Contacts of the helix formed by residues 271 - 287 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A THR* 4.1 17.5 - - + -
221A LEU* 4.7 11.2 - - + -
231A ALA* 4.7 6.5 - - + -
233A VAL* 3.7 29.8 - - + -
261A LEU* 4.6 10.1 - - + -
265A LEU* 4.3 22.6 - - + +
269A LYS 3.8 0.8 + - - -
270A PRO* 1.3 69.1 - - - +
272A PRO* 1.3 60.6 - - + +
274A ALA* 2.9 6.8 + - - +
275A ILE* 2.6 61.5 + - + +
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Residues in contact with PRO 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 5.5 9.7 - - + +
270A PRO* 3.2 13.0 - - + -
271A LEU* 1.3 94.7 - - + +
273A GLU* 1.3 65.1 + - - +
275A ILE* 3.8 10.4 - - + +
276A ARG* 2.9 23.9 + - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 3.5 36.9 + - + +
270A PRO* 2.9 31.4 + - + +
272A PRO* 1.3 79.7 - - - +
274A ALA* 1.3 58.1 + - - +
276A ARG* 3.2 13.0 + - + +
277A PHE* 2.8 26.9 + - - +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 4.0 8.0 - - + +
264A ALA* 3.5 30.1 - - + +
265A LEU* 3.7 32.1 - - + +
269A LYS* 4.4 3.3 - - + +
270A PRO 2.9 8.9 + - - +
271A LEU 3.4 6.7 - - - +
273A GLU* 1.3 74.7 - - - +
275A ILE* 1.3 65.4 + - - +
277A PHE* 3.1 4.0 + - - +
278A ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.5 32.3 - - + -
229A VAL* 3.5 23.6 - - + -
231A ALA* 3.7 20.6 - - + -
240A VAL* 3.7 19.3 - - + -
257A PHE* 4.4 4.5 - - + -
261A LEU* 4.0 13.2 - - + -
271A LEU* 2.6 34.7 + - + +
272A PRO* 4.0 5.6 - - + +
274A ALA* 1.3 71.7 - - - +
276A ARG* 1.3 57.7 + - - +
278A ALA* 3.6 2.9 - - - +
279A HIS* 2.8 44.1 + - + +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 5.3 3.7 - - + +
243A PHE* 3.7 29.6 - - + -
272A PRO 2.9 14.8 + - - +
273A GLU* 3.3 16.2 - - + +
274A ALA 3.1 0.2 - - - -
275A ILE* 1.3 76.9 - - - +
277A PHE* 1.3 64.8 + - - +
279A HIS* 3.3 7.4 + - - +
280A ALA* 3.1 22.5 + - - +
305A LEU* 3.6 18.3 + - + +
308A GLN* 3.7 32.7 - - - +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 3.8 20.2 - - - -
260A ALA* 3.4 31.0 - - + -
263A THR* 4.6 6.1 - - + -
264A ALA* 3.9 14.6 - - + -
269A LYS* 3.8 19.7 - - - +
273A GLU 2.8 13.5 + - - +
274A ALA 3.4 8.1 - - - +
276A ARG* 1.3 75.4 - - - +
278A ALA* 1.3 62.5 + - - +
280A ALA* 3.4 4.5 + - - +
281A ALA* 3.1 18.5 + - - +
298A ARG* 3.7 40.4 - - - -
301A ILE* 3.6 33.0 - - + +
302A ASP* 4.3 6.3 - - - -
305A LEU* 4.1 16.1 - - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PHE* 3.5 44.5 - - + +
260A ALA* 4.1 11.4 - - - -
261A LEU* 3.7 13.0 - - + +
274A ALA 3.0 15.5 + - - +
275A ILE* 3.6 4.5 - - - +
276A ARG 3.1 0.2 - - - -
277A PHE* 1.3 75.2 - - - +
279A HIS* 1.3 62.7 + - - +
281A ALA* 2.9 16.8 + - - +
282A ALA* 2.9 15.1 + - - +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLY* 3.6 24.9 - - - -
229A VAL* 3.6 15.6 - - + +
240A VAL* 2.8 26.6 + - + -
241A PRO 3.3 19.2 + - - -
242A GLY* 3.8 6.6 - - - -
243A PHE* 3.8 16.5 + - + -
257A PHE* 3.7 7.6 - + - -
275A ILE* 2.8 27.0 + - + +
276A ARG* 3.7 5.6 - - - +
278A ALA* 1.3 72.2 - - - +
280A ALA* 1.3 67.9 + - - +
282A ALA* 3.3 1.6 + - - +
283A ALA* 2.9 25.1 + - - +
1310A ACP 2.7 39.8 + - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PHE* 3.4 20.4 - - + -
276A ARG 3.1 10.6 + - - +
277A PHE 3.5 9.4 - - - +
279A HIS* 1.3 81.6 - - - +
281A ALA* 1.3 62.9 + - - +
283A ALA* 3.2 3.5 + - - +
284A ILE* 3.2 26.9 + - - +
301A ILE* 4.1 7.6 - - + -
304A PHE* 3.8 20.5 - - + -
305A LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 5.1 0.2 - - - +
256A THR* 3.5 14.9 - - + +
260A ALA* 3.8 26.2 - - + -
277A PHE 3.1 9.4 + - - +
278A ALA 2.9 8.8 + - - +
280A ALA* 1.3 77.2 - - - +
282A ALA* 1.3 64.0 + - - +
284A ILE* 3.4 1.3 + - - -
285A ALA 3.1 15.4 + - - -
296A PRO* 3.4 27.1 - - + +
301A ILE* 3.9 15.9 - - + -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 3.7 15.3 - - - +
256A THR* 3.7 10.3 - - - +
257A PHE* 4.3 7.4 - - + +
278A ALA 2.9 14.0 + - - +
279A HIS 3.8 2.2 - - - +
281A ALA* 1.3 79.4 - - - +
283A ALA* 1.3 57.6 + - - +
285A ALA* 2.8 20.5 + - - +
286A VAL* 2.8 18.9 + - - +
1310A ACP 3.5 33.2 - - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PHE* 4.2 16.8 - - + +
245A VAL* 4.0 27.5 - - + +
279A HIS 2.9 18.7 + - - +
280A ALA 3.7 4.7 - - - +
282A ALA* 1.3 77.0 - - - +
284A ILE* 1.3 62.8 + - - +
286A VAL* 3.2 24.9 - - - +
287A THR* 3.4 11.3 - - - +
304A PHE* 4.5 7.2 - - + -
1310A ACP 4.4 8.9 + - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA 3.2 16.6 + - - +
281A ALA 3.8 4.9 - - - +
282A ALA 3.2 0.2 - - - -
283A ALA* 1.3 75.3 - - - +
285A ALA* 1.3 64.4 + - - +
287A THR* 2.7 30.1 + - - +
288A ARG* 3.6 40.5 + - - +
296A PRO* 3.9 26.0 - - + -
300A GLU* 3.8 26.0 - - + +
301A ILE* 4.0 11.4 - - + -
304A PHE* 4.0 24.7 - - + -
307A ARG* 5.4 3.4 - - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE 5.8 0.4 - - - +
252A ALA 5.0 0.9 - - - +
253A ALA* 5.0 7.4 - - - -
256A THR* 3.7 24.2 - - + +
281A ALA 3.1 12.7 + - - +
282A ALA* 2.8 14.3 + - - +
284A ILE* 1.3 78.4 - - - +
286A VAL* 1.3 57.9 + - - +
287A THR 3.1 0.2 - - - -
288A ARG 3.2 7.6 + - - +
294A SER* 3.3 27.2 - - - +
296A PRO* 4.3 0.6 - - + +
1309A CS 2.9 25.0 - - - -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 3.7 22.4 - - + -
247A ALA* 4.3 12.1 - - + -
248A VAL 2.6 33.4 + - - -
249A ASP 3.0 21.6 + - - +
250A THR* 4.3 5.8 - - + -
251A ILE 6.0 0.2 - - - +
253A ALA* 3.7 27.4 - - + -
282A ALA 2.8 16.5 + - - +
283A ALA* 3.2 18.6 - - - +
285A ALA* 1.3 76.4 - - - +
287A THR* 1.3 52.8 + - - +
288A ARG 3.3 0.7 - - - -
1310A ACP 4.2 25.8 - - + +
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 4.5 15.3 - - + -
246A GLN* 4.1 16.4 - - + +
248A VAL* 4.1 19.9 - - - +
283A ALA 3.4 16.6 - - - +
284A ILE* 2.7 23.5 + - - +
286A VAL* 1.3 78.4 - - - +
288A ARG* 1.3 69.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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