Contacts of the helix formed by residues 1680 - 1690 (chain D) 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 PRO1680 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678D ASP 3.3 5.2 - - - +
1679D TYR* 1.3 71.5 - - - +
1681D ILE* 1.3 65.4 + - - +
1682D TYR 3.3 2.7 - - - -
1683D ASP* 3.0 15.6 + - - -
1684D VAL* 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1681 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1679D TYR 3.4 5.3 + - - -
1680D PRO* 1.3 71.4 - - - +
1682D TYR* 1.3 56.6 + - - +
1684D VAL* 3.1 4.8 + - - +
1685D LEU* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1682 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680D PRO 3.3 1.4 + - - -
1681D ILE* 1.3 71.5 - - - +
1683D ASP* 1.3 65.0 + - - +
1685D LEU* 3.3 2.7 + - - +
1686D GLN* 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1683 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680D PRO* 3.0 10.1 + - - -
1682D TYR* 1.3 76.2 - - - +
1684D VAL* 1.3 57.4 + - - +
1686D GLN* 2.8 19.2 + - - +
1687D MET* 2.9 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1684 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1679D TYR* 6.1 0.4 - - - +
1680D PRO 3.3 7.0 + - - -
1681D ILE* 3.1 8.3 + - - +
1683D ASP* 1.3 74.4 - - - +
1685D LEU* 1.3 56.4 + - - +
1687D MET* 3.4 2.7 + - - +
1688D VAL* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1685 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352D THR* 5.9 1.6 - - - -
1681D ILE 2.9 14.0 + - - -
1682D TYR* 3.3 4.5 + - - +
1683D ASP 3.2 0.2 - - - -
1684D VAL* 1.3 75.9 - - - +
1686D GLN* 1.3 57.1 + - - +
1688D VAL* 3.3 2.1 + - - +
1689D GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1686 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651D CYS 5.4 6.0 - - - +
1682D TYR 2.9 10.3 + - - -
1683D ASP* 2.8 9.1 + - - +
1685D LEU* 1.3 74.0 - - - +
1687D MET* 1.3 64.5 + - - +
1689D GLY* 3.0 4.5 + - - -
1690D HIS* 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651D CYS* 5.6 10.1 + - - +
1661D VAL* 5.6 5.2 - - - -
1683D ASP 2.9 11.8 + - - -
1684D VAL* 3.8 3.8 - - - +
1686D GLN* 1.3 73.5 - - - +
1688D VAL* 1.3 62.6 + - - +
1690D HIS* 3.1 15.7 + - - +
1691D ALA 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684D VAL 2.9 15.3 + - - -
1685D LEU* 3.7 4.3 - - - +
1687D MET* 1.3 75.3 - - - +
1689D GLY* 1.3 60.2 + - - +
1691D ALA* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1689 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352D THR* 3.9 25.0 - - - +
1353D GLY* 4.9 7.1 - - - -
1685D LEU 2.9 14.8 + - - -
1686D GLN* 3.0 6.2 + - - -
1688D VAL* 1.3 75.1 - - - +
1690D HIS* 1.3 59.7 + - - +
1691D ALA* 3.1 10.5 + - - +
1692D ASN* 4.0 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657D ALA* 3.9 8.9 - - - +
1658D ALA* 3.2 22.9 + - - -
1661D VAL* 6.2 1.1 - - - -
1686D GLN 3.0 11.2 + - - -
1687D MET* 3.1 9.8 + - - +
1688D VAL 3.0 2.0 - - - -
1689D GLY* 1.3 77.3 - - - +
1691D ALA* 1.3 56.6 + - - +
1692D ASN 3.5 1.9 + - - -
----------------------------------------------------------
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