8     5.2    -      -       -      +
     71A  TYR*     3.5    26.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS*     2.5    28.5    +      -       +      +
     61A  VAL*     1.3    72.5    -      -       -      +
     63A  GLY*     1.3    69.5    +      -       -      +
     70A  VAL*     3.4    25.1    -      -       +      +
     71A  TYR      4.3     1.3    -      -       -      +
     72A  GLN*     3.1    52.0    -      -       +      +
     83A  ALA*     5.2     2.5    -      -       +      -
    134A  TYR*     3.9    20.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  VAL*     3.8    12.4    -      -       -      +
     62A  ILE*     1.3    87.8    -      -       -      +
     64A  ASN*     1.3    61.7    +      -       -      +
     65A  GLY      4.7     0.2    -      -       -      -
     69A  VAL*     4.2     0.3    -      -       -      -
     70A  VAL*     2.9    40.1    +      -       -      +
----------------------------------------------------------
 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