Contacts of the helix formed by residues 285 - 296 (chain V) in PDB entry 3FKS
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 LEU 285 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278S VAL* 5.3 2.9 - - + -
281S ARG* 4.6 19.1 - - - +
282S GLN* 4.4 0.6 + - - -
262V THR* 4.2 15.9 - - + -
277V SER* 5.4 0.4 - - - +
278V ALA 5.5 0.2 - - - +
281V TYR* 3.7 36.8 - - + -
282V GLN* 3.4 19.9 + - - +
283V PRO 3.0 8.8 + - - +
284V THR* 1.3 72.1 - - - +
286V ALA* 1.3 64.7 + - - +
287V THR 3.3 1.1 - - - -
288V ASP* 4.6 0.3 - - - +
289V MET* 3.3 23.1 + - + +
320V PRO* 3.7 24.0 - - + +
324V THR* 3.2 29.4 - - + +
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Residues in contact with ALA 286 (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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209S GLY* 6.6 0.2 - - - -
238S ALA* 3.9 10.8 - - - +
245S GLN* 5.1 13.0 + - - +
275S LYS* 5.7 4.7 - - + +
278S VAL* 4.2 24.5 - - + +
279S ALA* 5.7 2.9 - - - +
282S GLN* 4.6 6.3 + - - +
285V LEU* 1.3 78.8 - - - +
287V THR* 1.3 64.5 + - + +
289V MET* 4.4 1.1 - - - +
290V GLY* 3.4 17.2 + - - -
324V THR* 4.4 12.1 - - + -
328V HIS* 5.0 2.6 + - - -
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Residues in contact with THR 287 (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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238S ALA 4.3 4.9 - - - +
239S SER 5.4 1.3 - - - +
240S GLU 4.2 18.2 - - - +
241S ALA* 4.5 2.7 - - - -
242S ALA* 4.3 12.6 - - - +
245S GLN* 4.8 5.8 - - - +
279S ALA* 6.6 0.2 - - + -
282S GLN* 3.3 36.6 + - - +
284V THR* 3.3 15.2 - - - +
285V LEU 4.2 0.2 - - - +
286V ALA* 1.3 78.2 - - + +
288V ASP* 1.3 73.5 + - - +
289V MET 3.1 1.1 - - - -
290V GLY* 2.9 11.3 + - - -
291V LEU* 2.9 27.2 + - - +
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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
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261V PHE* 3.8 27.1 - - + -
265V GLY* 5.3 5.9 - - - +
274V ARG* 4.5 4.6 + - - -
282V GLN* 4.5 13.9 + - - +
284V THR* 3.2 42.3 + - - +
285V LEU 4.6 0.9 - - - +
287V THR* 1.3 82.9 + - - +
289V MET* 1.3 61.6 + - - +
290V GLY 3.5 0.2 + - - -
291V LEU* 3.7 12.8 + - - +
292V LEU* 3.6 13.2 + - - +
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Residues in contact with MET 289 (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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258V ILE* 4.5 14.1 - - + -
261V PHE* 4.4 13.0 - - + -
262V THR* 3.6 25.8 - - + +
285V LEU* 3.3 20.2 + - + +
286V ALA 4.4 1.1 - - - +
287V THR 3.1 0.8 - - - -
288V ASP* 1.3 78.9 - - - +
290V GLY* 1.3 60.7 + - - +
292V LEU* 3.6 2.8 + - - +
293V GLN* 3.2 45.3 + - - +
321V ALA 4.8 2.2 - - - +
324V THR* 3.7 20.0 - - + +
325V THR* 3.5 28.7 - - - +
328V HIS* 3.7 22.0 - - + +
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Residues in contact with GLY 290 (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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238S ALA* 4.2 10.8 - - - -
239S SER* 4.6 3.1 - - - -
286V ALA 3.4 11.5 + - - -
287V THR 2.9 8.7 + - - -
289V MET* 1.3 75.7 - - - +
291V LEU* 1.3 59.0 + - - -
292V LEU 3.0 2.0 + - - -
294V GLU* 2.8 39.4 + - - +
328V HIS* 3.8 19.3 - - - -
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Residues in contact with LEU 291 (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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239S SER* 3.4 38.1 - - - +
121V PRO* 4.9 11.4 - - + +
234V LEU* 5.4 3.3 - - + +
287V THR* 2.9 28.4 + - - +
288V ASP* 4.2 12.1 - - - +
289V MET 3.5 0.2 - - - -
290V GLY* 1.3 74.4 - - - +
292V LEU* 1.3 56.3 + - - +
294V GLU* 4.5 1.1 - - - +
295V ARG* 3.2 33.3 + - - +
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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
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233V ALA* 4.1 21.5 - - + +
234V LEU* 3.5 34.5 - - + +
237V LEU* 3.7 27.1 - - + +
255V ILE* 5.9 3.4 - - + -
258V ILE* 3.7 29.6 - - + -
261V PHE* 3.8 28.7 - - + -
288V ASP 3.6 10.6 + - - +
289V MET* 3.6 9.1 + - - +
290V GLY 3.0 0.6 - - - -
291V LEU* 1.3 82.0 - - - +
293V GLN* 1.3 69.4 + - - +
295V ARG* 4.0 2.6 - - - +
296V ILE* 3.8 13.3 - - + +
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Residues in contact with GLN 293 (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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152V LYS* 3.6 21.3 - - - +
258V ILE* 3.9 16.4 - - - +
289V MET* 3.2 32.4 + - - +
290V GLY 3.2 1.2 + - - +
292V LEU* 1.3 80.7 - - + +
294V GLU* 1.3 57.8 + - - +
296V ILE* 2.8 43.3 + - - +
308V GLN* 2.7 47.1 + - - +
325V THR* 5.4 2.9 - - - +
328V HIS* 3.5 33.2 - - + +
329V LEU* 5.5 1.4 - - - +
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Residues in contact with GLU 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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210S GLN 3.7 5.7 - - - +
211S LYS* 3.1 41.5 - - - +
212S ARG* 3.2 19.3 + - - +
213S SER* 4.7 4.9 + - - -
237S THR* 3.8 6.2 + - - -
238S ALA* 3.8 12.4 + - + +
239S SER* 3.7 29.2 + - - +
121V PRO* 4.1 10.5 - - + -
122V PRO* 4.1 2.5 - - - +
127V GLN* 5.1 4.6 + - - -
152V LYS* 4.3 4.6 + - - +
290V GLY* 2.8 25.0 + - - +
291V LEU 5.0 0.4 - - - +
293V GLN* 1.3 72.9 - - - +
295V ARG* 1.3 64.7 + - - +
296V ILE 3.0 10.3 + - - +
297V THR* 3.6 13.7 - - - +
328V HIS* 5.1 1.8 - - + -
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Residues in contact with ARG 295 (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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117V ILE 2.7 24.5 + - - -
118V HIS* 4.2 1.0 - - - +
119V ALA* 3.1 34.9 + - - +
120V ASP 4.4 0.6 + - - +
121V PRO* 3.8 22.0 - - + +
122V PRO* 3.9 10.6 - - + +
234V LEU* 3.7 8.8 - - - +
237V LEU* 3.4 35.9 - - + +
238V THR* 3.7 20.0 + - - +
241V GLU* 2.7 29.7 + - - +
244V ARG* 2.9 31.6 + - - +
291V LEU 3.2 22.4 + - - +
292V LEU 4.0 6.7 + - - +
293V GLN 3.1 0.6 + - - -
294V GLU* 1.3 77.3 - - - +
296V ILE* 1.3 59.2 + - - +
297V THR* 3.2 4.3 + - - +
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Residues in contact with ILE 296 (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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152V LYS* 3.7 21.4 + - + +
237V LEU* 3.5 23.3 - - + -
244V ARG* 4.0 2.9 - - - +
253V LEU* 4.0 18.2 - - + -
255V ILE* 4.3 8.1 - - + -
292V LEU* 3.8 11.2 - - + +
293V GLN* 2.8 24.2 + - - +
294V GLU 3.3 1.6 - - - +
295V ARG* 1.3 71.2 - - - +
297V THR* 1.3 65.4 + - - +
304V VAL* 3.4 32.8 - - + +
306V SER* 3.5 35.0 - - - +
308V GLN* 4.3 9.4 - - - +
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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