Contacts of the strand formed by residues 430 - 434 (chain s) in PDB entry 6QX2


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 430 (chain s).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428s  GLU      4.8     5.1    -      -       -      +
    429s  CYS*     1.3    76.4    -      -       -      +
    431s  ILE*     1.3    53.7    +      -       -      +
    432s  PHE*     4.1     9.6    -      -       +      -
    451s  THR*     2.9    15.6    +      -       -      +
    452s  GLN*     3.0    28.1    +      -       +      +
    453s  ALA*     2.8    31.5    +      -       -      +
    500s  TYR*     3.8     5.4    -      -       -      -
    502s  LYS*     3.1    39.2    +      -       +      +
    504s  VAL*     4.6     3.4    -      -       +      -
    598s  PRO*     5.3     2.3    -      -       -      +
    601s  ARG*     2.6    47.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 431 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418s  LEU*     3.7    26.5    -      -       +      -
    430s  GLU*     1.3    73.1    -      -       -      +
    432s  PHE*     1.3    66.1    +      -       -      +
    433s  LEU*     4.6     2.7    -      -       +      -
    453s  ALA*     3.5    13.5    -      -       +      +
    455s  LEU*     4.1    11.9    -      -       +      +
    484s  ALA*     3.9    13.9    -      -       +      -
    485s  PHE*     3.8    11.9    -      -       +      -
    500s  TYR*     3.8    38.1    -      -       +      -
    502s  LYS      2.9     7.1    +      -       -      +
    503s  ILE*     3.7    32.6    -      -       +      +
    504s  VAL*     2.8    33.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 432 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430s  GLU*     4.0    17.7    -      -       +      -
    431s  ILE*     1.3    73.9    -      -       -      +
    433s  LEU*     1.3    59.5    +      -       -      +
    434s  VAL*     4.0     1.9    +      -       +      -
    443s  THR*     4.6     0.9    -      -       +      -
    452s  GLN*     3.6    43.5    -      -       +      -
    453s  ALA      2.9    19.9    +      -       -      +
    454s  ILE*     3.4    13.7    -      -       +      +
    455s  LEU      2.9    31.4    +      -       -      +
    504s  VAL*     3.4    36.1    -      -       +      -
    506s  MET*     3.8    38.6    -      -       +      -
    595s  THR      4.6     4.3    -      -       -      -
    596s  MET*     4.0    24.2    -      -       +      -
    601s  ARG*     4.0     8.3    -      -       -      -
    603s  LEU*     5.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 433 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431s  ILE*     4.6     7.6    -      -       +      +
    432s  PHE*     1.3    72.0    -      -       -      +
    434s  VAL*     1.3    58.1    +      -       -      +
    455s  LEU*     3.5    38.8    -      -       +      +
    457s  LEU*     4.6    14.1    -      -       +      -
    481s  MET*     4.4    15.7    -      -       +      -
    485s  PHE*     4.4     8.5    -      -       +      -
    503s  ILE*     3.7    16.4    -      -       +      -
    504s  VAL      2.9    13.3    +      -       -      +
    505s  ILE*     4.1    14.2    -      -       +      +
    506s  MET*     2.9    30.3    +      -       -      +
    507s  THR*     5.3     2.4    -      -       -      +
    520s  LEU*     4.5     9.0    -      -       +      -
    524s  PHE*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 434 (chain s). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432s  PHE      4.6     4.5    -      -       -      +
    433s  LEU*     1.3    77.3    -      -       -      +
    435s  GLU*     1.3    57.3    +      -       -      +
    436s  GLY      4.1     0.2    -      -       -      +
    439s  ALA*     4.0    11.9    -      -       +      -
    440s  GLY*     3.9    19.5    -      -       -      +
    443s  THR*     4.0    13.2    -      -       +      +
    454s  ILE*     4.0    11.4    -      -       +      -
    455s  LEU      3.3     2.6    +      -       -      +
    456s  PRO*     3.6    25.8    -      -       +      -
    457s  LEU*     2.9    35.3    +      -       -      +
    506s  MET*     3.6    41.7    -      -       +      +
    507s  THR*     6.1     1.6    -      -       -      -
    583s  LEU*     4.8     0.4    -      -       +      -
----------------------------------------------------------
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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