Contacts of the helix formed by residues 309 - 329 (chain F) in PDB entry 5U07
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 GLY 309 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLY 3.9 2.4 + - - -
301E GLU* 3.3 19.1 - - - -
302E THR* 3.6 30.2 - - - +
303E ALA 4.6 2.8 - - - +
308F ASP* 1.3 75.1 - - - +
310F TYR* 1.3 62.7 + - - -
311F THR 3.4 2.9 + - - -
312F LEU* 4.2 6.8 + - - +
313F ARG* 4.1 14.6 - - - +
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Residues in contact with TYR 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLY* 3.9 6.5 - - - -
32E GLY* 3.7 25.3 - - - -
301E GLU* 2.4 28.3 + - - +
195F HIS* 3.3 46.9 - + + +
196F GLY 5.2 1.2 + - - -
230F THR* 4.2 14.6 - - + +
304F LEU* 3.6 38.0 + - + +
305F TYR 3.2 7.8 + - - -
306F GLY* 3.0 41.3 - - - -
308F ASP 3.3 4.0 + - - -
309F GLY* 1.3 67.7 - - - -
311F THR* 1.3 64.2 + - - +
312F LEU 3.4 0.4 - - - -
313F ARG* 3.9 9.6 - - - -
314F ALA* 2.8 25.2 + - + +
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Residues in contact with THR 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E PRO 4.9 5.5 + - - +
301E GLU* 3.2 29.9 + - + +
302E THR* 3.8 10.7 - - - +
9F ILE* 5.8 3.8 - - + -
11F THR* 3.7 15.5 - - + -
230F THR* 4.6 2.9 - - + -
282F ASP* 3.4 28.5 - - - +
309F GLY 3.4 0.4 - - - -
310F TYR* 1.3 75.5 - - - +
312F LEU* 1.3 70.1 + - - +
314F ALA* 3.6 4.9 - - - +
315F CYS* 3.0 30.2 + - - -
341F GLU* 5.0 6.9 + - - -
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E THR* 5.7 4.0 - - + -
309F GLY 4.2 6.3 + - - +
310F TYR 3.4 0.2 - - - -
311F THR* 1.3 82.7 + - - +
313F ARG* 1.3 61.9 + - + +
315F CYS* 3.3 3.9 + - + +
316F GLN* 3.0 57.9 + - + +
341F GLU* 4.2 28.7 + - + +
343F LYS* 4.5 29.2 - - + -
344F THR* 4.5 1.1 - - - +
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Residues in contact with ARG 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F LEU* 4.2 30.5 - - + +
305F TYR* 4.3 15.6 - - - +
306F GLY* 3.6 23.8 + - - +
308F ASP* 3.3 37.1 + - - +
309F GLY 4.1 10.1 + - - +
310F TYR* 3.3 11.7 + - - +
311F THR 3.3 0.6 - - - -
312F LEU* 1.3 79.7 - - + +
314F ALA* 1.3 56.9 + - - +
316F GLN* 3.4 7.3 + - - +
317F GLU* 3.0 35.4 + - + +
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Residues in contact with ALA 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 4.5 16.8 - - + -
194F VAL* 4.3 26.7 - - + -
230F THR* 5.1 2.9 - - - +
300F PHE* 3.8 14.2 - - + -
304F LEU* 4.1 6.9 - - + +
310F TYR 2.8 19.7 + - - +
311F THR* 3.6 4.0 - - - +
313F ARG* 1.3 74.8 - - - +
315F CYS* 1.3 66.8 + - - +
317F GLU* 3.1 2.8 + - - +
318F LEU* 2.9 24.5 + - - +
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Residues in contact with CYS 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 5.1 12.3 - - - -
282F ASP* 5.2 4.9 - - - -
283F LEU* 3.9 32.5 - - + +
311F THR* 3.0 22.3 + - - +
312F LEU* 3.7 5.2 - - + +
314F ALA* 1.3 77.9 - - - +
316F GLN* 1.3 64.9 + - + +
317F GLU 3.3 0.2 + - - -
318F LEU* 3.3 5.6 + - - +
319F ASN* 2.9 23.3 + - - +
341F GLU* 2.9 39.9 - - - +
346F LEU* 5.0 1.4 - - - +
349F LEU* 5.5 0.5 - - - +
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Residues in contact with GLN 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F LEU* 3.0 42.2 + - + +
313F ARG* 3.8 7.0 - - - +
315F CYS* 1.3 76.9 - - - +
317F GLU* 1.3 61.3 + - + +
319F ASN* 3.3 17.7 + - - +
320F ASN* 2.9 28.2 + - - +
344F THR* 2.8 42.8 + - - +
346F LEU* 5.9 0.2 - - - +
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Residues in contact with GLU 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F ALA* 4.5 12.0 - - - +
300F PHE* 4.2 16.2 - - + -
304F LEU* 4.5 18.4 - - + -
313F ARG* 3.0 22.5 + - + +
314F ALA* 3.1 4.2 + - - +
316F GLN* 1.3 78.2 - - - +
318F LEU* 1.3 64.5 + - - +
320F ASN* 3.3 14.9 + - - +
321F TYR* 2.9 25.8 + - - +
343G LYS* 5.6 3.5 + - - -
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Residues in contact with LEU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F HIS* 4.7 7.9 - - + -
8F ALA 5.5 0.2 - - - +
9F ILE* 4.1 22.4 - - + -
232F TYR* 3.9 27.6 - - + -
283F LEU* 4.4 11.7 - - + -
285F HIS* 4.8 5.4 - - + -
296F PHE* 4.0 22.8 - - + -
299F ALA* 4.9 2.2 - - - -
300F PHE* 4.0 12.0 - - + -
314F ALA 2.9 15.8 + - - +
315F CYS* 3.8 5.6 - - - +
317F GLU* 1.3 76.4 - - - +
319F ASN* 1.3 56.5 + - - +
321F TYR* 3.8 4.7 - - - +
322F ALA* 2.9 30.3 + - - +
349F LEU* 3.9 32.3 - - + -
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Residues in contact with ASN 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F CYS 2.9 12.2 + - - +
316F GLN* 3.4 22.2 + - - +
318F LEU* 1.3 77.4 - - - +
320F ASN* 1.3 65.2 + - - +
322F ALA* 3.1 5.9 + - - +
323F GLU* 2.9 23.7 + - - +
344F THR* 5.9 1.8 - - - +
346F LEU* 2.6 49.5 - - + +
347F ALA* 4.0 1.8 - - - +
348F ALA* 3.2 20.3 + - - +
349F LEU* 4.6 3.4 - - - -
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Residues in contact with ASN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F GLN 2.9 16.7 + - - +
317F GLU* 3.8 18.2 + - - +
319F ASN* 1.3 76.4 - - - +
321F TYR* 1.3 63.5 - - - +
323F GLU* 3.0 38.0 + - - +
324F ARG* 3.0 18.4 + - - +
343G LYS* 4.9 13.0 - - - +
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Residues in contact with TYR 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F ILE* 5.9 0.2 - - - +
295F SER 4.5 1.7 + - - -
296F PHE* 3.8 32.1 - + - -
298F PRO* 3.7 26.3 - - + +
299F ALA* 3.5 35.4 - - + -
317F GLU 2.9 17.0 + - - +
318F LEU* 4.0 2.9 - - - +
320F ASN* 1.3 78.0 - - - +
322F ALA* 1.3 62.8 + - - +
324F ARG* 3.3 3.9 + - - +
325F LEU* 2.9 56.2 + - + +
279G THR* 5.2 0.7 - - - +
280G LEU 4.4 6.4 + - - -
282G ASP* 3.9 8.8 + - - -
340G VAL* 3.9 29.6 - - + +
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Residues in contact with ALA 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F HIS* 5.5 0.9 - - - +
296F PHE* 4.0 25.1 - - + -
318F LEU 2.9 18.7 + - - +
319F ASN 3.1 3.3 + - - +
321F TYR* 1.3 78.0 - - - +
323F GLU* 1.3 62.4 + - - +
325F LEU* 3.8 1.9 - - - +
326F ARG* 2.9 25.3 + - - +
335F ARG* 5.4 5.4 + - - +
348F ALA* 4.2 8.7 - - + +
349F LEU* 3.5 27.6 - - + -
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Residues in contact with GLU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F ASN* 2.9 11.6 + - - +
320F ASN* 3.0 43.0 + - - +
322F ALA* 1.3 76.4 - - - +
324F ARG* 1.3 72.9 + - + +
326F ARG* 3.2 6.8 + - - +
327F GLU* 3.0 23.3 + - - +
348F ALA* 3.5 23.3 + - + +
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Residues in contact with ARG 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F ASN* 3.0 28.3 + - - +
321F TYR* 3.9 2.9 - - - +
323F GLU* 1.3 86.7 - - - +
325F LEU* 1.3 59.6 + - - +
327F GLU* 3.3 28.3 + - - +
328F VAL* 2.9 36.4 + - - +
339G THR 3.6 5.9 + - - -
340G VAL* 3.0 46.7 + - + +
342G ASN* 3.1 39.4 - - - +
352G ARG* 3.0 31.3 - - - +
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Residues in contact with LEU 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F ILE* 3.6 33.4 - - + -
296F PHE* 3.6 13.5 - - + -
321F TYR* 2.9 58.0 + - + +
322F ALA* 4.0 3.8 - - - +
324F ARG* 1.3 75.4 - - - +
326F ARG* 1.3 61.6 + - - +
328F VAL* 4.3 9.6 - - + +
329F TRP* 2.8 34.7 + - + +
335F ARG* 5.4 0.9 - - - +
280G LEU* 4.5 25.6 - - + +
281G PRO 5.8 2.2 - - - +
340G VAL* 5.0 7.6 - - + -
356G TYR* 6.1 0.9 - - + -
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Residues in contact with ARG 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ALA 2.9 18.7 + - - +
323F GLU* 3.8 4.9 - - - +
325F LEU* 1.3 77.0 - - - +
327F GLU* 1.3 62.9 + - - +
329F TRP 3.7 15.0 - - - +
330F PRO* 3.8 6.3 - - - +
331F ASP 3.1 27.6 + - - +
332F ASP* 5.1 0.8 - - - +
333F ALA 4.5 3.8 + - - -
335F ARG* 2.7 61.3 - - - +
348F ALA* 5.4 6.1 - - + +
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Residues in contact with GLU 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F GLU 3.0 12.1 + - - +
324F ARG* 3.3 37.7 + - - +
326F ARG* 1.3 80.8 - - - +
328F VAL* 1.3 63.9 + - + +
330F PRO* 4.0 6.6 - - - +
354G ASP* 4.4 27.5 - - + +
355G SER* 3.7 13.5 - - - -
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Residues in contact with VAL 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F ARG* 2.9 25.4 + - - +
325F LEU* 4.2 9.2 - - + +
327F GLU* 1.3 78.5 - - + +
329F TRP* 1.3 59.0 + - + +
330F PRO* 3.3 7.8 - - - +
338G ALA* 5.2 0.9 - - + -
339G THR 3.9 25.4 - - - +
340G VAL* 4.6 6.1 - - + +
354G ASP 3.9 17.3 - - - +
355G SER* 3.3 1.7 - - - -
356G TYR* 3.2 68.1 + - + +
357G PRO* 3.8 1.9 - - - +
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Residues in contact with TRP 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F ARG* 3.3 22.2 + - - +
291F ASP* 2.5 30.5 + - + -
292F ARG* 4.5 7.9 - - - +
294F ILE* 4.0 9.9 - - + +
325F LEU* 2.8 22.4 + - + +
326F ARG* 3.7 8.4 - - - +
328F VAL* 1.3 73.6 - - + +
330F PRO* 1.3 73.5 + - + +
331F ASP* 3.4 4.7 + - - +
335F ARG* 5.1 1.9 + - - -
261G ARG* 3.7 36.8 - - + -
264G LEU* 4.8 12.1 - - + -
265G SER* 3.9 30.3 - - - -
280G LEU* 3.6 32.5 - - + -
356G TYR* 4.0 27.1 - + + -
357G PRO* 4.8 9.2 - - + -
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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
------------------------------------------------------------
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