Contacts of the strand formed by residues 31 - 35 (chain K) in PDB entry 6A5T


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 ILE 31 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21K  ILE*     4.3    16.4    -      -       +      -
     22K  THR      3.9     4.0    -      -       -      +
     23K  PRO*     4.0    16.6    -      -       +      -
     24K  ASP*     3.6     7.2    -      -       -      +
     29K  ASN      5.5     0.2    -      -       -      -
     30K  CYS*     1.3    82.5    -      -       -      +
     32K  ILE*     1.3    68.8    +      -       -      +
     33K  ILE*     3.5    25.1    -      -       +      -
     74K  ARG*     3.2     6.1    -      -       -      +
     75K  LEU*     2.9    47.0    +      -       +      +
     83K  PRO*     4.1    27.4    -      -       +      -
     84K  LYS*     5.0     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 32 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552A  PHE*     4.4     8.5    -      -       +      -
     21K  ILE*     3.5     3.6    -      -       -      +
     22K  THR*     2.9    51.5    +      -       -      +
     23K  PRO      5.3     0.2    -      -       -      -
     24K  ASP*     4.2    14.4    -      -       +      +
     26K  ARG*     5.4     1.8    -      -       -      +
     31K  ILE*     1.3    85.9    -      -       -      +
     33K  ILE*     1.3    75.2    +      -       -      +
     34K  LYS*     4.9     1.6    -      -       +      +
     72K  VAL*     3.4    25.1    -      -       +      -
     73K  MET      3.3     2.2    -      -       -      +
     74K  ARG*     3.4    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 33 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262C  LEU*     5.5     1.6    -      -       +      -
     19K  LEU*     3.5    35.0    -      -       +      -
     20K  LYS      3.5     3.4    -      -       -      +
     21K  ILE*     4.2    16.6    -      -       +      -
     31K  ILE*     3.5    27.6    -      -       +      -
     32K  ILE*     1.3    82.1    -      -       -      +
     34K  LYS*     1.3    62.8    +      -       -      +
     35K  PHE*     3.7    26.3    +      -       +      -
     72K  VAL*     3.2     9.1    -      -       -      +
     73K  MET*     2.8    44.3    +      -       +      +
     75K  LEU*     5.0     8.5    -      -       +      -
     87K  LEU*     4.8    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18K  LYS      4.8     0.2    -      -       -      -
     19K  LEU*     3.4     4.7    -      -       -      -
     20K  LYS*     2.8    49.6    +      -       +      +
     22K  THR*     5.8     2.2    +      -       +      -
     32K  ILE*     4.3     1.7    -      -       +      +
     33K  ILE*     1.3    72.3    -      -       -      +
     35K  PHE*     1.3    63.4    +      -       -      +
     36K  GLU*     4.4    11.3    +      -       +      +
     64K  GLU*     4.6    17.5    +      -       -      +
     70K  ASN*     3.1    40.4    -      -       -      +
     71K  PHE      3.6    13.5    -      -       -      +
     72K  VAL*     4.5    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 35 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258C  VAL*     4.5    10.1    -      -       +      -
     18K  LYS*     4.2     5.4    -      -       -      -
     19K  LEU*     3.4    27.1    -      -       +      +
     33K  ILE*     3.7    22.7    -      -       +      -
     34K  LYS*     1.3    78.9    -      -       -      +
     36K  GLU*     1.3    70.1    +      -       -      +
     38K  GLU*     4.2    15.5    -      -       +      -
     42K  LEU*     3.9    17.7    -      -       +      -
     46K  LEU*     4.2    20.6    -      -       +      -
     70K  ASN*     3.4    18.0    -      -       -      +
     71K  PHE*     3.0    60.2    +      +       +      +
     73K  MET*     4.4    18.8    -      -       +      -
     87K  LEU*     5.8     4.9    -      -       +      -
----------------------------------------------------------
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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