Contacts of the helix formed by residues 793 - 798 (chain A) in PDB entry 2DQM
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 ASN 793 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ALA 2.9 26.7 + - - +
755A THR* 3.5 11.4 - - - +
756A SER 3.3 24.0 + - - +
761A VAL* 4.0 3.8 - - - +
788A ALA 3.3 1.5 + - - +
789A PHE* 3.2 20.3 + - + +
790A ALA 4.9 0.2 - - - -
792A SER* 1.3 79.6 - - - +
794A PRO* 1.3 58.1 - - - +
795A ALA* 3.1 8.4 + - - +
796A ALA* 3.2 29.2 + - + +
797A PHE 2.8 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A VAL* 3.9 27.4 - - + +
623A ASN* 4.6 10.5 - - - +
632A ILE* 6.3 0.4 - - + -
634A PRO* 3.7 12.7 - - + +
790A ALA 4.7 4.7 - - - +
791A GLY 4.0 10.1 - - - +
792A SER 3.2 9.2 - - - +
793A ASN* 1.3 90.0 - - - +
795A ALA* 1.3 57.1 + - - +
797A PHE* 4.1 5.4 - - + -
798A HIS* 2.8 53.1 + - + +
836A TYR* 4.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A PRO* 3.7 18.9 + - - +
635A ILE* 4.0 17.8 - - + +
638A ALA* 3.7 30.1 - - + -
793A ASN* 3.1 7.9 + - - +
794A PRO* 1.3 82.6 - - - +
796A ALA* 1.3 60.2 + - - +
798A HIS 3.8 2.4 - - - -
799A ALA* 3.6 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A VAL* 3.7 16.6 - - + -
762A LEU* 6.1 0.8 - - + +
789A PHE* 3.6 23.2 - - + -
793A ASN* 3.0 30.6 + - - +
795A ALA* 1.3 75.4 - - - +
797A PHE* 1.3 67.1 + - - +
798A HIS 3.1 1.6 - - - -
799A ALA* 3.1 22.3 + - - +
803A SER* 5.1 0.5 + - - -
804A GLY* 4.4 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A PHE* 3.8 19.6 - + + +
790A ALA* 3.6 31.9 - - + +
793A ASN 2.8 15.9 + - - +
794A PRO* 4.0 3.4 - - + +
796A ALA* 1.3 77.4 - - - +
798A HIS* 1.3 80.9 + + - +
799A ALA 3.4 2.1 + - - +
804A GLY* 3.4 43.6 + - - -
805A TYR* 3.4 33.6 + + - -
808A LEU* 3.7 33.0 - - + -
829A PRO* 3.7 23.8 - - + -
830A LEU* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A PRO* 3.6 14.1 - - + -
794A PRO* 2.8 36.0 + - + +
795A ALA 3.8 4.7 - - - +
797A PHE* 1.3 93.1 - + - +
799A ALA* 1.3 65.4 + - - -
805A TYR* 2.7 28.4 + + - -
829A PRO* 4.7 3.0 + - - +
836A TYR* 3.1 47.5 + + - -
840A ARG* 2.9 27.1 + - - +
844A MET* 3.5 33.2 - - + -
----------------------------------------------------------
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