Contacts of the helix formed by residues 316 - 334 (chain F) in PDB entry 5UHE
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 ALA 316 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ARG* 3.7 25.1 - - - +
350D ARG* 3.8 10.3 - - - +
315F MET* 1.3 79.6 - - - +
317F PHE* 1.3 66.9 + - - +
318F LEU* 3.4 3.1 - - + +
319F ASP* 3.1 25.7 + - - +
320F LEU* 3.0 19.8 + - - +
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Residues in contact with PHE 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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228F VAL* 4.1 28.7 - - + -
232F LEU* 6.0 1.1 - - + -
304F VAL* 4.2 14.1 - - + -
307F ALA* 3.6 13.9 - - + -
308F LYS* 3.5 41.5 - - + -
311F THR* 5.0 12.5 + - - +
315F MET 3.8 0.6 + - - -
316F ALA* 1.3 72.8 - - - +
318F LEU* 1.3 59.7 + - + +
320F LEU* 2.9 14.6 + - + +
321F ILE* 2.9 56.3 + - + +
8H G 3.8 23.8 - - - -
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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
----------------------------------------------------------
350D ARG* 4.8 11.7 - - - +
369D ASN* 4.3 23.1 - - - +
372D ARG* 5.2 1.8 - - - +
373D MET* 3.5 25.6 - - + -
376D GLU* 4.8 5.2 - - - +
227F SER* 3.6 27.8 - - - +
228F VAL* 4.2 30.5 - - + -
231F TYR* 4.8 4.5 - - + -
316F ALA* 3.4 1.9 - - + +
317F PHE* 1.3 76.5 - - + +
319F ASP* 1.3 56.9 + - - +
320F LEU 3.0 0.2 - - - -
321F ILE* 3.3 18.2 + - + +
322F GLN* 2.9 34.8 + - - +
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Residues in contact with ASP 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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346D ARG* 4.7 7.4 + - - +
349D ASN* 6.0 1.3 - - - -
350D ARG* 2.7 45.3 + - - +
353D ARG* 2.8 38.2 + - - +
373D MET* 3.8 1.6 - - - +
315F MET* 4.0 17.8 - - + +
316F ALA* 3.1 19.0 + - - +
318F LEU* 1.3 76.6 - - - +
320F LEU* 1.3 58.5 + - - +
322F GLN 4.0 0.7 - - - -
323F GLU* 3.3 31.9 + - - +
362F GLN* 5.3 1.1 - - - -
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Residues in contact with LEU 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ALA* 4.0 17.7 - - + +
310F TYR* 3.3 48.7 - - + +
311F THR* 4.1 5.2 - - - +
315F MET* 3.5 44.6 - - + +
316F ALA 3.0 10.1 + - - +
317F PHE* 2.9 19.6 + - + +
319F ASP* 1.3 76.9 - - - +
321F ILE* 1.3 57.9 + - - +
322F GLN 3.3 0.2 - - - -
323F GLU* 3.6 2.1 + - - +
324F GLY* 2.9 25.1 + - - -
355F ILE* 3.7 27.8 - - + +
359F MET* 3.7 3.8 - - + -
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Residues in contact with ILE 321 (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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369D ASN* 6.1 0.7 - - - +
228F VAL* 5.6 2.5 - - + -
231F TYR* 3.5 45.5 - - + +
232F LEU* 6.1 0.2 - - + -
303F VAL* 3.3 10.4 - - + +
304F VAL* 3.8 20.6 - - + -
307F ALA* 4.1 8.5 - - + -
317F PHE* 2.9 53.3 + - + +
318F LEU* 3.3 19.5 + - + +
320F LEU* 1.3 73.7 - - - +
322F GLN* 1.3 55.7 + - + +
324F GLY 3.1 1.0 + - - -
325F ASN* 2.7 40.7 + - - +
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Residues in contact with GLN 322 (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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353D ARG* 3.7 16.0 - - - +
357D LEU* 3.7 10.5 - - + +
366D ILE* 3.2 29.0 + - - +
369D ASN* 3.2 25.9 + - - +
370D GLU* 2.7 42.0 + - - +
373D MET* 3.6 8.5 - - + -
231F TYR* 4.9 0.9 + - - -
318F LEU 2.9 21.0 + - - +
319F ASP 4.2 0.7 - - - +
321F ILE* 1.3 77.0 - - + +
323F GLU* 1.3 62.1 + - - +
325F ASN* 3.0 32.9 + - - +
326F LEU* 2.9 22.3 + - - +
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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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353D ARG* 3.4 26.2 + - - +
315F MET* 5.3 4.0 - - + -
319F ASP 3.3 19.9 + - - +
320F LEU* 4.0 4.0 - - + +
322F GLN* 1.3 77.8 - - - +
324F GLY* 1.3 60.8 + - - +
326F LEU* 3.5 20.6 + - - +
327F GLY 3.3 15.2 + - - -
354F ALA* 3.6 18.1 - - - +
355F ILE* 4.8 4.0 - - - -
358F ALA* 3.2 33.4 - - + +
362F GLN* 2.9 25.0 + - - +
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Residues in contact with GLY 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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303F VAL* 3.5 16.2 - - - -
320F LEU 2.9 15.4 + - - -
321F ILE 3.4 4.3 - - - -
322F GLN 3.1 0.2 - - - -
323F GLU* 1.3 75.3 - - - +
325F ASN* 1.3 58.0 + - - +
327F GLY* 3.0 4.5 + - - -
328F LEU* 2.9 23.6 + - - +
351F ILE* 3.5 22.3 - - - +
355F ILE* 3.8 9.8 - - - +
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Residues in contact with ASN 325 (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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357D LEU* 6.0 0.2 - - + -
366D ILE* 4.2 24.9 - - + +
231F TYR* 3.1 22.5 + - - -
300F LEU* 3.2 24.9 - - + +
303F VAL* 3.2 18.9 - - - +
321F ILE* 2.7 19.7 + - - +
322F GLN* 3.0 31.3 + - - +
324F GLY* 1.3 70.9 - - - +
326F LEU* 1.3 57.2 + - - +
328F LEU* 2.9 12.7 + - + +
329F ILE* 2.9 32.6 + - - +
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Residues in contact with LEU 326 (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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353D ARG* 4.3 20.2 - - + -
356D ARG* 4.7 23.8 - - + +
357D LEU* 3.6 30.5 - - + +
360D LEU* 3.8 25.5 - - + +
322F GLN 2.9 11.1 + - - +
323F GLU* 3.5 28.3 - - - +
324F GLY 3.2 0.2 - - - -
325F ASN* 1.3 76.6 - - - +
327F GLY* 1.3 60.9 + - - +
329F ILE* 3.4 14.8 + - + +
330F ARG* 3.5 30.5 + - - +
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Residues in contact with GLY 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 3.3 4.2 + - - -
324F GLY 3.0 8.4 + - - -
326F LEU* 1.3 76.6 - - - +
328F LEU* 1.3 65.1 + - - +
330F ARG* 3.3 14.4 + - - +
331F ALA* 3.1 20.9 + - - +
350F TRP* 4.0 16.5 - - - +
354F ALA* 3.6 23.7 - - - +
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Residues in contact with LEU 328 (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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366D ILE* 5.9 1.6 - - + -
296F LEU* 3.7 35.4 - - + +
299F ASN* 3.4 27.1 - - + +
300F LEU* 4.2 8.3 - - + -
303F VAL* 3.6 18.2 - - + -
324F GLY 2.9 11.0 + - - +
325F ASN* 2.9 13.8 + - - +
327F GLY* 1.3 77.4 - - - +
329F ILE* 1.3 60.1 + - - +
331F ALA* 3.0 15.2 + - + +
332F VAL 3.1 10.2 + - - -
343F PHE* 3.7 31.2 - - + -
347F ALA* 4.4 10.8 - - + -
351F ILE* 4.5 10.9 - - + +
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Residues in contact with ILE 329 (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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357D LEU* 3.9 16.8 - - + -
360D LEU* 4.1 32.5 - - + +
362D ALA* 3.7 31.4 - - + -
366D ILE* 4.8 7.4 - - + -
292F LYS* 4.8 7.4 - - - -
296F LEU* 3.8 27.8 - - + -
325F ASN 2.9 19.2 + - - +
326F LEU* 3.6 9.6 - - + +
327F GLY 3.2 0.4 - - - -
328F LEU* 1.3 75.9 - - - +
330F ARG* 1.3 61.6 + - + +
332F VAL* 3.1 21.4 - - + +
333F GLU* 3.2 18.7 - - + +
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Residues in contact with ARG 330 (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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356D ARG* 4.6 19.7 - - - +
360D LEU* 5.4 5.8 - - + -
326F LEU* 3.5 29.3 + - - +
327F GLY* 3.3 12.2 + - - +
329F ILE* 1.3 80.9 - - + +
331F ALA* 1.3 61.3 + - - +
333F GLU* 3.4 10.4 + - + -
334F LYS* 3.2 42.2 + - - +
350F TRP* 3.3 42.4 - - + -
353F GLN* 6.1 2.8 - - - +
354F ALA* 4.6 17.1 - - - +
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Residues in contact with ALA 331 (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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327F GLY 3.1 12.1 + - - +
328F LEU* 3.0 15.1 + - - +
330F ARG* 1.3 75.1 - - - +
332F VAL* 1.3 63.5 + - - +
333F GLU 3.1 2.2 - - - -
335F PHE* 3.2 24.8 + - - +
343F PHE* 4.1 7.7 - - + -
346F TYR* 3.5 8.7 - - + +
347F ALA* 4.2 18.8 - - + -
350F TRP* 3.8 30.7 - - + -
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Residues in contact with VAL 332 (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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253F ILE* 4.2 20.9 - - + +
292F LYS* 4.4 12.3 - - + +
295F LEU* 3.6 43.3 - - + -
296F LEU* 3.7 24.0 - - + -
328F LEU 3.1 10.1 + - - +
329F ILE* 3.1 20.6 - - + +
331F ALA* 1.3 75.3 - - - +
333F GLU* 1.3 74.1 + - + +
335F PHE* 4.0 8.5 + - + +
343F PHE* 3.7 14.1 - - + -
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Residues in contact with GLU 333 (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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360D LEU* 6.6 0.2 - - + -
253F ILE* 5.3 6.7 - - - +
257F LEU* 3.8 40.4 - - + +
292F LYS* 3.5 32.7 - - - +
329F ILE* 3.2 23.0 - - + +
330F ARG* 3.4 11.2 + - - +
331F ALA 3.1 0.6 - - - -
332F VAL* 1.3 84.3 - - - +
334F LYS* 1.3 74.5 + - + +
335F PHE 3.2 8.0 + - - +
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Residues in contact with LYS 334 (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* 3.2 42.0 + - - +
333F GLU* 1.3 88.5 - - + +
335F PHE* 1.3 61.9 + - - +
336F ASP* 4.8 0.5 - - - +
346F TYR* 3.4 22.2 + - - +
350F TRP* 4.7 14.4 - - + -
2H A 3.1 22.5 + - - -
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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