Contacts of the helix formed by residues 829 - 839 (chain A) in PDB entry 2QOQ
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 SER 829 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A GLU 3.5 2.8 + - - -
828A MET* 1.3 73.0 - - - +
830A ASN* 1.3 67.1 + - - +
831A GLN* 3.3 23.5 + - - +
832A ASP* 2.9 35.9 + - - +
833A VAL* 2.9 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ILE* 3.5 34.1 - - + +
789A ARG* 3.0 24.8 + - - +
828A MET 4.1 1.3 - - - +
829A SER* 1.3 72.6 + - - +
831A GLN* 1.3 62.7 + - - +
833A VAL* 3.2 9.2 + - - +
834A ILE* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A SER* 3.3 20.0 + - - +
830A ASN* 1.3 78.2 - - - +
832A ASP* 1.3 72.9 + - - +
834A ILE* 3.6 11.3 + - - +
835A LYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A MET* 3.8 18.2 - - + -
829A SER* 2.9 29.0 + - - +
831A GLN* 1.3 90.3 + - - +
833A VAL* 1.3 59.7 + - - +
835A LYS* 4.2 6.7 - - - +
836A ALA* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ILE* 4.2 17.9 - - + +
789A ARG* 4.0 23.3 - - - +
796A ILE* 6.0 1.6 - - + -
825A TYR* 3.8 53.2 - - + -
828A MET* 3.9 16.2 - - + -
829A SER 2.9 19.7 + - - +
830A ASN* 3.5 8.1 - - - +
832A ASP* 1.3 74.4 - - - +
834A ILE* 1.3 63.3 - - - +
836A ALA* 4.1 1.3 - - - +
837A VAL* 3.1 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ILE* 4.0 26.5 - - + -
796A ILE* 3.9 40.4 - - + -
830A ASN* 3.0 26.4 + - + +
831A GLN* 3.8 9.0 - - - +
833A VAL* 1.3 77.1 - - - +
835A LYS* 1.3 66.1 + - + +
837A VAL* 4.1 2.9 - - - +
838A ASP* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A GLN 3.0 18.7 + - - +
832A ASP* 4.2 7.0 - - - +
833A VAL 3.4 0.2 - - - -
834A ILE* 1.3 76.5 - - + +
836A ALA* 1.3 61.3 + - - +
838A ASP* 3.2 16.8 + - - +
839A GLU* 2.8 74.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A MET* 4.5 4.0 - - + -
832A ASP* 2.8 23.8 + - + +
833A VAL 4.1 1.8 - - - +
835A LYS* 1.3 72.8 - - - +
837A VAL* 1.3 63.8 + - - +
839A GLU* 3.2 14.0 + - - +
840A GLY 3.3 0.2 + - - -
841A TYR* 3.0 35.3 + - + +
901A LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A PRO* 3.9 15.8 - - + +
808A TRP* 3.6 34.3 - - + -
825A TYR* 3.4 37.9 - - + +
833A VAL* 3.1 22.4 + - + +
834A ILE* 4.1 2.5 - - - +
836A ALA* 1.3 76.3 - - + +
838A ASP* 1.3 64.3 + - - +
840A GLY* 3.0 5.0 + - - -
841A TYR 3.5 12.3 - - - +
842A ARG* 2.9 26.1 + - - +
863A LYS* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A PRO* 5.5 11.5 - - + +
834A ILE* 3.1 21.9 + - + +
835A LYS* 3.2 20.3 + - - +
837A VAL* 1.3 78.4 - - - +
839A GLU* 1.3 58.3 + - - +
840A GLY 3.1 3.7 + - - -
863A LYS* 2.9 38.6 + - - +
905A GLN* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LYS* 2.8 60.9 + - - +
836A ALA* 3.2 7.8 + - - +
838A ASP* 1.3 75.8 - - - +
840A GLY* 1.3 56.4 + - - +
841A TYR* 3.6 20.8 - - + -
903A LEU* 3.5 14.6 - - - +
905A GLN* 4.3 11.4 + - - +
----------------------------------------------------------
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