Contacts of the helix formed by residues 726 - 731 (chain D) in PDB entry 6PUO
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.
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 ASP 726 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D LEU* 3.7 15.3 - - - +
656D SER* 2.9 26.4 + - - -
660D LYS* 3.3 19.3 + - - +
683D GLU* 3.1 34.2 - - + +
721D ALA* 3.4 18.1 + - + +
724D ALA* 3.2 11.4 - - - +
725D LYS* 1.3 71.8 - - - +
727D MET* 1.3 64.4 + - - +
728D LYS 3.3 2.9 - - - -
729D PHE* 3.3 17.1 + - + -
730D VAL* 3.3 18.6 + - - +
1065D PHE* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 727 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D GLU* 3.6 1.4 + - - -
725D LYS* 2.8 22.1 + - + +
726D ASP* 1.3 72.7 - - - +
728D LYS* 1.3 64.6 + - + +
730D VAL* 3.7 1.6 + - - +
731D SER* 3.4 23.9 + - - -
1061D GLN* 3.9 38.3 - - + +
1062D ILE* 4.9 15.9 - - + -
1065D PHE* 3.6 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 728 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D GLU* 2.8 30.1 + - - +
683D GLU* 3.3 17.6 + - - +
684D HIS* 3.7 20.1 + - + +
687D ILE* 3.5 19.6 - - + +
726D ASP 3.3 0.4 - - - -
727D MET* 1.3 81.1 - - + +
729D PHE* 1.3 62.8 + - - +
731D SER* 3.8 14.9 + - - -
732D HIS* 3.9 8.1 + - - +
1061D GLN* 4.4 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 729 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649D ILE* 4.7 7.6 - - + -
653D LEU* 4.2 18.6 - - + -
683D GLU* 3.6 6.9 + - + +
686D ALA* 4.2 17.7 - - + -
687D ILE* 3.6 29.6 - - + +
690D PHE* 4.2 27.1 - + + -
705D LEU* 4.6 13.2 - - + -
717D CYS* 5.0 4.0 - - - -
718D LEU* 5.2 7.0 - - + -
721D ALA* 3.6 27.4 - - + -
726D ASP* 3.3 18.7 + - + +
727D MET 3.3 0.6 - - - -
728D LYS* 1.3 77.7 - - - +
730D VAL* 1.3 66.0 + - + +
732D HIS* 3.4 20.5 - - + +
735D ILE* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718D LEU* 5.8 4.7 - - + -
721D ALA* 4.2 22.9 - - + +
722D LEU* 4.8 14.6 - - + -
726D ASP 3.3 17.8 + - - +
727D MET 3.7 1.5 + - - +
728D LYS 3.4 0.2 - - - -
729D PHE* 1.3 79.3 - - + +
731D SER* 1.3 56.2 + - - +
732D HIS 3.2 3.9 + - - -
735D ILE* 3.6 23.7 - - + +
736D GLN* 2.9 21.7 + - - +
739D LEU* 5.2 6.5 - - + -
1064D LYS* 4.2 18.4 - - - +
1065D PHE* 4.1 31.2 - - + +
1068D HIS* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 731 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727D MET 3.4 16.2 + - - -
728D LYS* 3.8 8.1 + - - +
729D PHE 3.2 1.2 - - - -
730D VAL* 1.3 77.4 - - - +
732D HIS* 1.3 61.5 + - - +
733D GLY* 3.4 3.2 + - - -
736D GLN* 3.9 9.4 - - - +
1061D GLN* 4.0 24.9 + - - +
1064D LYS* 4.0 35.9 + - - -
1065D PHE 5.8 0.2 - - - -
----------------------------------------------------------
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