Contacts of the helix formed by residues 286 - 301 (chain C) in PDB entry 4ACR
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 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL* 4.3 3.6 - - + -
237C VAL* 3.7 19.3 - - + -
283C GLN* 3.5 20.2 - - - +
284C ALA 3.1 1.4 - - - -
285C ASP* 1.3 76.6 - - - +
287C ASP* 1.3 64.8 + - - +
288C ALA 3.3 1.2 + - - -
289C GLU* 3.5 3.4 + - - -
290C TRP* 2.9 24.0 + - - +
393C TRP* 3.6 42.8 - - + +
453C ILE* 4.0 19.3 - - + +
456C GLN* 4.1 9.6 - - + -
457C ILE* 3.6 27.8 - - + +
460C LEU* 3.9 21.1 - - + +
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ALA 3.3 16.2 + - - +
285C ASP 3.1 2.2 - - - -
286C LEU* 1.3 77.2 - - - +
288C ALA* 1.3 60.4 + - - +
290C TRP* 3.5 4.9 - - - +
291C ARG* 2.8 76.4 + - - +
390C GLN 4.2 4.7 - - - +
391C ASP 4.9 0.7 - - - +
393C TRP* 4.2 9.8 - - + +
394C ILE* 3.7 29.0 + - + +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ASP 4.4 4.9 + - - +
286C LEU 3.4 0.4 - - - -
287C ASP* 1.3 84.9 + - - +
289C GLU* 1.3 66.8 + - + +
291C ARG* 3.4 6.4 + - - +
292C ASN* 2.9 35.6 + - - +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ASP 5.4 1.3 + - - +
286C LEU 3.5 4.4 + - - +
287C ASP 3.4 0.2 - - - -
288C ALA* 1.3 80.7 - - + +
290C TRP* 1.3 60.1 + - - +
292C ASN* 3.5 25.8 + - - +
293C LEU* 2.9 29.1 + - - +
457C ILE* 3.8 25.4 - - + +
460C LEU* 3.9 26.7 - - + +
461C LYS* 3.5 41.3 + - - +
464C THR* 4.2 5.2 + - - +
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Residues in contact with TRP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 4.3 13.9 - - + -
100C LEU* 4.3 8.7 - - + -
230C ALA* 4.0 32.1 - - + -
233C VAL* 4.8 4.0 - - + -
234C VAL* 3.9 28.0 - - + -
286C LEU 2.9 19.4 + - - +
287C ASP* 3.5 3.8 - - - +
289C GLU* 1.3 77.1 - - - +
291C ARG* 1.3 56.8 + - - +
293C LEU* 3.3 3.0 + - + +
294C LEU* 3.0 61.0 + - + +
389C VAL* 3.1 31.4 + - + -
390C GLN* 3.5 22.4 - - - -
392C PHE* 4.3 1.7 - - + +
393C TRP* 3.2 36.0 - + + +
460C LEU* 3.7 21.4 - - + +
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASP* 2.8 44.0 + - - +
288C ALA* 3.7 6.1 - - - +
290C TRP* 1.3 78.7 - - - +
292C ASN* 1.3 57.1 + - - +
294C LEU* 3.4 5.4 + - - +
295C ASP* 2.9 43.4 + - - +
390C GLN* 3.6 49.3 - - + +
391C ASP* 3.6 17.0 - - - +
394C ILE* 3.4 29.5 - - - +
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Residues in contact with ASN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ALA* 2.9 25.9 + - - +
289C GLU* 3.5 33.2 + - - +
291C ARG* 1.3 77.6 - - - +
293C LEU* 1.3 56.7 + - - +
295C ASP* 3.3 11.0 + - - +
296C SER* 2.9 29.6 + - - -
464C THR* 4.0 14.1 - - + +
468C ARG* 4.2 17.9 + - - +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLY 4.4 5.8 - - - +
229C VAL* 4.9 2.9 - - + -
230C ALA* 4.1 25.6 - - + +
289C GLU 2.9 19.4 + - - +
290C TRP* 3.6 5.2 - - + +
292C ASN* 1.3 76.6 - - - +
294C LEU* 1.3 65.8 + - + +
296C SER* 2.5 18.8 + - - -
297C MET* 2.9 29.0 + - + +
460C LEU* 3.6 27.6 - - + +
463C MET* 3.6 29.8 - - + -
464C THR* 3.4 17.0 + - - +
467C LEU* 3.7 13.7 - - + -
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 6.4 0.2 - - + -
230C ALA* 5.3 2.5 - - + -
290C TRP* 3.0 62.5 + - + +
291C ARG* 3.9 3.8 - - - +
293C LEU* 1.3 89.3 - - + +
295C ASP* 1.3 58.9 + - - +
297C MET* 3.2 9.2 + - - +
298C VAL* 2.9 36.7 + - + +
386C LEU* 3.3 50.7 - - + +
389C VAL* 4.2 7.2 - - + -
390C GLN* 3.7 14.8 - - + +
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Residues in contact with ASP 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ARG* 2.9 32.5 + - - +
292C ASN* 3.6 11.3 - - - +
294C LEU* 1.3 78.6 - - - +
296C SER* 1.3 57.5 + - - +
298C VAL* 3.1 14.1 - - - +
299C LEU* 2.9 37.1 + - + +
390C GLN* 5.1 6.1 - - - +
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ASN 2.9 11.8 + - - -
293C LEU* 2.5 27.4 + - - +
295C ASP* 1.3 76.2 - - - +
297C MET* 1.3 57.3 + - - +
299C LEU* 3.2 14.3 + - - +
300C ILE* 2.9 29.8 + - - +
464C THR* 4.1 14.4 - - - +
467C LEU* 3.3 33.0 - - - +
468C ARG* 4.7 9.4 - - - -
471C TYR* 6.1 0.5 - - - +
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Residues in contact with MET 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.3 46.8 - - + +
226C GLY* 3.7 19.7 - - - +
227C LEU* 3.5 28.7 - - + +
230C ALA* 5.2 2.7 - - - -
293C LEU* 2.9 32.3 + - + +
294C LEU* 3.2 13.4 + - - +
296C SER* 1.3 75.3 + - - +
298C VAL* 1.3 63.4 + - - +
300C ILE* 3.3 23.3 - - - +
301C THR* 3.4 12.1 - - - +
386C LEU* 4.2 14.6 - - + -
467C LEU* 3.6 18.2 - - + -
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 2.9 15.5 + - + +
295C ASP* 3.1 23.6 - - - +
297C MET* 1.3 74.7 - - - +
299C LEU* 1.3 62.8 + - + +
301C THR* 3.0 24.1 + - - -
302C ASP* 4.0 5.7 - - - +
383C LYS* 4.3 30.0 - - + +
386C LEU* 4.0 27.4 - - + -
387C ARG* 5.7 6.1 - - + +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ASP* 2.9 27.7 + - + +
296C SER* 3.3 14.1 - - - +
297C MET 3.1 0.2 - - - -
298C VAL* 1.3 81.3 - - + +
300C ILE* 1.3 60.5 + - - +
301C THR 3.2 1.9 + - - -
302C ASP* 3.4 19.5 + - - +
468C ARG* 6.5 1.6 - - + -
471C TYR* 3.6 48.9 - - + +
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Residues in contact with ILE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ALA* 3.9 24.4 - - - +
223C PHE* 3.6 26.9 - - + -
296C SER 2.9 12.3 + - - +
297C MET 3.3 16.6 - - - +
299C LEU* 1.3 74.9 - - - +
301C THR* 1.3 59.7 + - - +
302C ASP 3.1 0.4 - - - -
303C LYS* 3.0 30.3 + - + +
304C PHE* 3.9 4.0 + - - -
467C LEU* 3.8 30.7 - - + +
470C ALA* 3.9 12.1 - - + +
471C TYR* 3.6 37.9 - - + +
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.6 22.7 - - + -
297C MET 3.4 18.2 - - - +
298C VAL* 3.0 18.9 + - - +
300C ILE* 1.3 73.2 - - - +
302C ASP* 1.3 68.9 + - - +
303C LYS 3.1 2.0 - - - -
304C PHE* 3.3 33.3 + - + -
305C TRP* 3.3 21.1 - - - -
379C VAL* 3.9 19.4 - - + +
382C ALA* 6.0 1.1 - - + -
383C LYS* 3.7 15.8 - - + -
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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