Contacts of the strand formed by residues 289 - 292 (chain A) in PDB entry 7UUT


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 289 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  ASP*     6.0     0.4    -      -       -      +
    259A  GLY      5.7     0.3    +      -       -      -
    260A  GLY      3.0    12.2    +      -       -      -
    261A  THR*     3.3     9.4    -      -       +      +
    262A  ILE*     2.6    34.8    +      -       -      +
    287A  HIS      3.4     6.6    +      -       -      -
    288A  LYS*     1.3    73.0    -      -       -      +
    290A  ILE*     1.3    57.6    +      -       -      +
    291A  LYS*     4.1    20.9    -      -       +      -
     99B  TYR*     5.5     2.8    +      -       -      -
    289B  THR*     3.6    28.0    -      -       +      -
    290B  ILE      3.6     4.9    -      -       -      -
    291B  LYS*     3.8    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  MET*     4.0    18.2    -      -       +      -
    253A  VAL*     4.4    10.8    -      -       +      -
    262A  ILE*     3.4    20.0    -      -       +      +
    276A  VAL*     4.1    27.1    -      -       +      -
    281A  TRP*     3.9    24.0    -      -       +      +
    288A  LYS      3.8     7.9    -      -       -      +
    289A  THR*     1.3    77.2    -      -       -      +
    291A  LYS*     1.3    64.6    +      -       -      +
    281B  TRP*     3.8    26.2    -      -       +      -
    288B  LYS      4.1     1.9    -      -       -      +
    289B  THR*     3.5     5.2    -      -       -      +
    290B  ILE*     2.9    53.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     3.0    57.2    +      -       +      +
    163A  ASP*     2.7    34.8    +      -       -      -
    261A  THR*     4.3     4.3    -      -       +      -
    262A  ILE      2.7    13.1    +      -       -      +
    263A  ALA*     4.5     0.9    -      -       -      -
    264A  ASN*     2.7    35.1    +      -       -      +
    289A  THR*     4.1    17.9    -      -       +      -
    290A  ILE*     1.3    78.2    -      -       -      +
    292A  GLY*     1.3    54.1    +      -       -      +
    281B  TRP*     4.1     5.7    -      -       -      -
    289B  THR*     3.9    25.4    -      -       +      +
    291B  LYS*     6.1     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     4.6     1.1    -      -       -      -
    264A  ASN      3.2     7.9    -      -       -      -
    291A  LYS*     1.3    77.4    -      -       -      +
    293A  GLY*     1.3    51.5    +      -       -      -
    281B  TRP*     4.0    16.4    -      -       -      -
    284B  GLY      3.1    20.1    -      -       -      +
    285B  MET      4.0     0.2    +      -       -      -
    286B  ALA      3.3     5.4    +      -       -      -
    287B  HIS*     2.6    35.5    +      -       -      +
    288B  LYS      4.1     3.8    +      -       -      -
----------------------------------------------------------
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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