Contacts of the helix formed by residues 342 - 363 (chain F) in PDB entry 5UH6
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 LYS 342 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU 4.3 10.9 + - - -
243F ALA* 4.0 28.5 - - + +
246F GLU* 3.3 29.5 + - - +
335F PHE* 4.2 3.3 - - - -
340F GLY 3.7 3.8 + - - +
341F TYR* 1.3 78.2 - - - +
343F PHE* 1.3 63.7 + - - +
344F SER* 3.2 4.3 - - - +
345F THR* 3.1 17.3 - - + +
346F TYR* 4.2 0.5 + - - +
4H A 3.2 21.5 + - - +
5H A 3.2 33.6 + - - +
6H T 3.8 22.8 + - - +
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Residues in contact with PHE 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F GLU* 3.3 29.2 + - + +
295F LEU* 4.3 15.5 - - + -
299F ASN* 3.3 45.3 - - + -
302F LEU* 5.0 0.7 - - + -
328F LEU* 3.6 22.2 - - + -
331F ALA* 4.9 1.3 - - + -
332F VAL* 3.9 37.7 - - + -
335F PHE* 3.7 37.2 - + + -
341F TYR 3.9 0.4 + - - -
342F LYS* 1.3 74.5 - - - +
344F SER* 1.3 65.0 + - - +
345F THR 3.1 1.0 + - - -
346F TYR* 3.5 3.7 + + - +
347F ALA* 3.1 37.5 + - + +
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Residues in contact with SER 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F LEU* 4.1 14.8 - - - +
342F LYS* 4.0 2.8 - - - +
343F PHE* 1.3 81.4 - - - +
345F THR* 1.3 61.8 + - - +
347F ALA* 4.0 0.9 - - - +
348F THR* 2.8 29.8 + - - -
4H A 3.8 4.5 - - - +
5H A 2.6 44.5 + - - +
6H T 3.7 30.8 + - - -
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Residues in contact with THR 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341F TYR* 3.8 11.9 - - + -
342F LYS* 3.1 20.4 - - + +
344F SER* 1.3 81.7 + - - +
346F TYR* 1.3 66.5 + - + +
347F ALA 3.5 0.2 + - - -
348F THR* 3.6 5.4 + - - -
349F TRP* 3.0 27.4 + - - -
2H A 4.3 6.0 + - - +
3H T 4.1 16.7 + - - -
4H A 3.1 54.6 + - - +
5H A 3.3 9.9 + - - -
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Residues in contact with TYR 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F ALA 3.8 12.6 - - - -
334F LYS* 3.3 42.3 + - - +
335F PHE* 3.8 23.8 - + + -
343F PHE* 3.5 6.1 + + - +
345F THR* 1.3 80.4 - - + +
347F ALA* 1.3 65.5 + - - +
349F TRP* 3.8 7.9 + - + +
350F TRP* 3.0 44.3 + + - -
1H T 4.7 14.3 - - - -
2H A 3.5 67.5 + + + +
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Residues in contact with ALA 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F LEU* 3.9 16.2 - - + -
328F LEU* 4.4 4.7 - - + -
331F ALA* 4.2 9.6 - - - -
343F PHE* 3.1 45.7 + - + +
344F SER 4.0 0.2 - - - +
346F TYR* 1.3 77.2 - - - +
348F THR* 1.3 56.5 + - - +
350F TRP* 2.7 25.3 + - - +
351F ILE* 3.0 21.5 + - + +
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Residues in contact with THR 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F LEU* 4.3 7.4 - - - +
306F LEU* 3.6 27.7 - - + +
344F SER 2.8 21.1 + - - -
345F THR 4.0 0.7 - - - -
346F TYR 3.5 0.4 - - - -
347F ALA* 1.3 77.4 - - - +
349F TRP* 1.3 61.9 + - - +
350F TRP 3.1 1.4 + - - -
351F ILE* 3.2 8.9 + - - -
352F ARG* 3.1 42.3 + - - +
5H A 3.3 42.2 + - + +
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Residues in contact with TRP 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F THR* 3.0 25.0 + - - -
346F TYR* 4.2 7.9 - - + +
347F ALA 3.2 0.8 - - - -
348F THR* 1.3 75.9 - - - +
350F TRP* 1.3 57.7 + - - +
352F ARG* 3.2 34.2 - - - +
353F GLN* 3.4 11.3 + - - +
1H T 3.0 64.8 - - - +
2H A 3.9 18.1 - - - -
3H T 4.0 21.2 + - + -
4H A 4.9 7.6 - - - +
5H A 3.3 18.0 - - - +
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Residues in contact with TRP 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F GLY* 4.3 6.2 - - - +
330F ARG* 3.5 53.6 + - + -
331F ALA* 3.7 26.3 - - + +
334F LYS* 4.6 21.1 - - + -
346F TYR* 3.0 52.6 + + - -
347F ALA 2.7 9.8 + - - +
349F TRP* 1.3 81.5 - - - +
351F ILE* 1.3 59.1 + - - +
352F ARG 3.5 0.4 - - - -
353F GLN* 3.4 7.6 + - + +
354F ALA* 3.1 26.7 + - - +
1H T 4.1 47.7 + + + -
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Residues in contact with ILE 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F LEU* 4.2 25.4 - - + -
303F VAL* 3.6 29.2 - - + -
306F LEU* 3.6 23.3 - - + -
324F GLY* 3.5 28.5 - - - +
327F GLY* 4.9 1.1 - - - -
328F LEU* 4.4 19.3 - - + +
347F ALA* 3.0 25.9 + - + +
348F THR* 3.2 4.5 + - - +
350F TRP* 1.3 74.7 - - - +
352F ARG* 1.3 65.6 + - - +
353F GLN 3.1 0.9 - - - -
354F ALA* 3.4 3.8 + - - +
355F ILE* 3.1 25.5 + - + +
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Residues in contact with ARG 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C THR* 6.2 2.2 - - - +
306F LEU* 4.5 16.4 - - + -
309F ARG* 5.9 6.0 - - - +
310F TYR* 3.8 24.2 - - + +
348F THR* 3.1 36.4 + - + +
349F TRP* 3.2 53.9 - - - +
351F ILE* 1.3 76.6 - - - +
353F GLN* 1.3 57.3 + - - +
355F ILE* 3.3 6.9 + - - +
356F THR* 3.0 37.7 + - + +
5H A 4.6 10.2 + - - +
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Residues in contact with GLN 353 (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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330F ARG* 5.7 2.7 - - - +
349F TRP 3.4 15.3 + - - +
350F TRP* 3.4 12.7 + - + +
351F ILE 3.1 0.2 - - - -
352F ARG* 1.3 81.5 - - - +
354F ALA* 1.3 60.6 + - - +
356F THR* 3.5 11.9 + - - -
357F ARG* 3.2 26.4 + - + +
1H T 2.8 46.2 + - - +
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Residues in contact with ALA 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F GLU* 3.5 25.4 - - - +
326F LEU* 5.7 0.2 - - + -
327F GLY* 3.7 24.2 - - - +
330F ARG* 4.6 18.3 - - - +
350F TRP 3.1 9.2 + - - +
351F ILE 3.9 3.6 - - - +
352F ARG 3.3 0.4 - - - -
353F GLN* 1.3 74.5 - - - +
355F ILE* 1.3 66.5 + - - +
357F ARG* 3.8 3.6 - - - +
358F ALA* 3.1 27.4 + - - +
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Residues in contact with ILE 355 (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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306F LEU* 3.7 30.7 - - + +
307F ALA* 3.9 21.8 - - + -
310F TYR* 3.9 26.0 - - + -
315F MET* 4.7 1.5 - - - +
320F LEU* 3.6 32.8 - - + +
323F GLU* 5.2 3.8 - - + -
324F GLY* 4.2 18.8 - - - +
351F ILE* 3.1 18.5 + - + +
352F ARG* 3.7 5.2 - - - +
354F ALA* 1.3 78.5 - - - +
356F THR* 1.3 55.1 + - - +
357F ARG 3.1 0.2 + - - -
358F ALA* 3.8 2.0 - - - +
359F MET* 2.7 39.0 + - - +
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Residues in contact with THR 356 (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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310F TYR* 3.8 30.3 - - + +
352F ARG* 3.0 17.9 + - + +
353F GLN* 3.5 17.2 + - - -
355F ILE* 1.3 76.7 - - - +
357F ARG* 1.3 64.6 + - - +
359F MET* 3.9 6.5 - - - +
360F ALA* 3.3 21.0 + - - +
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Residues in contact with ARG 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F GLN* 3.2 18.5 + - - +
354F ALA* 3.8 4.9 - - - +
355F ILE 3.1 0.6 - - - -
356F THR* 1.3 80.2 + - - +
358F ALA* 1.3 70.8 + - + +
359F MET 3.1 0.3 + - - -
360F ALA* 3.2 6.7 + - - +
361F ASP* 2.6 50.2 + - - +
367F ARG* 5.1 4.4 - - - +
370F VAL* 4.3 33.0 - - - +
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Residues in contact with ALA 358 (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 MET* 4.6 3.8 - - + -
323F GLU* 3.5 38.4 - - + +
354F ALA 3.1 16.2 + - - +
355F ILE 4.0 1.6 - - - +
357F ARG* 1.3 82.2 - - + +
359F MET* 1.3 52.2 + - - +
361F ASP* 3.4 8.0 - - - +
362F GLN* 2.8 46.2 + - - +
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Residues in contact with MET 359 (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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310F TYR* 3.2 49.4 - - + +
313F ARG* 3.6 26.9 - - + +
315F MET* 3.7 28.2 - - + +
320F LEU* 3.6 25.1 - - + -
355F ILE* 2.7 18.4 + - - +
356F THR* 3.9 7.4 - - - +
358F ALA* 1.3 77.6 - - - +
360F ALA* 1.3 57.5 + - - +
361F ASP 3.1 0.3 + - - -
363F ALA* 2.9 45.1 + - + +
364F ARG* 4.3 1.7 + - - +
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Residues in contact with ALA 360 (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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356F THR 3.3 14.5 + - - +
357F ARG* 3.2 5.1 + - - +
359F MET* 1.3 77.7 - - - +
361F ASP* 1.3 58.6 + - - +
363F ALA 4.8 0.9 - - - -
364F ARG* 4.2 21.3 - - - +
367F ARG* 5.4 0.3 - - - +
368F ILE 3.8 18.5 + - - +
370F VAL* 5.6 9.5 - - + -
373F VAL* 3.6 37.0 - - + +
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Residues in contact with ASP 361 (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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31D PRO* 6.2 0.3 - - - +
32D GLU* 4.7 3.6 - - - +
357F ARG* 2.6 52.9 + - - +
358F ALA* 3.4 10.0 - - - +
359F MET 3.0 0.6 - - - -
360F ALA* 1.3 81.6 - - - +
362F GLN* 1.3 64.0 + - + +
364F ARG* 5.1 2.2 - - - +
367F ARG* 2.8 58.7 + - - +
368F ILE 5.3 1.0 - - - +
369F PRO* 6.1 0.2 - - - +
370F VAL* 5.6 5.3 - - - +
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Residues in contact with GLN 362 (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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31D PRO* 6.1 2.0 - - + -
345D ARG* 3.0 24.1 + - - -
349D ASN* 3.4 43.3 + - - +
353D ARG* 3.9 14.9 + - - +
315F MET* 3.6 21.2 - - + +
319F ASP* 5.1 1.0 - - - +
323F GLU* 2.9 28.7 + - - +
358F ALA* 2.8 21.6 + - - +
361F ASP* 1.3 85.4 - - + +
363F ALA* 1.3 64.9 + - - +
364F ARG 3.0 8.7 + - - +
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Residues in contact with ALA 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D ARG* 4.8 5.8 + - - +
313F ARG 4.1 15.5 - - - +
314F GLY* 4.0 26.5 - - - +
315F MET* 4.6 5.6 - - + -
359F MET* 2.9 26.4 + - + +
362F GLN* 1.3 77.9 - - - +
364F ARG* 1.3 73.7 + - - +
365F THR* 3.5 5.4 + - - -
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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