Contacts of the helix formed by residues 273 - 290 (chain A) in PDB entry 2HQQ
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 SER 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.1 1.1 - - - -
271A GLY 4.0 0.2 + - - -
272A ARG* 1.3 78.8 - - - +
274A VAL* 1.3 58.0 + - - +
275A GLN* 3.5 9.3 + - - +
276A GLU* 3.1 23.9 + - - +
277A ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 5.6 1.8 - - - +
220A VAL* 4.1 31.4 - - + -
222A VAL* 5.8 1.3 - - + -
232A ALA* 3.6 31.2 - - + -
233A LEU 6.4 0.2 - - - -
240A LEU* 3.6 18.2 - - + -
268A LEU* 4.1 21.1 - - + +
272A ARG 4.0 0.2 + - - -
273A SER* 1.3 70.7 - - - +
275A GLN* 1.3 66.7 + - - +
277A ALA* 3.2 1.9 + - + +
278A LEU* 2.9 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.0 33.1 - - + +
241A HIS 2.9 33.9 + - - +
242A SER* 4.5 4.0 - - - +
273A SER* 3.2 9.0 + - - +
274A VAL* 1.3 79.0 - - - +
276A GLU* 1.3 62.2 + - - +
278A LEU* 3.6 5.7 + - - +
279A ARG* 3.2 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER* 4.3 2.4 + - - -
272A ARG* 2.2 61.4 + - + +
273A SER* 3.1 21.5 + - - +
275A GLN* 1.3 75.1 - - - +
277A ALA* 1.3 61.1 + - - +
279A ARG* 3.3 24.6 + - - +
280A PHE* 2.8 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 3.5 23.0 - - + +
267A SER* 3.2 25.9 + - - +
268A LEU* 3.7 26.9 - - + -
273A SER 2.9 16.6 + - - +
274A VAL* 3.2 4.9 + - + +
276A GLU* 1.3 77.6 - - - +
278A LEU* 1.3 55.1 + - - +
280A PHE* 3.4 2.1 + - - +
281A GLY 2.8 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 4.1 8.7 - - + -
230A ALA* 3.8 30.3 - - + +
231A ASP 3.9 13.5 - - - +
232A ALA* 3.8 15.5 - - + +
240A LEU* 3.7 41.1 - - + +
241A HIS* 3.8 7.0 - - - +
242A SER* 3.9 8.7 - - - -
260A PHE* 4.1 12.3 - - + -
264A VAL* 4.6 5.8 - - + -
274A VAL* 2.9 18.5 + - + +
275A GLN* 3.7 5.8 - - - +
277A ALA* 1.3 73.1 - - - +
279A ARG* 1.3 67.8 + - - +
281A GLY* 3.3 1.0 + - - -
282A CYS* 3.0 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER* 3.4 20.0 + - - +
245A PHE* 4.3 7.8 - - + -
275A GLN* 3.2 37.6 + - - +
276A GLU* 3.3 26.6 + - - +
278A LEU* 1.3 79.4 - - - +
280A PHE* 1.3 63.0 + - - +
282A CYS* 3.2 3.5 + - - +
283A GLN* 3.0 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.0 19.1 - - + -
263A SER* 3.4 39.0 - - - -
266A PHE* 4.0 24.2 - + - -
267A SER* 3.9 8.3 - - - -
276A GLU* 2.8 33.3 + - - +
277A ALA* 3.7 6.1 - - - +
279A ARG* 1.3 69.9 - - - +
281A GLY* 1.3 66.0 + - - +
283A GLN* 3.2 13.9 + - + +
284A VAL* 2.9 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.6 24.0 - - - -
263A SER* 3.8 18.4 - - - -
264A VAL* 4.2 1.3 - - - -
277A ALA 2.8 17.9 + - - -
278A LEU 3.7 1.6 - - - -
279A ARG 3.3 0.2 - - - -
280A PHE* 1.3 78.0 - - - +
282A CYS* 1.3 60.6 + - - +
284A VAL* 4.1 0.5 - - - +
285A ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLY* 4.2 5.4 - - - -
230A ALA* 3.7 36.3 - - - -
242A SER* 3.8 11.2 - - - +
243A ASP 3.7 19.3 - - - +
244A ALA* 4.5 4.3 - - - -
245A PHE* 3.8 13.5 + - + +
260A PHE* 4.2 6.7 - - - -
278A LEU 3.0 20.0 + - - +
279A ARG 3.7 4.7 - - - +
281A GLY* 1.3 75.7 - - - +
283A GLN* 1.3 58.1 + - - +
285A ALA* 4.0 3.7 - - - +
286A GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.3 48.7 - - + +
279A ARG* 3.0 37.2 + - - +
280A PHE* 3.7 13.5 - - + +
282A CYS* 1.3 74.9 - - - +
284A VAL* 1.3 61.8 + - + +
286A GLY* 3.3 1.4 + - - -
287A LYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.8 5.2 - - + -
259A THR* 3.6 12.8 - - + -
263A SER* 3.3 22.7 - - - +
280A PHE* 2.9 53.9 + - + +
283A GLN* 1.3 77.9 - - + +
285A ALA* 1.4 57.5 + - - +
287A LYS* 3.3 7.5 + - + +
288A LYS* 2.9 27.5 + - - +
297A ILE* 3.9 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 3.6 26.2 - - + +
259A THR* 3.8 13.1 - - - +
260A PHE* 4.0 12.6 - - + +
281A GLY 3.0 19.8 + - - +
282A CYS* 4.0 4.5 - - - +
284A VAL* 1.4 77.0 - - - +
286A GLY* 1.3 61.7 + - - +
288A LYS* 3.3 4.4 + - - +
289A CYS* 3.1 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE 3.2 28.0 - - - -
246A PRO* 4.8 0.4 - - - -
247A PRO* 3.4 24.8 - - - +
282A CYS 2.9 15.4 + - - -
283A GLN 3.7 0.4 - - - -
284A VAL 3.3 0.2 - - - -
285A ALA* 1.3 76.7 - - - +
287A LYS* 1.3 63.5 + - - +
289A CYS* 3.1 12.9 + - - -
290A GLY 3.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE 4.4 0.2 + - - -
247A PRO* 4.8 3.5 - - - +
283A GLN 2.9 16.5 + - - +
284A VAL* 3.6 9.4 - - + +
286A GLY* 1.3 74.5 - - - +
288A LYS* 1.3 64.7 + - - +
290A GLY* 2.9 16.8 + - - -
291A LEU* 3.6 20.4 - - + +
296A GLY 3.7 12.9 + - - -
297A ILE* 2.8 34.9 + - + +
298A VAL* 4.3 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP* 2.9 29.5 + - - -
253A THR 4.7 0.2 - - - -
254A LEU 3.3 25.1 - - - +
256A ALA* 4.2 10.8 - - + +
259A THR* 3.7 18.8 - - + +
284A VAL 2.9 16.0 + - - +
285A ALA 3.4 6.5 - - - +
287A LYS* 1.3 76.9 - - - +
289A CYS* 1.3 57.6 + - - +
291A LEU* 2.8 41.6 + - - +
293A GLY* 2.8 31.2 + - - +
294A PHE* 3.9 17.0 - - + -
297A ILE* 3.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 3.9 12.3 - - + -
250A VAL* 3.5 12.7 - - + +
251A VAL 2.8 24.3 + - - -
252A ASP 3.2 15.4 + - - -
253A THR* 3.9 17.0 - - - -
256A ALA* 3.5 26.9 - - - -
285A ALA 3.1 20.0 + - - -
286A GLY* 3.1 11.8 + - - +
288A LYS* 1.3 76.1 - - - +
290A GLY* 1.3 56.3 + - - +
291A LEU 3.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 3.5 12.5 - - - +
249A ARG* 3.4 23.4 + - - +
251A VAL* 3.5 14.1 - - - +
286A GLY 3.5 3.8 + - - -
287A LYS 2.9 9.6 + - - -
289A CYS* 1.3 78.4 - - - +
291A LEU* 1.3 63.3 + - - +
----------------------------------------------------------
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