Contacts of the strand formed by residues 530 - 535 (chain C) in PDB entry 5HP1


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 LYS 530 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428C  GLN      5.6     1.1    -      -       -      -
    430C  GLU*     3.7    29.6    +      -       -      +
    434C  ILE*     3.5    27.4    -      -       +      +
    491C  LEU      3.1     4.1    +      -       -      +
    492C  GLU*     3.2    32.7    +      -       +      +
    493C  VAL*     3.1    23.4    +      -       -      +
    528C  LYS      3.8     0.4    -      -       -      -
    529C  GLU*     1.3    87.9    -      -       +      +
    531C  VAL*     1.3    65.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 531 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428C  GLN      4.8     4.5    +      -       -      +
    429C  LEU*     3.4    19.5    -      -       +      +
    430C  GLU*     2.6    37.7    +      -       -      +
    486C  LEU*     4.4     5.4    -      -       +      -
    493C  VAL*     3.5    17.9    -      -       +      +
    495C  ILE*     4.7     4.9    -      -       +      -
    525C  LEU*     4.0    29.4    -      -       +      +
    528C  LYS*     3.5    32.3    -      -       +      -
    530C  LYS*     1.3    79.5    -      -       -      +
    532C  TYR*     1.3    63.1    +      -       -      +
    533C  LEU*     4.6     8.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 532 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430C  GLU*     3.4    27.4    -      -       +      +
    431C  LYS      3.5    21.6    +      -       -      -
    432C  GLU      3.5    15.7    -      -       -      +
    433C  PRO*     3.5    19.7    -      -       +      +
    434C  ILE*     4.0     2.4    -      -       +      +
    493C  VAL      3.1     7.7    +      -       -      +
    494C  ASN*     3.4    14.6    -      -       -      +
    495C  ILE*     2.9    30.0    +      -       -      +
    531C  VAL*     1.3    74.2    -      -       -      +
    533C  LEU*     1.3    74.2    +      -       -      +
    534C  ALA*     3.6    10.2    -      -       +      +
    255D  ASN*     2.7    34.2    +      -       -      -
    259D  LYS*     3.5    19.9    -      -       -      -
    289D  LEU*     3.5    22.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 533 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429C  LEU*     3.9    26.1    -      -       +      +
    430C  GLU      5.1     1.5    +      -       -      +
    482C  ILE*     4.8    11.2    -      -       +      -
    495C  ILE*     3.5    35.4    -      -       +      +
    497C  THR*     4.7     5.4    -      -       +      -
    503C  LEU*     3.7    33.8    -      -       +      +
    506C  ILE*     3.5    35.4    -      -       +      -
    507C  GLN*     5.1     8.2    +      -       +      +
    525C  LEU*     5.8     1.1    -      -       +      -
    531C  VAL*     4.1    10.4    +      -       +      +
    532C  TYR*     1.3    87.6    -      -       -      +
    534C  ALA*     1.3    60.8    +      -       -      +
    259D  LYS*     5.0     1.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 534 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495C  ILE      3.0    10.5    +      -       -      +
    496C  VAL*     3.4    16.6    -      -       +      +
    497C  THR*     3.0    27.7    +      -       -      +
    503C  LEU*     4.3     4.7    -      -       -      -
    532C  TYR*     3.6    28.5    -      -       +      +
    533C  LEU*     1.3    75.9    -      -       -      +
    535C  TRP*     1.3    62.0    +      -       -      +
    255D  ASN*     4.4     4.5    -      -       -      +
    258D  GLN*     4.8     6.5    -      -       +      +
    259D  LYS*     4.2     9.4    -      -       -      +
    289D  LEU*     4.5     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 535 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497C  THR      3.4     4.9    -      -       -      -
    498C  ASP      3.5    31.8    +      -       -      -
    499C  SER      4.2     4.7    -      -       -      -
    500C  GLN*     3.6    35.3    -      -       +      +
    503C  LEU*     3.5    20.4    -      -       +      +
    534C  ALA*     1.3    74.9    -      -       -      +
    536C  VAL*     1.3    74.3    +      -       -      +
    537C  PRO*     3.6    39.3    -      -       +      -
    538C  ALA      5.1     0.4    -      -       -      -
    258D  GLN*     4.9     5.5    -      -       -      +
    259D  LYS*     4.0    17.2    +      -       -      +
    262D  GLY*     4.3     8.0    -      -       -      -
    265D  ASN*     4.9     6.5    -      -       -      -
    266D  TRP*     5.7     7.0    -      +       -      -
    422D  LEU*     4.0    33.9    -      -       +      +
    423D  VAL*     3.9    28.5    -      -       +      -
----------------------------------------------------------
 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