Contacts of the helix formed by residues 711 - 721 (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 LEU 711 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697N LEU* 5.7 9.6 - - - +
710N LYS* 1.3 76.8 - - - +
712N TRP* 1.3 60.9 + - - +
714N MET* 4.1 0.4 - - - +
715N LYS* 3.3 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 712 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710N LYS 3.3 2.8 - - - +
711N LEU* 1.3 75.4 - - - +
713N MET* 1.3 60.9 + - - +
715N LYS* 3.8 0.5 + - - -
716N GLY* 3.3 18.9 + - - -
731N ALA 5.9 2.3 - - - -
735N GLY* 6.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 713 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710N LYS* 3.3 12.6 + - - +
711N LEU 3.2 0.8 - - - -
712N TRP* 1.3 74.7 - - - +
714N MET* 1.3 64.0 + - - +
716N GLY* 3.7 2.0 + - - -
717N GLN* 3.6 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 714 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710N LYS 2.9 16.0 + - - -
711N LEU* 4.1 0.7 - - - +
713N MET* 1.3 77.2 - - - +
715N LYS* 1.3 64.8 + - - +
717N GLN* 3.1 12.3 + - - -
718N ILE* 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 715 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711N LEU 3.3 14.6 + - - -
712N TRP 4.3 0.7 - - - -
714N MET* 1.3 75.4 - - - +
716N GLY* 1.3 51.8 + - - +
718N ILE* 3.2 3.4 + - - +
719N GLU* 2.8 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 716 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712N TRP 3.3 15.6 + - - -
713N MET 4.1 2.7 - - - -
714N MET 3.2 1.0 - - - -
715N LYS* 1.3 76.2 - - - +
717N GLN* 1.3 50.5 + - - +
719N GLU* 3.2 3.5 + - - -
720N GLU* 2.5 34.3 + - - -
728N ALA* 4.9 13.8 - - - -
731N ALA* 6.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 717 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713N MET 3.6 7.5 + - - -
714N MET 3.1 8.1 + - - -
716N GLY* 1.3 75.4 - - - +
718N ILE* 1.3 64.1 + - - +
720N GLU* 3.0 4.0 + - - +
721N GLN* 3.0 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 718 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714N MET 3.3 8.9 + - - -
715N LYS* 3.2 6.7 + - - +
717N GLN* 1.3 75.6 - - - +
719N GLU* 1.3 60.6 - - - +
721N GLN* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 719 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715N LYS 2.8 18.2 + - - -
716N GLY* 3.3 4.9 - - - -
718N ILE* 1.3 71.0 - - - +
720N GLU* 1.3 65.2 + - - +
721N GLN 3.2 6.2 + - - -
727N LYS 6.1 0.4 - - - -
728N ALA* 5.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716N GLY 2.5 19.1 + - - -
717N GLN* 3.0 7.1 + - - +
719N GLU* 1.3 72.2 - - - +
721N GLN* 1.3 61.0 + - - +
728N ALA* 5.2 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 721 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717N GLN 3.0 12.2 + - - -
718N ILE* 3.3 12.7 + - - +
719N GLU 3.1 8.9 - - - -
720N GLU* 1.3 80.9 - - - +
----------------------------------------------------------
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