Contacts of the helix formed by residues 308 - 324 (chain F) in PDB entry 5YUS
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 ASN 308 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267F TYR* 4.0 4.0 - - - -
286F GLN* 3.0 24.3 + - - +
304F TRP* 3.3 32.8 - - - +
306F ARG 3.5 0.7 - - - +
307F LEU* 1.3 78.5 + - - +
309F LYS* 1.3 63.7 + - - +
310F ALA* 3.2 9.8 + - - +
311F ASP* 2.7 32.7 + - - +
312F LEU* 3.3 9.7 + - - +
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Residues in contact with LYS 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F ILE* 5.2 3.6 - - + -
264F GLU* 2.9 33.6 + - - +
267F TYR* 3.6 57.7 + - + -
268F PRO* 6.0 0.9 - - - -
308F ASN* 1.3 73.1 + - - +
310F ALA* 1.3 64.5 + - - +
312F LEU* 3.0 6.2 + - + +
313F ILE* 2.9 43.1 + - + +
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Residues in contact with ALA 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F ASN* 3.2 8.5 + - - +
309F LYS* 1.3 79.0 - - - +
311F ASP* 1.3 58.2 + - - +
313F ILE* 3.3 12.3 + - - +
314F ALA* 2.8 30.9 + - - +
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Residues in contact with ASP 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F GLN* 2.8 26.0 + - - +
302F HIS* 2.8 32.3 + - - -
304F TRP* 3.4 32.9 - - + -
308F ASN* 2.7 21.6 + - - +
310F ALA* 1.3 73.2 - - - +
312F LEU* 1.3 57.8 + - - +
314F ALA* 3.7 7.4 - - - +
315F THR* 2.8 35.5 + - - -
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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
----------------------------------------------------------
263F ILE* 5.0 4.0 - - + -
267F TYR* 4.0 22.9 - - + -
270F LEU* 4.2 5.2 - - + -
286F GLN* 3.6 29.2 - - + +
287F GLY* 3.5 38.6 - - - +
288F VAL* 3.5 12.2 - - + +
302F HIS* 6.2 0.2 - - + -
307F LEU* 4.2 10.1 - - + -
308F ASN 3.3 15.9 + - - +
309F LYS* 3.0 7.8 + - + +
311F ASP* 1.3 76.3 - - - +
313F ILE* 1.3 60.9 + - - +
315F THR* 3.3 2.6 + - - -
316F ALA* 2.8 30.9 + - - +
334F LEU* 4.0 22.2 - - + -
335F HIS 4.6 0.4 - - - +
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Residues in contact with ILE 313 (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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256F TRP* 3.5 23.2 - - + -
260F GLU* 3.1 35.0 - - + +
263F ILE* 3.8 26.5 - - + -
264F GLU* 3.8 3.8 - - - +
309F LYS* 2.9 42.1 + - + +
310F ALA* 3.6 10.1 - - - +
312F LEU* 1.3 76.4 - - - +
314F ALA* 1.3 58.3 + - - +
316F ALA 3.2 1.0 + - - -
317F ARG* 2.8 28.7 + - + +
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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
----------------------------------------------------------
310F ALA 2.8 20.6 + - - +
311F ASP* 3.7 9.6 - - - +
313F ILE* 1.3 73.9 - - - +
315F THR* 1.3 63.8 + - - +
317F ARG* 3.2 8.3 + - - +
318F LYS* 3.0 26.3 + - - +
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Residues in contact with THR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F GLY* 5.2 0.9 - - - -
288F VAL* 3.9 11.4 - - + -
300F GLN* 3.5 44.9 - - + +
302F HIS* 3.3 28.8 - - + +
311F ASP* 2.8 23.0 + - - -
312F LEU* 3.7 5.8 - - - -
314F ALA* 1.3 76.4 - - - +
316F ALA* 1.3 61.9 + - - +
318F LYS* 3.2 10.6 + - - +
319F THR* 2.8 26.9 + - - -
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Residues in contact with ALA 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TRP* 3.8 7.5 - - + -
259F CYS* 4.8 4.5 - - - -
263F ILE* 3.4 33.2 - - + -
288F VAL* 3.9 20.6 - - + +
290F LEU* 4.6 7.9 - - + +
312F LEU 2.8 12.5 + - - +
313F ILE 3.6 2.2 - - - +
315F THR* 1.3 77.2 - - - +
317F ARG* 1.3 51.8 + - - +
319F THR* 3.7 2.6 - - - -
320F TRP* 2.7 36.2 + - - +
332F VAL* 5.6 0.9 - - + -
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Residues in contact with ARG 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TRP* 3.5 58.9 - - + +
313F ILE* 2.8 13.6 + - + +
314F ALA* 3.2 11.9 + - - +
316F ALA* 1.3 73.9 - - - +
318F LYS* 1.3 59.8 + - - +
320F TRP* 3.5 2.2 - - - +
321F ASP* 2.7 77.8 + - - +
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Residues in contact with LYS 318 (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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300F GLN* 4.4 17.0 - - - +
314F ALA* 3.0 14.1 + - - +
315F THR* 3.5 11.6 - - - +
317F ARG* 1.3 77.7 - - - +
319F THR* 1.3 56.9 + - - +
321F ASP* 4.7 3.8 - - - -
322F GLU* 2.8 66.7 + - - +
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Residues in contact with THR 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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288F VAL* 3.8 5.9 - - + +
290F LEU* 3.9 18.2 - - + +
298F THR* 3.6 34.8 - - + +
300F GLN* 2.3 44.5 + - + +
315F THR 2.8 16.4 + - - -
316F ALA* 3.7 5.6 - - - -
318F LYS* 1.3 75.2 - - - +
320F TRP* 1.3 63.7 + - - +
322F GLU* 4.8 2.7 - - - -
323F ARG* 3.0 30.3 + - + +
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Residues in contact with TRP 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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253F ILE* 3.9 16.8 - - + -
254F HIS 3.7 5.2 - - - -
255F HIS* 3.4 41.3 - - - -
256F TRP* 3.8 33.3 - + + +
259F CYS* 3.7 27.6 - - + -
290F LEU* 3.9 14.3 - - + +
316F ALA 2.7 21.7 + - - +
317F ARG* 3.5 4.3 - - - +
319F THR* 1.3 73.9 - - - +
321F ASP* 1.3 78.3 + - - +
324F ARG* 3.0 72.8 + - - +
329F VAL* 3.5 24.0 - - + -
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Residues in contact with ASP 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F ARG* 2.7 63.1 + - - +
318F LYS* 3.9 4.7 - - - +
320F TRP* 1.3 85.0 - - - +
322F GLU* 1.3 66.0 + - + +
324F ARG* 4.7 4.9 + - - +
325F GLY 5.4 1.7 + - - -
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Residues in contact with GLU 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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300F GLN* 5.1 2.9 + - - +
318F LYS* 2.8 46.2 + - + +
319F THR* 4.4 1.3 - - - +
320F TRP 3.2 0.2 - - - -
321F ASP* 1.3 83.9 - - + +
323F ARG* 1.3 64.9 + - + +
324F ARG 3.6 1.2 + - - -
325F GLY 5.3 0.9 + - - -
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Residues in contact with ARG 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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317A ARG* 3.3 17.4 - - - +
321A ASP* 2.7 40.3 + - + +
292F PHE* 3.0 27.2 - - - -
296F GLN* 3.3 22.2 + - - +
297F GLN 5.3 1.2 + - - -
298F THR* 3.5 35.5 - - + +
319F THR* 3.0 16.9 + - + +
322F GLU* 1.3 83.2 - - + +
324F ARG* 1.3 58.2 + - - +
325F GLY 4.0 0.2 - - - -
327F ARG* 3.2 10.4 + - - -
868H G 3.3 25.2 + - - -
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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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254F HIS* 3.6 20.0 + - - +
292F PHE* 3.7 20.9 - - + -
320F TRP* 3.0 87.4 + - - +
321F ASP* 4.7 3.8 + - - +
322F GLU 3.6 2.0 - - - -
323F ARG* 1.3 78.3 - - - +
325F GLY* 1.3 67.8 + - - +
326F GLY* 4.2 20.5 - - - +
327F ARG* 3.1 46.2 + - - +
329F VAL* 4.1 3.4 - - - -
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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
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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