Contacts of the strand formed by residues 279 - 288 (chain C) in PDB entry 5AQM
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 GLN 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C THR* 3.9 3.5 - - - +
274C LEU* 3.7 4.0 - - - -
277C SER* 3.3 18.4 + - - -
278C THR* 1.3 84.8 + - - +
280C ALA* 1.3 68.8 + - - +
281C SER* 4.9 7.7 + - - -
296C SER* 3.8 19.2 + - - -
297C ILE 3.5 19.1 - - - +
298C THR* 4.1 16.0 - - + +
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Residues in contact with ALA 280 (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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270C ALA* 3.8 34.5 - - + +
273C THR* 3.9 20.2 - - + -
274C LEU* 4.0 7.4 - - + -
279C GLN* 1.3 76.0 - - - +
281C SER* 1.3 64.2 + - - +
282C ILE* 5.1 0.6 - - - +
296C SER* 3.2 5.0 - - - -
297C ILE* 2.9 36.6 + - + +
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Residues in contact with SER 281 (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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269C ARG* 5.0 8.3 + - - -
270C ALA* 5.5 0.5 - - - +
279C GLN* 4.9 7.4 + - - -
280C ALA* 1.3 75.9 + - - +
282C ILE* 1.3 67.2 + - - +
283C GLU* 5.7 2.0 - - - -
295C THR 3.6 9.9 - - - -
296C SER* 4.2 8.0 - - - +
225D ILE* 3.8 31.3 - - - +
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Residues in contact with ILE 282 (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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241C PHE* 3.9 33.0 - - + -
263C LEU* 5.3 2.5 - - + -
266C ALA* 3.9 25.6 - - + +
267C CYS* 4.5 2.9 - - - +
270C ALA* 4.0 26.0 - - + -
280C ALA 5.1 1.8 - - - +
281C SER* 1.3 81.5 - - - +
283C GLU* 1.3 66.1 + - - +
284C ILE* 3.7 32.8 - - + +
293C PHE* 3.6 3.5 - - + +
294C TYR* 3.4 2.8 - - - -
295C THR* 2.9 47.4 + - + +
296C SER* 6.0 0.2 - - - -
297C ILE* 5.1 2.0 - - + -
222D ASP 5.5 2.7 - - - +
225D ILE* 4.4 0.2 - - - -
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Residues in contact with GLU 283 (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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281C SER* 5.7 2.2 - - - -
282C ILE* 1.3 78.9 - - - +
284C ILE* 1.3 61.9 + - - +
285C ASP 4.0 1.7 + - - -
293C PHE 3.7 3.4 - - - -
294C TYR* 3.7 22.4 - - + +
295C THR 5.5 0.2 - - - +
221D ILE 4.9 0.5 - - - +
222D ASP* 3.6 26.1 + - - +
224D LEU 3.9 6.3 - - - +
225D ILE* 3.6 27.2 - - + +
226D LEU 3.0 18.1 + - - +
234D ARG* 3.7 18.6 + - - -
237D ARG* 2.9 42.7 + - - +
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Residues in contact with ILE 284 (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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262C ARG* 3.3 39.3 - - + +
263C LEU* 4.0 28.3 - - + +
266C ALA* 3.9 15.9 - - + -
282C ILE* 3.7 24.0 - - + -
283C GLU* 1.3 77.5 - - - +
285C ASP* 1.3 63.9 + - - +
287C LEU* 3.9 25.7 + - + -
292C ASP* 3.5 0.2 - - - -
293C PHE* 2.8 44.8 + - + +
294C TYR* 4.0 1.1 - - - -
222D ASP* 3.7 16.6 - - + +
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Residues in contact with ASP 285 (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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262C ARG* 2.9 23.7 + - - +
283C GLU 4.0 1.4 + - - -
284C ILE* 1.3 71.5 - - - +
286C SER* 1.3 71.2 + - - +
287C LEU 3.2 0.5 + - - -
292C ASP* 3.3 9.2 - - - +
294C TYR* 2.6 36.4 + - - -
222D ASP* 4.4 1.6 + - - -
234D ARG 4.4 1.0 - - - +
237D ARG* 3.7 19.9 + - + +
238D LYS* 3.2 40.4 + - + +
241D VAL* 3.6 22.6 - - + +
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Residues in contact with SER 286 (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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262C ARG* 3.2 1.4 + - - -
284C ILE 3.6 1.0 + - - -
285C ASP* 1.3 71.8 - - - +
287C LEU* 1.3 65.7 + - - +
288C TYR* 3.3 2.2 - - - -
290C GLY* 3.4 24.1 + - - -
291C ILE 3.5 6.8 + - - -
292C ASP* 2.7 15.1 + - - -
1383C TRS 4.3 1.0 - - - -
238D LYS* 4.0 14.1 - - - -
241D VAL* 3.9 7.2 - - - -
242D LYS* 5.2 6.4 - - - +
245D GLN* 2.6 49.3 + - - -
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Residues in contact with LEU 287 (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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245C PHE* 3.9 15.3 - - + -
253C ILE* 4.0 14.8 - - + -
259C ALA* 3.4 38.1 - - + +
262C ARG* 3.9 9.9 - - + +
263C LEU* 4.6 4.7 - - + +
284C ILE* 3.9 29.6 - - + -
285C ASP 3.2 2.4 + - - -
286C SER* 1.3 75.1 - - - +
288C TYR* 1.3 61.4 + - + +
291C ILE 2.8 14.5 + - - +
293C PHE* 3.7 39.5 - - + -
1383C TRS 2.7 28.7 + - - +
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Residues in contact with TYR 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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245C PHE* 4.1 6.3 - + + -
251C LYS* 4.1 21.8 - - + -
252C ASP 3.5 24.8 + - - -
253C ILE* 3.4 33.7 - - + -
256C ASN* 3.8 41.7 - - + -
259C ALA* 4.5 0.9 - - + -
286C SER 3.3 1.2 - - - -
287C LEU* 1.3 81.4 - - + +
289C GLU* 1.3 107.0 + - + +
290C GLY 3.1 1.3 - - - +
291C ILE* 2.9 23.3 + - - +
1383C TRS 4.2 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
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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