Contacts of the helix formed by residues 271 - 287 (chain B) in PDB entry 1GQT
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 LEU 271 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 6.3 0.2 - - + -
219B THR* 4.2 15.7 - - + +
221B LEU* 4.2 17.7 - - + -
231B ALA* 4.9 6.3 - - + -
233B VAL* 3.7 31.0 - - + -
261B LEU* 4.8 1.1 - - + -
265B LEU* 4.1 27.6 - - + +
269B LYS 3.8 0.4 + - - -
270B PRO* 1.3 71.2 - - - +
272B PRO* 1.3 61.5 - - + +
274B ALA* 3.3 4.4 + - - +
275B ILE* 2.8 68.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 4.8 20.4 - - - +
240B VAL* 4.6 15.5 - - + +
270B PRO* 3.4 12.8 - - + -
271B LEU* 1.3 98.5 - - + +
273B GLU* 1.3 57.3 + - - +
275B ILE* 3.3 8.3 + - + +
276B ARG* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LYS* 3.5 36.7 + - + +
270B PRO* 3.2 26.1 + - + +
272B PRO* 1.3 77.4 - - + +
274B ALA* 1.3 61.3 + - - +
276B ARG* 2.9 11.0 + - + +
277B PHE* 2.8 29.4 + - + +
305B LEU* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.0 8.9 - - + +
264B ALA* 3.7 27.7 - - + +
265B LEU* 3.6 30.1 - - + -
269B LYS* 4.0 5.9 - - - +
270B PRO 2.8 20.3 + - - +
271B LEU 3.4 5.2 - - - +
273B GLU* 1.3 73.3 - - - +
275B ILE* 1.3 62.2 + - - +
277B PHE* 3.3 3.8 + - - +
278B ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.7 34.1 - - + -
229B VAL* 3.6 26.7 - - + -
231B ALA* 3.8 15.0 - - + -
240B VAL* 3.9 11.2 - - + -
257B PHE* 4.1 8.3 - - + -
261B LEU* 4.2 5.4 - - + -
271B LEU* 2.8 45.9 + - + +
272B PRO* 3.7 6.5 - - + +
273B GLU 3.1 0.2 - - - -
274B ALA* 1.3 74.2 - - - +
276B ARG* 1.3 57.8 + - - +
278B ALA* 3.2 6.8 + - - +
279B HIS* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 3.8 21.1 - - - +
241B PRO* 3.0 40.5 + - - +
242B GLY 3.8 13.3 + - - -
243B PHE* 3.5 39.8 - - + -
272B PRO 3.1 11.8 + - - +
273B GLU* 2.9 15.4 + - + +
275B ILE* 1.3 78.6 - - - +
277B PHE* 1.3 56.7 - - - +
279B HIS* 3.3 7.6 + - - +
280B ALA* 3.0 23.9 + - - +
305B LEU* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 2.9 29.6 - - - -
260B ALA* 3.5 29.8 - - + -
263B THR* 4.7 1.6 - - + -
264B ALA* 3.8 15.9 - - + -
267B GLU* 5.8 0.2 - - - -
269B LYS* 3.3 22.7 - - - +
273B GLU* 2.8 13.1 + - + +
274B ALA 3.5 7.4 - - - +
276B ARG* 1.3 75.6 - - - +
278B ALA* 1.3 63.3 + - - +
280B ALA* 3.1 4.2 + - - +
281B ALA* 3.1 19.4 + - - +
298B ARG* 3.5 37.9 - - - -
301B ILE* 3.7 27.6 - - + +
302B ASP* 4.1 3.8 - - - -
305B LEU* 4.0 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 3.4 45.3 - - + +
260B ALA* 4.0 12.3 - - - -
261B LEU* 3.6 13.0 - - + +
274B ALA 3.0 13.4 + - - +
275B ILE* 3.2 7.2 + - - +
277B PHE* 1.3 76.9 - - - +
279B HIS* 1.3 63.2 + - - +
281B ALA* 3.1 4.2 + - - +
282B ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLY* 3.7 19.5 - - - -
229B VAL* 3.7 7.1 - - + +
240B VAL* 3.0 25.3 + - + -
241B PRO 3.0 21.4 + - - -
242B GLY* 3.5 10.4 - - - -
243B PHE* 3.9 16.3 + - + -
257B PHE* 4.0 10.5 - + - -
275B ILE* 2.8 27.7 + - + -
276B ARG* 3.4 11.7 - - - +
278B ALA* 1.3 72.3 - - - +
280B ALA* 1.3 65.0 + - - +
282B ALA* 3.3 1.4 + - - +
283B ALA* 2.9 26.0 + - - +
1310B ACP 2.9 44.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.6 23.6 - - + -
276B ARG 3.0 9.5 + - - +
277B PHE 3.1 7.8 + - - +
279B HIS* 1.3 78.4 - - - +
281B ALA* 1.3 62.5 + - - +
283B ALA* 3.2 2.5 + - - +
284B ILE* 3.2 29.0 + - - +
301B ILE* 4.2 7.0 - - + -
304B PHE* 3.7 20.4 - - + -
305B LEU* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 3.5 19.5 - - + +
260B ALA* 3.9 19.1 - - + -
277B PHE 3.1 11.4 + - - +
278B ALA 3.1 7.8 + - - +
280B ALA* 1.3 77.7 - - - +
282B ALA* 1.3 62.7 + - - +
283B ALA 3.2 0.2 + - - -
284B ILE* 3.3 1.1 + - - -
285B ALA 2.9 16.6 + - - -
296B PRO* 3.4 25.3 - - + +
301B ILE* 4.2 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ALA 3.6 23.1 - - - +
256B THR* 3.5 9.4 - - - +
257B PHE* 4.1 7.6 - - + +
278B ALA 2.9 14.8 + - - +
279B HIS 3.9 0.2 - - - +
281B ALA* 1.3 79.5 - - - +
283B ALA* 1.3 57.8 + - - +
285B ALA* 2.9 4.1 + - - +
286B VAL* 2.9 35.5 + - - +
1310B ACP 3.7 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 4.3 22.0 - - + +
245B VAL* 3.8 21.6 - - + +
279B HIS 2.9 18.3 + - - +
280B ALA* 3.6 5.4 - - - +
282B ALA* 1.3 75.1 - - - +
284B ILE* 1.3 63.9 + - - +
286B VAL* 2.7 30.2 - - - +
287B THR* 3.6 7.6 - - - +
304B PHE* 4.5 4.0 - - + -
1310B ACP 4.5 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 6.1 0.2 - - - -
280B ALA 3.4 13.0 - - - +
281B ALA 3.5 6.1 - - - +
283B ALA* 1.3 77.9 - - - +
285B ALA* 1.3 63.6 + - - +
287B THR* 2.9 29.5 + - - +
288B ARG* 3.6 38.5 + - - +
296B PRO* 4.0 20.6 - - + -
300B GLU* 3.7 31.4 - - + +
301B ILE* 4.3 5.6 - - + -
304B PHE* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE 5.6 0.9 - - - +
252B ALA 5.1 3.4 - - - +
253B ALA* 5.1 3.1 - - - -
256B THR* 3.6 24.9 - - + +
281B ALA 2.9 14.9 + - - +
282B ALA* 2.9 12.0 + - - +
284B ILE* 1.3 77.2 - - - +
286B VAL* 1.3 61.1 + - + +
288B ARG 3.2 8.5 + - - +
294B SER* 3.2 30.7 - - - +
296B PRO* 4.5 0.7 - - + -
1309B CS 3.1 23.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 3.6 20.9 - - + -
247B ALA* 3.8 9.1 - - + -
248B VAL 3.2 22.2 + - - -
249B ASP 3.2 23.7 + - - +
250B THR* 4.5 8.7 - - + -
253B ALA* 4.0 23.8 - - + -
282B ALA 2.9 14.3 + - - +
283B ALA* 2.7 28.3 - - - +
285B ALA* 1.3 79.3 - - - +
287B THR* 1.3 59.2 + - + +
288B ARG 3.3 0.7 - - - -
1309B CS 4.5 0.2 - - - -
1310B ACP 4.2 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 4.3 15.3 - - + -
246B GLN 3.6 18.4 - - - +
248B VAL* 3.6 22.1 - - - +
283B ALA 3.6 14.8 - - - +
284B ILE* 2.9 20.7 + - - +
286B VAL* 1.3 82.3 - - + +
288B ARG* 1.3 65.8 + - - +
----------------------------------------------------------
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