Contacts of the strand formed by residues 28 - 32 (chain C) in PDB entry 6I4X


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 GLU 28 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  LYS*     3.0    12.8    +      -       +      +
     12B  THR*     3.5    20.5    +      -       +      +
     13B  THR*     2.8    28.4    +      -       -      +
     20C  LYS*     3.1    42.2    +      -       +      +
     21C  LEU      3.7     3.6    -      -       -      -
     22C  ILE*     4.3    17.0    -      -       +      +
     26C  GLY      3.4    12.4    +      -       -      +
     27C  HIS*     1.3    71.6    -      -       -      +
     29C  PHE*     1.3    61.9    +      -       -      +
     30C  ILE*     4.0     1.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 29 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  THR*     3.4    14.1    -      -       -      +
     15B  PHE*     3.5    23.3    -      +       +      -
     93B  PHE*     3.4    33.4    -      +       -      -
     19C  VAL      3.7     0.7    -      -       -      +
     20C  LYS*     3.5     0.9    -      -       -      -
     21C  LEU*     2.7    54.0    +      -       +      +
     23C  SER*     4.1    11.9    -      -       -      -
     27C  HIS*     3.6    26.0    -      -       +      -
     28C  GLU*     1.3    71.5    -      -       -      +
     30C  ILE*     1.3    61.6    +      -       -      +
     31C  VAL      3.7     1.3    +      -       -      -
     67C  SER*     3.6    20.0    -      -       -      -
     70C  LEU*     3.8    14.8    -      -       +      -
     71C  SER*     3.5    23.1    -      -       -      -
     74C  CYS*     4.0    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  THR*     3.8    28.0    -      -       +      -
     13B  THR      2.8    13.6    +      -       -      +
     14B  ILE*     3.7     9.9    -      -       +      +
     15B  PHE*     3.1    30.1    +      -       -      +
     34B  ILE*     3.8    22.9    -      -       +      -
     35B  LEU*     3.8    22.7    -      -       +      -
     18C  TYR*     3.9    21.4    -      -       +      -
     19C  VAL      3.3    10.1    -      -       -      +
     20C  LYS*     4.2    28.0    -      -       +      +
     28C  GLU*     5.0     1.1    -      -       -      +
     29C  PHE*     1.3    73.8    -      -       -      +
     31C  VAL*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  PHE*     4.7    13.7    -      -       +      -
     18C  TYR*     3.1    11.7    -      -       -      -
     19C  VAL*     2.7    61.4    +      -       +      +
     21C  LEU*     3.9    17.7    -      -       +      -
     29C  PHE      4.9     0.9    -      -       -      +
     30C  ILE*     1.3    74.3    -      -       -      +
     32C  LYS*     1.3    72.1    +      -       -      +
     35C  HIS*     3.7    20.2    -      -       +      +
     36C  ALA*     3.6    17.3    -      -       +      +
     74C  CYS*     4.9    12.3    -      -       +      +
     77C  PHE*     4.6    12.1    -      -       +      -
     78C  THR*     5.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  PHE      4.7     6.8    +      -       -      +
     16B  THR*     5.8     2.2    -      -       -      +
     17B  ASP*     4.3    16.4    +      -       -      -
     17C  MET*     3.5    15.9    -      -       +      +
     18C  TYR*     3.6    33.2    -      -       +      +
     31C  VAL*     1.3    80.3    -      -       -      +
     33C  ARG*     1.3    67.1    +      -       -      +
     34C  GLU*     3.3     2.9    -      -       +      +
     35C  HIS*     3.0    46.9    +      -       +      +
     36C  ALA*     2.9    21.0    +      -       -      +
----------------------------------------------------------
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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