Contacts of the helix formed by residues 169 - 173 (chain 2) in PDB entry 1QJX
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 ASP 169 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2641 TYR* 2.5 32.9 + - - +
2661 LEU* 3.6 23.1 - - - +
1352 VAL* 3.6 8.1 - - - +
1672 SER* 3.1 5.9 + - - -
1682 ASP* 1.3 75.8 - - - +
1702 ASN* 1.3 65.6 + - - +
1712 TRP* 3.2 22.6 + - - +
1722 LEU* 3.1 9.5 + - + -
1742 PHE* 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS* 2.8 46.3 + - - +
1562 VAL* 4.8 1.3 - - + -
1682 ASP 3.2 7.5 + - - +
1692 ASP* 1.3 72.7 - - - +
1712 TRP* 1.3 87.1 + - - +
1722 LEU 3.1 1.3 + - - -
1732 ASN* 3.2 18.2 + - - -
1742 PHE* 3.6 24.9 - - + -
1792 LEU* 3.8 10.4 - - - +
2242 ILE* 4.0 11.9 - - + +
2252 PRO* 5.6 0.4 + - - +
633 GLY 5.5 0.2 - - - +
643 ASN* 5.7 0.7 - - - -
653 VAL* 3.8 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 171 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2661 LEU* 4.5 6.1 - - + +
2701 VAL* 4.0 30.7 - - + +
2741 VAL* 4.0 36.1 - - + -
2761 ILE* 5.3 0.4 - - + -
1692 ASP* 4.0 25.1 + - + +
1702 ASN* 1.3 89.5 + - - +
1722 LEU* 1.3 80.0 + - + +
1732 ASN 3.4 1.1 - - - -
1782 LEU* 3.7 15.6 - - + +
1792 LEU* 3.1 32.3 + - + +
623 ILE* 4.7 1.6 - - + -
633 GLY* 3.4 46.6 + - - -
643 ASN 4.4 7.4 - - - +
653 VAL* 4.7 2.2 - - + +
673 MET* 3.6 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2531 ALA* 4.5 2.5 - - + -
2541 VAL* 4.2 22.4 - - + -
2641 TYR* 3.7 33.2 - - + +
2661 LEU* 4.3 10.5 - - + -
2741 VAL* 4.7 0.9 - - + -
1692 ASP* 3.1 13.2 + - + +
1702 ASN 3.1 0.6 - - - -
1712 TRP* 1.3 113.1 - - + +
1732 ASN* 1.3 58.1 - - - +
1742 PHE 2.9 10.6 + - - -
1752 ASP 2.9 10.6 + - - -
1762 GLY* 3.0 15.1 + - - +
1772 THR 2.8 30.0 - - - +
1782 LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 173 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2501 PRO* 4.4 1.9 - - - +
1272 ILE* 5.8 0.2 - - + -
1302 HIS* 2.9 27.0 + - - +
1702 ASN 3.2 9.8 + - - -
1722 LEU* 1.3 77.2 - - - +
1742 PHE* 1.3 71.4 + - - +
1752 ASP* 2.9 6.8 + - - +
1772 THR* 2.9 27.9 + - - +
1782 LEU 2.9 19.4 - - - +
1792 LEU* 3.1 25.7 - - - +
1822 LEU* 3.2 39.5 - - + +
----------------------------------------------------------
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