Contacts of the helix formed by residues 288 - 302 (chain V) in PDB entry 3MQT
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 288 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103V SER* 3.4 12.2 + - - -
106V ASP* 3.7 3.4 - - - -
107V MET* 5.4 0.9 - - - -
283V TYR 3.4 21.0 + - - -
286V CYS* 3.7 4.8 - - - -
287V GLY* 1.3 78.2 - - - +
289V VAL* 1.3 55.7 + - - -
290V THR 3.3 2.7 - - - -
291V GLU* 3.2 1.9 + - - +
292V LEU* 2.7 42.0 + - - +
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Residues in contact with VAL 289 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106V ASP* 3.0 4.4 + - - +
107V MET* 4.9 12.9 - - + +
110V TYR* 3.5 34.3 - - + +
125V MET* 3.7 41.1 - - + -
283V TYR* 4.8 10.3 + - + +
288V GLY* 1.3 69.0 - - - -
290V THR* 1.3 65.8 + - - +
292V LEU* 3.7 8.1 - - - +
293V LEU* 2.9 30.2 + - + +
319V ALA* 4.9 16.8 - - + +
323V PHE* 4.5 7.9 - - + -
369V LEU* 6.2 0.4 - - + -
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Residues in contact with THR 290 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78V PHE* 3.6 18.7 + - + +
79V ARG* 4.3 13.9 - - + +
82V TYR* 3.9 26.7 - - + -
106V ASP* 2.6 30.3 + - - -
110V TYR* 2.7 25.0 + - - +
289V VAL* 1.3 78.3 - - - +
291V GLU* 1.3 61.2 + - - +
293V LEU* 3.5 12.1 + - + +
294V ARG* 3.6 18.1 + - - +
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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
----------------------------------------------------------
82V TYR* 3.5 23.9 + - + +
86V TYR* 6.0 0.2 - - - -
263V THR* 3.3 9.0 - - - -
264V ARG* 2.7 63.8 + - - +
265V PHE* 5.0 0.7 - - - -
286V CYS* 3.6 17.0 - - - +
287V GLY 3.9 16.3 + - - -
288V GLY 3.2 8.1 + - - +
290V THR* 1.3 79.1 - - - +
292V LEU* 1.3 60.7 + - - +
294V ARG* 3.0 15.7 + - - +
295V ILE* 2.9 32.3 + - + +
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Residues in contact with LEU 292 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281V SER* 3.6 25.1 - - - +
283V TYR* 3.4 52.0 - - + -
286V CYS* 3.7 15.0 - - - -
288V GLY 2.7 24.4 + - - +
289V VAL* 3.2 7.4 + - - +
291V GLU* 1.3 73.4 - - - +
293V LEU* 1.3 51.0 + - - +
295V ILE* 3.2 6.5 + - + -
296V MET* 2.7 34.3 + - - +
306V LEU* 3.6 22.0 - - + +
308V PRO* 4.0 14.6 - - + -
323V PHE* 3.9 15.3 - - + -
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Residues in contact with LEU 293 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N ARG* 3.9 18.5 + - - +
110V TYR* 3.9 17.9 - - + +
124V LEU 5.2 0.7 - - - +
125V MET* 3.8 36.8 - - + +
289V VAL* 2.9 27.1 + - + +
290V THR* 3.7 7.2 - - - +
291V GLU 3.2 0.2 - - - -
292V LEU* 1.3 77.6 - - - +
294V ARG* 1.3 59.6 + - - +
296V MET* 3.3 23.7 - - + +
297V ASP* 3.2 26.0 + - - +
323V PHE* 3.6 23.1 - - + -
326V VAL* 4.4 3.6 - - + -
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Residues in contact with ARG 294 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297N ASP* 3.3 55.2 + - + +
300N GLU* 2.7 31.9 + - - +
79V ARG* 4.2 13.7 - - - +
82V TYR* 6.3 0.9 - - - -
83V ASN* 6.0 0.4 + - - -
264V ARG* 3.1 56.4 - - + +
290V THR* 3.6 12.3 + - - +
291V GLU* 3.0 15.9 + - - +
293V LEU* 1.3 74.9 - - - +
295V ILE* 1.3 66.6 + - - +
297V ASP* 3.3 10.2 + - - +
298V ILE* 3.3 32.0 + - - +
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Residues in contact with ILE 295 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263V THR 4.0 7.6 - - - +
264V ARG* 3.7 31.4 - - + -
267V ALA* 4.1 9.6 - - + -
271V LEU* 6.0 0.7 - - + -
279V VAL* 4.1 13.9 - - + -
281V SER* 3.8 22.9 - - - +
286V CYS* 4.2 9.4 - - + -
291V GLU* 2.9 27.7 + - + +
292V LEU* 3.6 9.0 - - + +
294V ARG* 1.3 75.5 - - - +
296V MET* 1.3 63.2 + - - +
298V ILE* 3.1 9.2 + - + +
299V CYS* 2.9 26.4 + - - -
306V LEU* 3.8 27.1 - - + -
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Residues in contact with MET 296 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N ARG* 4.0 37.0 - - - +
129V GLN* 5.8 0.9 - - - +
292V LEU 2.7 16.9 + - - +
293V LEU* 3.3 26.2 - - + +
295V ILE* 1.3 73.8 - - - +
297V ASP* 1.3 59.9 + - - +
299V CYS* 3.3 6.4 + - - +
300V GLU* 3.0 29.6 + - + +
306V LEU* 3.8 11.2 - - + +
323V PHE* 4.3 8.7 - - + -
326V VAL* 4.2 11.0 - - + +
327V CYS* 3.9 33.9 - - - -
328V HIS* 4.9 14.1 - - + +
329V ILE* 3.7 21.1 - - + +
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Residues in contact with ASP 297 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N ARG* 2.9 39.7 + - - -
294N ARG* 3.3 46.3 + - - +
297N ASP* 4.5 11.8 - - + +
79V ARG* 5.5 0.2 + - - -
293V LEU 3.2 11.6 + - - +
294V ARG* 3.3 9.2 + - - +
296V MET* 1.3 81.9 - - - +
298V ILE* 1.3 61.9 + - + +
300V GLU* 3.4 8.2 + - - +
301V HIS* 3.3 20.3 + - - +
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Residues in contact with ILE 298 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264V ARG* 4.1 34.8 - - + +
267V ALA* 6.0 1.1 - - + -
268V GLN* 3.5 42.0 - - + +
271V LEU* 3.9 18.4 - - + -
294V ARG* 3.3 20.6 - - - +
295V ILE* 3.1 9.1 + - + +
297V ASP* 1.3 75.7 - - + +
299V CYS* 1.3 64.6 + - - +
301V HIS* 3.3 7.8 + - + +
302V HIS* 3.2 29.9 + - + +
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Residues in contact with CYS 299 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271V LEU* 4.0 11.2 - - - -
279V VAL* 3.7 36.1 - - - -
295V ILE* 2.9 21.8 + - - -
296V MET 3.5 8.5 - - - +
298V ILE* 1.3 75.3 - - - +
300V GLU* 1.3 58.0 + - - +
302V HIS 3.1 2.8 + - - -
303V ASN 2.8 24.4 + - - -
304V ALA* 2.9 27.8 + - - +
305V GLN 4.2 3.4 - - - -
306V LEU* 4.2 13.9 - - - -
329V ILE* 3.6 9.6 - - + -
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Residues in contact with GLU 300 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K ASP* 4.4 7.6 - - - +
264N ARG* 3.5 21.8 + - - -
265N PHE* 5.6 1.1 - - - -
294N ARG* 3.0 21.3 + - - +
296V MET* 3.0 14.8 + - - +
297V ASP* 3.5 11.7 - - - +
298V ILE 3.2 0.4 - - - -
299V CYS* 1.3 77.4 - - - +
301V HIS* 1.3 62.9 + - - +
303V ASN* 3.2 12.4 + - - +
304V ALA 4.9 0.4 - - - -
328V HIS* 4.0 28.6 + - - -
329V ILE* 3.9 20.6 - - + +
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Residues in contact with HIS 301 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K ASP* 4.2 4.5 - - - +
242K ILE* 3.5 44.0 - - + +
273K LYS* 4.1 16.8 + - - -
265N PHE* 6.0 3.6 - - - -
268N GLN* 3.2 38.9 + - - +
272N GLU* 4.7 3.8 + - - -
297V ASP 3.3 10.4 + - - +
298V ILE* 3.3 10.1 + - + +
300V GLU* 1.3 79.8 - - - +
302V HIS* 1.3 78.1 + + - +
303V ASN 3.5 0.3 + - - -
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Residues in contact with HIS 302 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K ILE* 3.7 19.5 - - + +
246K LYS* 3.0 31.6 + - - +
268V GLN* 5.2 2.9 - - + -
271V LEU* 3.9 39.6 - - + +
272V GLU* 3.9 33.5 - - + +
298V ILE* 3.2 26.7 + - + +
299V CYS 3.1 8.0 + - - +
301V HIS* 1.3 94.1 + + - +
303V ASN* 1.3 69.0 + - - +
304V ALA* 3.2 4.5 + - + +
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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
------------------------------------------------------------
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