Contacts of the helix formed by residues 19 - 30 (chain D) in PDB entry 3QNQ
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 GLN 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LYS 3.4 14.3 + - - +
16D VAL* 3.2 17.1 + - - +
18D GLU* 1.3 74.9 - - - +
20D ARG* 1.3 62.8 + - - +
21D HIS* 2.8 41.9 + - - +
22D LEU* 3.4 28.4 + - + +
23D LEU* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU 3.2 5.2 + - - -
19D GLN* 1.3 79.7 - - - +
21D HIS* 1.3 71.2 + - - +
23D LEU* 3.1 10.7 - - - +
24D ALA* 2.7 36.4 + - - +
92D LEU* 4.1 7.0 - - + +
95D TYR* 3.3 56.0 + - + +
96D TYR* 3.3 34.3 + - - -
161D ARG* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLN* 2.8 27.2 + - - +
20D ARG* 1.3 90.3 - - - +
22D LEU* 1.3 58.7 + - - +
23D LEU 3.0 4.9 - - - -
24D ALA* 4.0 5.3 - - - +
25D ILE* 3.2 31.3 + - - +
92D LEU* 4.3 13.7 - - + -
154D ILE* 3.9 34.7 - - + +
158D GLU* 2.7 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 4.6 22.9 - - + +
19D GLN* 3.4 23.4 + - + +
21D HIS* 1.3 78.3 - - - +
23D LEU* 1.3 56.5 + - - +
25D ILE* 4.2 7.0 - - - +
26D ARG* 3.3 39.5 + - - +
254D ILE 4.5 5.2 - - - +
257D GLY 4.8 1.8 - - - +
258D VAL* 3.3 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ZDM 6.1 2.0 - - - -
17D ALA 4.8 4.7 - - - +
18D GLU* 4.4 6.7 - - - +
19D GLN 2.8 21.7 + - - +
20D ARG* 3.1 4.3 - - - +
21D HIS 3.0 0.2 - - - -
22D LEU* 1.3 77.5 - - - +
24D ALA* 1.3 69.3 + - - +
25D ILE 3.2 0.2 - - - -
26D ARG* 3.2 32.6 + - - +
27D ASP* 2.9 49.1 + - - +
91D ARG* 4.1 18.6 - - - +
95D TYR* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ARG 2.7 19.4 + - - +
21D HIS* 4.0 4.3 - - - +
23D LEU* 1.3 74.1 - - - +
25D ILE* 1.3 53.5 + - - +
28D GLY* 2.7 34.7 + - - -
88D ILE* 3.7 19.0 - - + +
91D ARG* 3.8 12.7 - - + +
92D LEU* 3.7 39.3 - - + +
95D TYR* 6.2 0.2 - - + -
154D ILE* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D HIS 3.2 18.8 + - - +
22D LEU* 4.2 7.4 - - - +
24D ALA* 1.3 73.8 - - - +
26D ARG* 1.3 68.4 + - - +
29D LEU* 3.0 48.5 + - + +
88D ILE* 3.7 20.9 - - + -
150D MET* 3.4 47.3 - - + -
154D ILE* 4.2 18.4 - - + -
257D GLY 4.0 10.8 - - - +
261D PRO* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 3.7 15.8 + - - +
17D ALA* 3.6 26.9 + - - +
22D LEU* 3.3 28.0 + - - +
23D LEU* 3.2 42.0 + - - +
25D ILE* 1.3 82.2 - - - +
27D ASP* 1.3 71.2 + - - +
29D LEU* 3.5 9.2 + - - +
30D VAL* 3.4 14.4 + - + +
33D MET* 5.1 2.1 - - - +
253D THR* 3.9 26.3 + - - +
254D ILE* 3.4 33.1 + - - +
257D GLY* 4.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.8 10.0 - - - +
443C ZDM 3.5 39.3 - - - +
23D LEU* 2.9 38.4 + - - +
26D ARG* 1.3 87.2 + - - +
28D GLY* 1.3 65.8 + - - +
30D VAL* 3.0 30.4 + - - +
31D LEU* 3.9 1.7 + - - +
91D ARG* 3.5 17.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ALA 2.7 24.5 + - - -
27D ASP* 1.3 73.6 - - - +
29D LEU* 1.3 60.3 + - - +
31D LEU* 3.1 23.4 + - - +
32D THR 4.5 0.2 + - - -
84D ALA* 4.7 4.5 - - - -
87D GLY* 3.7 22.2 - - - -
88D ILE* 3.6 17.3 - - - -
91D ARG* 4.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 3.0 38.9 + - + +
26D ARG* 3.8 6.5 - - - +
28D GLY* 1.3 70.5 - - - +
30D VAL* 1.3 64.7 + - - +
31D LEU 3.0 2.7 - - - -
32D THR* 2.7 31.8 + - - +
33D MET* 3.8 11.9 - - + +
84D ALA* 3.7 27.6 - - + -
88D ILE* 4.1 6.9 - - + +
146D LEU* 4.4 17.3 - - + -
150D MET* 5.8 2.0 - - + -
257D GLY 4.5 2.9 - - - +
260D SER* 3.4 26.9 - - - +
261D PRO* 4.3 15.5 - - + -
264D LEU* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.5 14.1 - - + +
183C SER* 3.4 22.6 + - - +
443C ZDM 4.1 19.4 - - + +
26D ARG* 3.4 14.8 + - + +
27D ASP* 3.0 30.7 + - + +
29D LEU* 1.3 77.0 - - - +
31D LEU* 1.3 60.0 + - - +
32D THR 3.0 1.4 + - - -
33D MET* 3.2 40.6 + - + +
34D PRO* 3.6 6.1 - - - +
1K NAG 4.4 9.2 - - + +
----------------------------------------------------------
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