Contacts of the helix formed by residues 271 - 287 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ILE* 6.4 0.9 - - + -
219C THR* 3.9 17.9 - - + -
221C LEU* 4.2 20.9 - - + -
231C ALA* 4.4 10.1 - - + -
233C VAL* 3.6 30.7 - - + -
261C LEU* 4.8 1.6 - - + -
265C LEU* 4.0 31.2 - - + +
269C LYS 3.8 0.2 + - - -
270C PRO* 1.3 69.4 - - - +
272C PRO* 1.3 67.6 - - + +
274C ALA* 3.0 2.6 + - - +
275C ILE* 2.7 50.6 + - + +
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Residues in contact with PRO 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 4.8 20.2 - - - +
240C VAL* 4.6 7.1 - - + +
270C PRO* 3.4 12.1 - - + -
271C LEU* 1.3 97.9 - - + +
273C GLU* 1.3 62.2 + - - +
275C ILE* 3.3 10.7 + - + +
276C ARG* 3.0 45.4 + - - +
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LYS* 3.7 33.0 + - + +
270C PRO* 3.1 35.0 + - + +
272C PRO* 1.3 78.5 - - - +
274C ALA* 1.3 64.4 + - - +
276C ARG* 3.0 19.4 + - + +
277C PHE* 2.9 21.8 + - + +
305C LEU* 5.8 2.4 - - + +
309C ARG* 4.4 21.9 + - - +
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU* 3.9 8.4 - - + +
264C ALA* 3.7 29.4 - - + +
265C LEU* 3.8 33.0 - - + +
269C LYS* 4.1 4.9 - - + +
270C PRO 3.0 10.3 + - - +
271C LEU 3.5 6.5 - - - +
273C GLU* 1.3 76.9 - - - +
275C ILE* 1.3 63.8 + - - +
277C PHE* 3.2 4.5 + - - +
278C ALA* 3.0 22.7 + - - +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 3.8 28.9 - - + -
229C VAL* 3.5 26.9 - - + -
231C ALA* 3.6 30.5 - - + -
240C VAL* 3.7 15.9 - - + -
257C PHE* 4.0 6.0 - - + -
261C LEU* 4.1 9.9 - - + -
271C LEU* 2.7 32.2 + - + +
272C PRO* 3.5 5.6 - - + +
274C ALA* 1.3 71.3 - - - +
276C ARG* 1.3 52.2 + - - +
278C ALA* 2.9 6.1 + - - +
279C HIS* 2.7 47.0 + - + +
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Residues in contact with ARG 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 5.9 1.6 - - - +
240C VAL* 4.2 18.0 - - + +
241C PRO 5.8 1.3 + - - +
243C PHE* 3.7 28.4 - - + -
272C PRO* 3.0 37.2 + - - +
273C GLU* 3.0 23.3 + - + +
275C ILE* 1.3 77.6 - - - +
277C PHE* 1.3 61.8 - - - +
279C HIS* 3.1 12.6 + - + +
280C ALA* 2.9 20.4 + - - +
305C LEU* 4.2 8.5 - - + -
309C ARG* 4.5 25.5 - - - +
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.8 10.1 - - - -
260C ALA* 3.5 40.4 - - + -
263C THR* 4.7 1.6 - - + -
264C ALA* 3.7 18.8 - - + -
269C LYS* 4.0 15.3 - - + +
273C GLU* 2.9 11.5 + - + +
274C ALA 3.5 7.2 - - - +
276C ARG* 1.3 76.6 - - - +
278C ALA* 1.3 62.3 + - - +
280C ALA* 3.3 3.3 + - - +
281C ALA* 3.1 20.6 + - - +
298C ARG* 3.6 43.3 - - - -
301C ILE* 3.4 34.0 - - + +
302C ASP* 4.1 4.5 - - - -
305C LEU* 3.7 26.1 - - + +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PHE* 3.5 42.3 - - + +
260C ALA* 4.0 12.3 - - - -
261C LEU* 3.7 15.3 - - + +
274C ALA 3.0 11.9 + - - +
275C ILE* 2.9 9.6 + - - +
277C PHE* 1.3 74.6 - - - +
279C HIS* 1.3 68.5 + - - +
281C ALA* 3.3 2.6 + - - +
282C ALA* 3.0 24.9 + - - +
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Residues in contact with HIS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C THR* 6.4 0.2 - - + -
228C GLY* 4.1 9.9 - - - -
229C VAL* 3.6 9.3 - - + +
240C VAL* 3.0 25.8 + - + -
241C PRO 3.2 19.6 + - - -
242C GLY* 3.7 12.1 - - - -
243C PHE* 3.9 17.6 + + + +
257C PHE* 3.6 12.4 - + - -
275C ILE* 2.7 33.0 + - + +
276C ARG* 3.4 10.3 - - + +
278C ALA* 1.3 77.6 - - - +
280C ALA* 1.3 62.7 + - - +
282C ALA* 3.3 1.6 + - - +
283C ALA* 3.1 23.9 + - - +
1311C ACP 2.8 41.8 + - - +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C PHE* 3.9 2.2 - - + -
276C ARG 2.9 13.7 + - - +
277C PHE 3.8 6.5 - - - +
278C ALA 3.2 0.4 - - - -
279C HIS* 1.3 76.1 - - - +
281C ALA* 1.3 64.3 + - - +
283C ALA* 3.3 2.9 + - - +
284C ILE* 3.2 29.6 + - - +
301C ILE* 4.4 12.1 - - + +
304C PHE* 3.4 34.7 - - + -
305C LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 5.2 0.2 - - - +
256C THR* 3.6 15.6 - - + +
260C ALA* 3.8 21.8 - - + -
277C PHE 3.1 16.0 + - - +
278C ALA 3.7 4.0 - - - +
279C HIS 3.2 0.2 - - - -
280C ALA* 1.3 78.8 - - - +
282C ALA* 1.3 62.6 + - - +
284C ILE* 3.5 0.7 + - - -
285C ALA 3.1 15.2 + - - -
296C PRO* 3.5 13.9 - - + +
301C ILE* 3.8 29.6 - - + +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ALA* 3.5 23.1 - - - +
256C THR* 3.9 8.7 - - - +
257C PHE* 4.2 4.3 - - + +
278C ALA 3.0 13.3 + - - +
279C HIS 4.0 1.1 - - - +
281C ALA* 1.3 78.2 - - - +
283C ALA* 1.3 55.6 + - - +
285C ALA* 2.8 20.0 + - - +
286C VAL* 2.9 19.9 + - - +
1311C ACP 3.6 35.4 - - - +
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C PHE* 3.8 23.1 - - + +
245C VAL* 3.8 5.1 - - + +
279C HIS 3.1 18.0 + - - +
280C ALA 3.5 5.2 - - - +
282C ALA* 1.3 76.3 - - - +
284C ILE* 1.3 62.9 + - - +
286C VAL* 3.0 19.6 + - - +
287C THR* 3.3 11.6 - - - +
304C PHE* 3.9 22.0 - - + -
1311C ACP 3.9 16.5 + - + -
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ALA 3.2 14.7 + - - +
281C ALA 3.8 5.6 - - - +
283C ALA* 1.3 75.6 - - - +
285C ALA* 1.3 64.4 + - - +
287C THR* 2.9 28.4 + - - +
288C ARG* 3.6 40.5 + - - +
296C PRO* 3.8 17.3 - - + -
300C GLU* 3.9 20.0 - - + +
301C ILE* 3.9 12.6 - - + +
304C PHE* 3.8 37.9 - - + -
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ILE 5.4 0.4 - - - +
252C ALA 4.8 1.1 - - - +
253C ALA* 4.8 7.6 - - - -
256C THR* 3.7 25.6 - - + +
281C ALA 3.1 13.2 + - - +
282C ALA* 2.8 14.3 + - - +
284C ILE* 1.3 77.9 - - - +
286C VAL* 1.3 59.1 + - - +
287C THR 3.2 0.9 + - - -
288C ARG 3.3 6.8 + - - +
294C SER* 3.5 29.3 - - - +
296C PRO* 4.4 0.9 - - + +
1310C CS 3.0 23.0 - - - -
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.6 21.1 - - + -
247C ALA* 4.1 11.0 - - + -
248C VAL 2.9 25.6 + - - -
249C ASP 3.4 16.9 + - - +
250C THR* 4.1 9.6 - - + -
253C ALA* 3.7 26.0 - - + -
282C ALA 2.9 14.8 + - - +
283C ALA* 3.0 22.0 - - - +
285C ALA* 1.3 76.6 - - - +
287C THR* 1.3 59.4 + - - +
288C ARG 3.3 0.6 + - - -
1311C ACP 3.8 33.2 - - + +
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Residues in contact with THR 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL* 4.0 19.3 - - + -
246C GLN 4.4 6.7 - - - +
248C VAL* 3.7 24.7 - - - +
283C ALA 3.3 17.3 - - - +
284C ILE* 2.9 18.6 + - - +
286C VAL* 1.3 81.1 - - - +
288C ARG* 1.3 66.4 + - - +
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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) + - + + + + + -
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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