Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 1XI1


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 THR 89 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.9     6.9    -      -       -      -
     80A  LYS*     3.0    38.4    -      -       +      +
     82A  SER*     3.3    12.6    -      -       -      -
     85A  GLY      2.5    17.7    +      -       -      -
     86A  LEU*     2.4    47.4    +      -       +      +
     87A  PRO      3.7     1.8    -      -       -      +
     88A  ASN*     1.3    84.4    -      -       -      +
     90A  TYR*     1.3    62.3    +      -       -      +
    106A  CYS*     2.9    28.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ILE*     3.0    39.9    -      -       +      +
     74A  LEU*     3.8    33.2    -      -       +      -
     75A  GLU*     3.1    28.0    +      -       +      +
     79A  PHE*     4.1     9.6    -      -       +      -
     80A  LYS*     3.1    11.2    +      -       -      -
     81A  TRP*     3.2    27.3    -      +       -      +
     82A  SER      3.0    21.0    +      -       -      -
     89A  THR*     1.3    77.6    -      -       -      +
     91A  ASN*     1.3    58.0    +      -       -      +
     92A  THR*     3.5    29.8    -      -       +      -
    103A  ILE*     4.5     1.8    -      -       +      -
    104A  ASP      3.0    14.8    -      -       -      +
    105A  ILE*     4.2     9.0    -      -       +      -
    404A  PRO*     3.6    13.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  TRP*     3.5    19.5    -      -       -      +
     82A  SER      3.5    11.9    -      -       -      +
     83A  ALA      3.3    24.1    +      -       -      +
     84A  ASP*     4.7     7.7    +      -       -      +
     85A  GLY      5.4     2.5    -      -       -      +
     90A  TYR*     1.3    72.9    -      -       -      +
     92A  THR*     1.3    91.1    +      -       -      +
     93A  ILE*     5.0     2.0    -      -       -      +
    102A  MET*     4.0    15.2    -      -       -      +
    103A  ILE*     3.7     0.7    -      -       -      -
    104A  ASP*     2.9    40.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ILE*     4.5     8.1    -      -       +      -
     81A  TRP*     3.0    22.7    +      -       +      +
     90A  TYR*     3.5    29.4    -      -       +      -
     91A  ASN*     1.3    97.1    +      -       -      +
     93A  ILE*     1.3    72.8    +      -       -      +
     94A  ILE*     4.0    16.4    -      -       +      +
    100A  TRP*     6.1     0.2    -      -       +      -
    102A  MET*     3.3    12.6    -      -       -      +
    103A  ILE*     4.6     5.6    -      -       +      -
    402A  LYS      4.3     4.5    +      -       -      -
    404A  PRO*     3.8    17.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ASN*     5.0     2.9    -      -       -      +
     92A  THR*     1.3    83.7    -      -       -      +
     94A  ILE*     1.3    61.2    +      -       -      +
     99A  GLN      3.8     0.5    -      -       -      +
    101A  TYR*     2.8    49.3    +      -       +      +
    102A  MET*     3.0    46.0    +      -       +      +
    188A  MET*     5.4     9.4    -      -       +      -
    399A  VAL*     5.3    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  THR*     4.0    22.5    +      -       +      +
     93A  ILE*     1.3    79.4    -      -       -      +
     95A  SER*     1.3    69.4    +      -       -      +
     98A  GLY*     4.2     8.5    -      -       -      -
     99A  GLN      3.2     9.2    -      -       -      +
    100A  TRP*     3.9    59.5    -      -       +      +
    102A  MET      5.4     0.9    -      -       -      +
    401A  GLY*     3.3     6.8    -      -       -      -
    402A  LYS*     3.1    40.9    +      -       +      +
    404A  PRO*     4.2    11.2    -      -       +      -
    414A  PHE*     4.1    16.4    -      -       +      -
----------------------------------------------------------
 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