Contacts of the helix formed by residues 710 - 723 (chain C) 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 ASN 710 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C THR 3.8 1.0 + - - -
709C TRP* 1.3 74.2 - - - +
711C ARG* 1.3 56.7 + - - +
712C LYS 3.2 2.7 - - - -
713C LYS* 3.1 6.3 + - - +
714C LEU* 2.6 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 711 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C TRP 3.8 1.0 + - - -
710C ASN* 1.3 70.5 - - - +
712C LYS* 1.3 57.8 + - - +
714C LEU* 5.2 0.4 - - - +
715C GLY* 2.9 28.9 + - - +
729C ALA 5.3 2.8 - - - +
730C ARG* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 712 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C ASN 3.2 0.4 - - - -
711C ARG* 1.3 77.4 - - - +
713C LYS* 1.3 61.9 + - - +
716C GLU* 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 713 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C ASN* 3.1 10.7 + - - +
712C LYS* 1.3 78.6 - - - +
714C LEU* 1.3 56.4 + - - +
716C GLU* 3.9 0.3 - - - -
717C PHE* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 714 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705C VAL* 6.4 2.7 - - - +
706C GLN 5.7 3.6 - - - -
709C TRP* 4.8 7.1 - - - +
710C ASN 2.6 21.6 + - - +
711C ARG* 5.2 0.4 - - - +
713C LYS* 1.3 70.4 - - - +
715C GLY* 1.3 58.4 + - - +
717C PHE* 3.2 1.8 + - - +
718C PHE* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 715 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C ARG* 2.9 18.3 + - - +
714C LEU* 1.3 74.4 - - - +
716C GLU* 1.3 58.3 + - - +
718C PHE* 3.2 2.2 + - - -
719C GLN* 2.9 26.5 + - - -
725C ASP 5.3 1.4 - - - +
726C LEU* 5.9 3.5 - - - -
729C ALA* 4.3 30.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 716 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C LYS 3.1 17.5 + - - -
713C LYS 3.9 0.7 - - - -
715C GLY* 1.3 74.7 - - - +
717C PHE* 1.3 64.7 + - - +
719C GLN* 3.2 2.4 + - - +
720C THR* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 717 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C LYS 2.9 16.2 + - - -
714C LEU* 3.2 3.1 + - - +
716C GLU* 1.3 75.2 - - - +
718C PHE* 1.3 61.9 + - - +
720C THR* 3.2 2.0 + - - +
721C LYS* 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 718 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C LEU 2.9 14.0 + - - -
715C GLY 3.7 2.9 - - - -
717C PHE* 1.3 75.7 - - - +
719C GLN* 1.3 64.6 + - - +
721C LYS* 3.2 0.6 + - - +
722C TYR* 3.0 23.6 + - - -
724C TRP* 3.8 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 719 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C GLY 2.9 14.1 + - - -
716C GLU* 3.2 2.9 + - - +
718C PHE* 1.3 77.6 - - - +
720C THR* 1.3 54.9 + - - +
723C ASP* 2.7 34.7 + - - -
724C TRP* 2.9 30.2 + - - +
725C ASP 5.3 0.2 - - - -
726C LEU* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 720 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C GLU 2.9 14.2 + - - -
717C PHE* 3.8 2.7 - - - +
719C GLN* 1.3 79.6 - - - +
721C LYS* 1.3 60.3 + - - +
723C ASP* 3.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 721 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717C PHE 2.9 15.7 + - - -
718C PHE 3.8 0.4 - - - -
720C THR* 1.3 78.3 - - - +
722C TYR* 1.3 56.2 - - - +
723C ASP 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 722 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718C PHE 3.0 10.7 + - - -
721C LYS* 1.3 76.0 - - - +
723C ASP* 1.3 65.8 + - - +
724C TRP* 3.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 723 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C GLN 2.7 19.9 + - - -
720C THR 3.9 3.0 + - - -
721C LYS 3.7 2.0 - - - -
722C TYR* 1.3 74.0 - - - +
724C TRP* 1.3 62.8 + - - +
725C ASP* 3.6 1.2 + - - -
----------------------------------------------------------
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