Contacts of the helix formed by residues 283 - 303 (chain F) in PDB entry 3JCK
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 HIS 283 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185F PHE* 4.4 16.0 - + - -
223F LEU* 3.6 26.0 - - + -
279F ILE* 3.3 28.8 - - + +
280F LEU 4.5 0.4 - - - -
282F GLN* 1.3 106.3 + - + +
284F GLU* 1.3 66.1 + - - +
285F SER* 3.1 8.7 - - - +
286F PHE* 3.2 47.5 + + + +
287F LEU* 3.4 14.4 + - - +
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Residues in contact with GLU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F ILE* 4.9 8.4 - - + +
274F ILE* 4.7 19.7 - - + +
280F LEU 4.5 3.6 - - - +
281F ALA 4.0 11.7 + - - +
282F GLN 3.3 4.4 + - - -
283F HIS* 1.3 76.8 - - - +
285F SER* 1.3 63.6 + - - +
287F LEU* 3.2 15.9 + - + +
288F ARG* 2.6 61.4 + - + +
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Residues in contact with SER 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F HIS* 4.2 5.2 - - - -
284F GLU* 1.3 76.4 - - - +
286F PHE* 1.3 91.5 + - - +
288F ARG* 3.0 13.2 + - - +
289F GLN* 2.9 28.2 + - - +
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Residues in contact with PHE 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F PHE* 6.1 2.0 - + - -
222F LEU 5.8 0.4 - - - +
223F LEU* 4.3 24.0 - - + +
225F ASP* 5.9 4.9 - - + -
283F HIS* 3.2 45.5 + + + +
285F SER* 1.3 95.4 + - - +
287F LEU* 1.3 69.3 + - + +
289F GLN* 2.8 27.9 + - - +
290F LYS* 2.8 19.5 + - + +
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Residues in contact with LEU 287 (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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222F LEU* 3.7 46.9 - - + +
223F LEU* 4.3 8.7 - - + -
266F PHE* 4.5 15.0 - - + -
270F ILE* 5.1 12.1 - - + -
274F ILE* 4.7 8.7 - - + -
280F LEU* 4.1 29.6 - - + +
283F HIS 3.6 14.1 - - - +
284F GLU* 3.2 16.0 + - + +
286F PHE* 1.3 73.6 - - + +
288F ARG* 1.3 64.4 + - + +
290F LYS* 3.4 6.8 + - + +
291F ILE* 2.9 31.1 + - - +
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Residues in contact with ARG 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PHE* 5.6 5.9 - - - -
266F PHE* 5.9 0.7 - - - -
267F ASP* 4.0 15.6 + - - -
270F ILE* 4.6 15.3 - - + +
271F LYS* 4.8 9.1 - - - +
284F GLU* 2.6 52.9 + - + +
285F SER* 3.0 10.0 + - - +
286F PHE 2.9 0.6 + - - -
287F LEU* 1.3 76.4 - - + +
289F GLN* 1.3 64.2 + - + +
291F ILE* 3.1 8.7 + - - +
292F CYS* 3.0 29.6 + - - -
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Residues in contact with GLN 289 (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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225F ASP* 5.5 1.9 - - - +
285F SER* 2.9 21.7 + - - +
286F PHE* 2.8 26.7 + - - +
288F ARG* 1.3 72.1 - - + +
290F LYS* 1.3 63.8 + - - +
292F CYS* 2.9 21.1 + - - +
293F LEU* 2.9 23.8 + - + +
327F LEU* 4.7 3.1 - - + +
330F ARG* 4.6 21.9 + - - +
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Residues in contact with LYS 290 (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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221F ALA 4.2 1.8 + - - -
222F LEU* 3.2 29.6 - - + +
223F LEU* 4.7 1.1 - - - +
224F GLY 2.6 30.6 + - - +
225F ASP* 4.0 0.6 + - - +
227F ILE 3.0 22.6 + - - -
228F TYR* 3.9 26.1 - - + +
230F PHE* 4.5 6.7 - - + -
258F LEU* 4.4 20.0 - - + -
286F PHE* 2.8 22.5 + - - +
287F LEU* 3.7 7.6 - - + +
289F GLN* 1.3 73.3 - - - +
291F ILE* 1.3 64.3 + - + +
293F LEU* 3.4 12.1 + - - +
294F MET* 3.0 33.6 + - + +
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Residues in contact with ILE 291 (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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258F LEU* 3.4 30.3 - - + -
261F GLY* 6.1 2.9 - - - -
262F ASP 5.6 0.4 - - - -
263F PHE* 3.5 39.3 - - + -
266F PHE* 3.2 50.3 - - + -
287F LEU 2.9 16.3 + - - +
288F ARG* 3.5 8.5 - - - +
290F LYS* 1.3 72.6 - - + +
292F CYS* 1.3 67.9 + - - +
294F MET* 3.0 3.1 + - - +
295F THR* 2.9 31.3 + - - +
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Residues in contact with CYS 292 (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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263F PHE* 4.6 9.2 - - - -
288F ARG* 3.0 23.1 + - - -
289F GLN* 2.9 13.5 + - - +
291F ILE* 1.3 73.2 - - - +
293F LEU* 1.3 63.9 + - - +
295F THR* 3.4 6.4 - - - -
296F LEU* 2.9 22.5 + - - +
317F THR* 3.7 28.6 - - - +
319F LEU* 5.1 14.4 - - + -
327F LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 293 (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 TYR* 3.3 40.2 - - + +
289F GLN* 2.9 22.1 + - + +
290F LYS* 3.4 9.2 - - - +
291F ILE 3.0 0.2 + - - -
292F CYS* 1.3 75.1 - - - +
294F MET* 1.3 66.4 + - - +
296F LEU* 2.7 18.7 + - + +
297F ILE* 2.9 16.1 + - + +
327F LEU* 3.6 23.3 - - + +
330F ARG* 4.7 9.6 - - + +
331F ALA* 3.6 37.2 - - + +
334F LEU* 4.5 8.7 - - + -
336F LEU* 5.0 5.8 - - + -
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Residues in contact with MET 294 (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 TYR* 3.8 44.0 - - + +
230F PHE* 5.2 3.4 - - + -
258F LEU* 3.6 43.5 - - + +
259F THR* 4.1 22.0 - - + +
261F GLY* 4.6 1.8 - - - -
290F LYS* 3.0 21.7 + - + +
291F ILE* 3.0 3.3 + - + +
293F LEU* 1.3 75.4 - - - +
295F THR* 1.3 63.6 + - - +
297F ILE* 3.2 17.6 + - + +
298F GLU* 3.0 33.3 + - + +
356F ARG* 4.4 16.8 - - - +
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Residues in contact with THR 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F GLY* 3.9 24.3 + - - +
263F PHE* 4.1 11.2 - - + +
291F ILE* 2.9 25.6 + - - +
292F CYS* 3.4 9.6 - - - -
294F MET* 1.3 74.9 - - - +
296F LEU* 1.3 63.9 + - - +
298F GLU* 3.1 5.6 + - - +
299F THR* 2.9 37.6 + - + +
316F ALA* 3.5 26.9 - - + +
317F THR* 4.0 11.2 - - + -
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Residues in contact with LEU 296 (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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292F CYS 2.9 13.1 + - - +
293F LEU* 2.7 13.9 + - + +
295F THR* 1.3 72.5 - - - +
297F ILE* 1.3 64.7 + - + +
299F THR* 2.7 21.3 + - - +
300F VAL* 3.0 27.4 + - + +
308F LEU* 4.2 2.2 - - + -
313F ILE* 3.8 36.6 - - + -
317F THR* 4.4 5.1 - - + +
327F LEU* 4.1 23.6 - - + -
328F VAL* 4.3 12.6 - - + -
331F ALA* 4.0 26.9 - - + -
337F LEU* 4.2 12.3 - - + -
348F VAL* 6.4 0.7 - - + -
350F ILE* 6.1 0.7 - - + -
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Residues in contact with ILE 297 (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 TYR* 5.2 0.9 - - + -
293F LEU* 2.9 20.9 + - + +
294F MET* 3.5 26.2 - - + +
296F LEU* 1.3 77.1 - - + +
298F GLU* 1.3 60.5 + - + +
300F VAL* 3.3 6.3 + - - +
301F PHE* 2.8 25.6 + - + +
331F ALA* 5.6 1.8 - - + -
336F LEU* 3.5 41.1 - - + +
337F LEU* 4.4 19.1 - - + -
353F VAL* 4.0 18.9 - - + +
356F ARG* 3.9 28.3 - - - +
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Residues in contact with GLU 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F LEU 3.8 0.9 - - - +
259F THR* 2.6 29.7 - - - +
260F VAL* 2.6 24.7 - - - +
261F GLY* 2.7 29.2 + - - +
294F MET* 3.0 15.8 + - + +
295F THR* 3.6 4.6 - - - +
297F ILE* 1.3 73.8 - - + +
299F THR* 1.3 61.3 + - + +
300F VAL 2.9 2.0 - - - -
301F PHE* 2.6 29.3 + - + +
302F VAL* 2.9 22.0 + - + +
356F ARG* 4.7 12.8 - - - +
362F GLN* 4.5 3.6 - - - +
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Residues in contact with THR 299 (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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295F THR* 2.9 19.7 + - + +
296F LEU* 2.7 27.9 + - - +
298F GLU* 1.3 73.8 - - + +
300F VAL* 1.3 60.5 + - - +
302F VAL* 4.4 3.6 - - - +
303F LYS* 3.5 23.0 + - - +
308F LEU* 4.6 11.2 - - - +
313F ILE* 5.7 0.9 - - - +
316F ALA* 4.1 27.2 - - + +
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Residues in contact with VAL 300 (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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296F LEU* 3.0 23.3 + - + +
297F ILE* 3.5 8.1 - - - +
298F GLU 2.9 0.8 - - - -
299F THR* 1.3 77.9 - - - +
301F PHE* 1.3 65.5 + - - +
302F VAL 3.2 0.4 - - - -
303F LYS* 3.1 20.4 + - - +
306F ARG* 3.9 19.5 - - + +
307F MET 5.9 0.2 - - - +
308F LEU* 3.6 28.7 - - + -
337F LEU* 5.4 2.2 - - + -
350F ILE* 3.6 43.1 - - + -
353F VAL* 3.7 12.8 - - + -
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Residues in contact with PHE 301 (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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230E GLN* 4.4 27.4 - - + -
233E PHE* 4.6 14.1 - + + -
234E ASN* 6.0 0.2 - - - -
297F ILE* 2.8 18.4 + - + +
298F GLU* 2.6 17.6 + - + +
300F VAL* 1.3 75.0 - - - +
302F VAL* 1.3 70.8 + - + +
306F ARG* 4.5 18.0 + - - +
353F VAL* 4.6 17.7 - - + -
354F GLN 5.9 1.6 - - - -
356F ARG* 4.9 14.1 - - - +
358F ILE* 4.6 13.9 - - + -
362F GLN* 5.0 11.2 - - + -
365F LYS* 6.1 2.2 - - + -
366F MET* 4.2 32.3 - - + -
369F ARG* 3.4 17.2 + - - -
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Residues in contact with VAL 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F GLU* 2.9 17.7 + - + +
299F THR* 4.9 2.7 - - - +
301F PHE* 1.3 84.5 - - + +
303F LYS* 1.3 57.4 + - - +
304F ASN* 3.4 7.7 + - - +
365F LYS* 4.0 44.0 - - + -
369F ARG* 2.3 29.3 + - - +
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Residues in contact with LYS 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F THR 3.5 17.4 + - - +
300F VAL* 3.1 14.6 + - - +
302F VAL* 1.3 77.0 - - - +
304F ASN* 1.3 64.2 + - - +
305F ILE* 3.2 22.7 - - - +
306F ARG* 4.0 9.8 - - - +
307F MET* 2.5 35.4 + - - +
308F LEU* 3.6 22.1 - - + +
312F ASP* 4.4 7.7 + - - -
369F ARG* 2.5 17.3 + - - -
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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
------------------------------------------------------------
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