Contacts of the helix formed by residues 761 - 771 (chain N) in PDB entry 6AH0
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 ARG 761 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760N THR* 1.3 71.6 - - - +
762N ALA* 1.3 63.8 + - - +
764N ALA* 2.9 15.2 + - - -
765N ILE* 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 762 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750N SER* 4.5 25.2 - - - +
753N GLU* 5.5 3.8 - - - +
754N GLU* 5.1 10.9 - - - +
760N THR* 3.3 2.6 - - - +
761N ARG* 1.3 75.9 - - - +
763N ARG* 1.3 56.7 + - - +
765N ILE* 3.0 6.2 + - - +
766N LEU* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 763 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760N THR 4.1 4.5 + - - -
761N ARG 3.1 1.0 + - - -
762N ALA* 1.3 74.5 - - - +
764N ALA* 1.3 57.1 + - - +
766N LEU* 3.3 4.0 + - - +
767N GLU* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 764 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760N THR 4.8 1.8 + - - -
761N ARG 2.9 9.8 + - - -
763N ARG* 1.3 76.5 - - - +
765N ILE* 1.3 52.3 - - - +
767N GLU* 2.9 1.5 + - - +
768N LYS* 2.5 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 765 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746N TRP* 5.4 7.4 - - - +
750N SER* 5.8 4.3 - - - +
761N ARG 3.4 5.5 + - - -
762N ALA* 3.0 9.6 + - - +
764N ALA* 1.3 77.6 - - - +
766N LEU* 1.3 60.6 + - - +
768N LYS* 4.4 0.8 - - - +
769N SER* 3.5 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 766 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746N TRP* 5.4 6.7 + - - +
750N SER* 5.6 1.6 - - - +
762N ALA 2.9 13.1 + - - -
763N ARG* 3.3 4.7 + - - +
765N ILE* 1.3 76.2 - - - +
767N GLU* 1.3 57.5 + - - +
769N SER* 3.6 0.9 + - - -
770N ARG* 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 767 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763N ARG 2.8 14.3 + - - -
764N ALA* 3.5 2.7 - - - +
766N LEU* 1.3 76.5 - - - +
768N LYS* 1.3 67.2 + - - +
770N ARG* 3.2 10.2 + - - +
771N LEU* 3.7 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 768 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764N ALA 2.5 22.1 + - - -
765N ILE* 4.4 1.1 - - - +
767N GLU* 1.3 73.2 - - - +
769N SER* 1.3 56.5 - - - +
771N LEU* 4.0 5.2 + - - -
772N LYS* 4.1 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 769 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765N ILE 3.5 13.3 + - - -
766N LEU 3.9 2.5 - - - -
767N GLU 3.2 0.4 - - - -
768N LYS* 1.3 74.1 - - - +
770N ARG* 1.3 65.7 + - - +
771N LEU 3.2 2.5 - - - -
772N LYS* 3.1 12.7 + - - +
773N ASN* 3.4 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 770 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766N LEU 3.0 16.8 + - - -
767N GLU* 3.2 5.4 + - - +
769N SER* 1.3 78.7 - - - +
771N LEU* 1.3 60.4 + - - +
773N ASN* 3.3 8.5 + - - -
774N PRO* 3.3 14.6 - - - +
775N LYS 4.3 1.7 + - - -
779N LEU* 6.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 771 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767N GLU 3.7 9.4 + - - -
768N LYS 4.0 1.7 + - - -
769N SER 3.2 0.8 - - - -
770N ARG* 1.3 73.0 - - - +
772N LYS* 1.3 63.2 + - - +
773N ASN 3.1 0.8 + - - -
774N PRO* 3.6 10.6 - - - +
----------------------------------------------------------
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