Contacts of the helix formed by residues 286 - 308 (chain V) in PDB entry 5Z58
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 THR 286 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284V ARG 3.3 6.8 + - - -
285V PRO* 1.3 74.2 - - - +
287V ASP* 1.3 69.3 + - - +
288V ASP* 3.2 8.1 - - - -
289V SER* 3.8 13.2 - - - -
290V VAL* 2.8 24.4 + - - +
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Residues in contact with ASP 287 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286V THR* 1.3 74.0 - - - +
288V ASP* 1.3 59.0 + - - +
290V VAL* 3.9 4.1 - - - +
291V GLU* 3.1 29.0 + - - +
331V ARG* 5.4 12.3 - - + -
332V VAL* 5.2 11.1 - - + +
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Residues in contact with ASP 288 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250V LYS* 4.6 22.1 - - + +
286V THR* 3.2 5.0 - - - -
287V ASP* 1.3 78.3 - - - +
289V SER* 1.3 65.5 - - - +
291V GLU* 3.2 7.3 + - - +
292V VAL* 3.0 23.9 + - - +
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Residues in contact with SER 289 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281V LEU* 3.3 36.2 - - - +
284V ARG 4.6 3.8 - - - -
286V THR* 3.1 23.3 + - - -
288V ASP* 1.3 78.0 - - - +
290V VAL* 1.3 59.0 + - - +
292V VAL* 3.5 4.9 + - - +
293V ALA* 3.1 26.9 + - - +
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Residues in contact with VAL 290 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281V LEU 4.8 1.1 + - - -
282V LEU* 6.5 0.4 - - - +
285V PRO* 5.2 10.3 - - + +
286V THR 2.8 17.3 + - - +
287V ASP* 3.9 4.0 - - - +
289V SER* 1.3 75.2 - - - +
291V GLU* 1.3 59.4 + - - +
293V ALA* 3.2 6.5 + - - +
294V ILE* 2.9 32.8 + - - +
332V VAL* 4.9 19.1 - - + +
335V MET* 5.7 5.2 - - + -
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Residues in contact with GLU 291 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287V ASP 3.1 19.1 + - - +
288V ASP* 3.2 8.5 + - - +
290V VAL* 1.3 76.0 - - - +
292V VAL* 1.3 63.9 + - - +
294V ILE* 4.2 3.6 - - - +
295V GLY* 3.2 19.8 + - - -
335V MET* 5.5 6.5 - - - -
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Residues in contact with VAL 292 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250V LYS* 5.5 1.3 - - - +
253V CYS* 4.5 28.5 - - + +
254V LEU* 5.0 9.9 - - + +
257V SER* 5.1 4.6 - - - -
281V LEU* 5.6 3.4 - - + -
288V ASP 3.0 15.6 + - - +
289V SER* 3.8 6.1 - - - +
291V GLU* 1.3 75.7 - - - +
293V ALA* 1.3 64.5 + - - +
295V GLY* 3.9 0.9 - - - -
296V PHE* 3.0 26.7 + - - +
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Residues in contact with ALA 293 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278V LEU* 5.0 15.9 - - + +
281V LEU* 3.9 19.7 - - + +
282V LEU* 5.4 5.4 - - + +
289V SER 3.1 18.6 + - - +
290V VAL* 3.2 7.8 + - - +
292V VAL* 1.3 77.0 - - - +
294V ILE* 1.3 56.9 + - - +
296V PHE* 3.4 7.2 + - - +
297V LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 294 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290V VAL 2.9 16.9 + - - +
291V GLU* 4.2 2.9 - - - +
293V ALA* 1.3 75.8 - - - +
295V GLY* 1.3 65.1 + - - +
297V LEU* 3.9 6.4 - - - +
298V LYS* 3.1 23.6 + - - +
335V MET* 4.3 27.4 - - + +
336V ILE* 5.9 0.7 - - - -
339V MET* 4.7 13.6 - - + +
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Residues in contact with GLY 295 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258V LYS* 6.0 1.5 - - - +
291V GLU 3.2 14.8 + - - -
292V VAL* 3.9 1.1 - - - -
294V ILE* 1.3 78.6 - - - +
296V PHE* 1.3 60.5 + - - +
298V LYS* 3.5 17.7 - - - +
299V GLU* 3.6 9.5 + - - +
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Residues in contact with PHE 296 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257V SER* 4.2 25.6 - - - +
258V LYS* 5.5 2.0 - - - +
261V ALA* 4.0 8.6 - - + +
292V VAL 3.0 19.3 + - - +
293V ALA* 3.4 7.2 - - - +
295V GLY* 1.3 74.7 - - - +
297V LEU* 1.3 65.3 + - - +
299V GLU* 3.2 15.8 + - - +
300V CYS* 3.2 13.0 + - - +
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Residues in contact with LEU 297 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278V LEU* 6.4 2.2 - - + -
293V ALA 2.9 17.2 + - - +
294V ILE* 3.4 7.6 + - - +
296V PHE* 1.3 74.0 - - - +
298V LYS* 1.3 58.0 + - - +
300V CYS* 5.2 1.1 - - - -
301V GLY* 2.7 38.4 + - - +
339V MET* 6.1 4.0 - - + -
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Residues in contact with LYS 298 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294V ILE 3.1 14.2 + - - +
295V GLY* 3.5 13.7 - - - +
297V LEU* 1.3 78.5 - - - +
299V GLU* 1.3 59.6 + - - +
301V GLY* 4.0 3.5 + - - -
302V LEU 5.0 1.2 + - - -
342V VAL* 5.8 10.5 - - + -
347V PHE* 5.2 2.1 - - - +
350V HIS* 3.1 30.4 - - + +
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Residues in contact with GLU 299 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258V LYS* 5.0 9.6 - - + +
261V ALA* 3.5 24.8 - - + +
262V HIS* 5.4 1.5 - - + +
265V ASN* 5.1 6.8 - - - +
295V GLY 3.6 8.5 + - - +
296V PHE* 3.2 5.8 + - - +
298V LYS* 1.3 81.6 - - + +
300V CYS* 1.3 58.4 + - - +
301V GLY 4.0 0.2 + - - -
302V LEU* 5.1 1.6 + - - +
303V LYS* 5.7 0.3 + - - +
350V HIS* 4.8 7.7 - - - +
351V PRO 4.6 10.9 - - - +
352V ILE* 5.4 2.4 - - - -
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Residues in contact with CYS 300 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261V ALA* 3.6 33.4 - - + +
264V ILE* 4.7 9.2 - - + -
265V ASN* 5.8 0.9 - - - -
274V CYS* 5.2 12.6 - - + -
296V PHE 3.2 8.7 + - - +
297V LEU* 4.7 1.6 - - - -
299V GLU* 1.3 76.7 - - - +
301V GLY* 1.3 58.1 + - - +
302V LEU 3.4 2.5 - - - -
303V LYS* 3.3 12.4 + - + +
304V LEU* 2.8 29.7 + - + +
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Residues in contact with GLY 301 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297V LEU* 2.7 29.2 + - - -
298V LYS 4.0 1.9 + - - -
299V GLU 3.5 1.4 - - - -
300V CYS* 1.3 73.6 - - - +
302V LEU* 1.3 57.2 + - - +
304V LEU* 3.2 8.4 + - - +
305V THR* 2.9 29.0 + - - -
312V ILE* 5.3 2.4 - - - +
347V PHE* 5.4 1.3 - - - -
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Residues in contact with LEU 302 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298V LYS 5.0 1.8 + - - -
299V GLU 5.1 1.9 + - - +
300V CYS 3.4 0.2 - - - -
301V GLY* 1.3 74.0 - - - +
303V LYS* 1.3 62.8 + - - +
305V THR* 3.2 17.6 + - - -
306V GLN* 3.3 12.6 + - - +
346V GLY 5.2 1.6 - - - +
347V PHE* 3.9 21.6 - - + +
350V HIS 3.9 21.3 + - - +
351V PRO* 5.3 0.7 - - + -
352V ILE* 4.9 11.7 - - + +
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Residues in contact with LYS 303 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264V ILE* 5.1 5.4 - - + +
265V ASN* 4.6 23.1 - - + +
299V GLU 5.8 0.4 - - - +
300V CYS* 3.3 15.1 + - + +
302V LEU* 1.3 77.6 - - - +
304V LEU* 1.3 63.2 + - - +
306V GLN* 3.0 16.6 + - - +
307V VAL* 3.1 16.2 + - - +
352V ILE* 4.9 14.1 - - + +
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Residues in contact with LEU 304 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271V GLU* 5.7 8.3 - - + -
274V CYS* 6.1 4.9 - - + -
300V CYS* 2.8 15.4 + - + +
301V GLY* 3.2 13.2 + - - +
303V LYS* 1.3 77.8 - - - +
305V THR* 1.3 54.8 + - - +
307V VAL* 4.7 1.8 - - - +
308V SER* 2.7 45.0 + - - +
312V ILE* 4.4 15.5 - - + +
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Residues in contact with THR 305 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301V GLY 2.9 12.8 + - - -
302V LEU* 3.2 13.0 + - - -
304V LEU* 1.3 77.5 - - - +
306V GLN* 1.3 60.1 + - - +
309V PRO* 3.5 28.9 - - - +
312V ILE* 4.7 7.6 - - - +
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Residues in contact with GLN 306 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302V LEU 3.3 7.9 + - - +
303V LYS* 3.0 11.5 + - - +
305V THR* 1.3 81.2 - - - +
307V VAL* 1.3 60.0 + - + +
309V PRO* 5.1 0.7 - - - +
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Residues in contact with VAL 307 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271V GLU* 5.3 11.7 - - + -
303V LYS 3.1 13.4 + - - +
304V LEU* 5.3 0.9 - - - -
306V GLN* 1.3 76.7 - - + +
308V SER* 1.3 62.4 + - - +
309V PRO 4.1 0.7 - - - -
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Residues in contact with SER 308 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271V GLU* 5.4 10.3 - - - -
304V LEU* 2.7 24.1 + - - +
307V VAL* 1.3 79.3 - - - +
309V PRO* 1.3 65.2 - - - +
310V ARG 3.2 3.1 - - - -
311V GLY* 3.1 18.3 + - - +
312V ILE* 3.1 11.1 + - - +
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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