Contacts of the strand formed by residues 283 - 292 (chain A) in PDB entry 1EBF
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 LYS 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LYS 5.0 0.3 - - - +
278A ALA* 2.7 33.7 + - + +
279A ALA* 3.7 2.3 + - - +
281A GLU* 3.5 41.4 + - + +
282A ASN* 1.3 75.6 - - - +
284A VAL* 1.3 59.9 + - - +
304A LYS* 3.5 42.1 + - + +
305A TYR 3.3 15.9 - - - +
306A ASP* 3.9 22.2 - - - +
307A TYR* 3.3 15.9 + - - -
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 2.8 52.5 - - - +
186A THR 3.7 12.3 - - - +
278A ALA* 4.7 1.3 - - - -
283A LYS* 1.3 74.6 - - - +
285A LEU* 1.3 63.0 + - - +
286A ARG* 3.6 24.2 - - + +
303A GLU 3.8 0.3 - - - +
304A LYS* 3.4 4.7 - - - -
305A TYR* 2.9 41.1 + - + +
307A TYR* 4.2 9.0 - - + -
312A ALA* 3.8 24.0 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 3.3 18.5 - - + -
184A PHE* 4.3 13.0 - - + -
185A SER* 3.1 14.6 + - - +
271A LEU* 4.4 1.6 - - + +
274A LEU* 3.7 25.6 - - + -
275A LYS* 3.5 38.1 - - + +
278A ALA* 3.7 22.7 - - + -
284A VAL* 1.3 72.4 - - - +
286A ARG* 1.3 85.0 + - - +
302A ILE* 4.0 22.9 - - + -
303A GLU 3.9 1.8 - - - -
304A LYS* 3.8 18.4 - - + -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.0 16.8 - - + -
178A SER* 5.7 1.1 - - - +
181A PHE* 3.1 26.3 + - - -
182A ASN* 3.3 28.4 + - - +
185A SER 3.0 28.5 + - - -
186A THR* 4.9 2.2 - - - +
284A VAL* 3.6 20.2 - - + +
285A LEU* 1.3 100.9 + - - +
287A PHE* 1.3 61.7 + - - +
288A ILE* 3.7 7.6 + - + +
302A ILE* 3.3 3.6 - - - -
303A GLU 3.0 30.7 + - - +
305A TYR* 3.9 23.8 - - + -
311A PHE* 2.9 28.5 + - + +
312A ALA* 3.6 24.0 + - - +
314A LEU 5.6 0.2 - - - +
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 3.7 24.3 - - - +
173A PHE 5.0 0.9 + - - -
174A SER* 6.2 0.2 - - - -
177A LEU* 3.3 40.3 + - + +
178A SER* 6.4 0.4 - - - +
181A PHE* 4.0 21.8 - + + +
215A LEU 5.1 1.1 - - - -
217A GLY* 4.4 10.8 - - - -
220A VAL* 4.1 14.3 - - + +
244A GLN 3.3 20.2 - - - -
246A LEU* 3.3 41.5 - - + -
286A ARG* 1.3 70.8 - - - +
288A ILE* 1.3 62.7 + - - +
300A VAL* 3.7 27.4 - - + -
301A GLY* 3.7 12.8 - - - -
302A ILE* 4.0 12.1 - - + -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU* 5.0 1.3 - - + -
171A GLY 3.2 13.2 - - - +
172A ILE* 4.2 11.9 - - + -
220A VAL* 4.5 3.8 - - - -
286A ARG* 4.2 5.2 - - + +
287A PHE* 1.3 80.2 - - - +
289A GLY* 1.3 65.9 + - - +
290A LYS* 3.5 30.5 - - + +
299A SER* 4.7 2.7 - - - +
300A VAL* 3.4 8.8 - - - +
301A GLY 2.9 44.2 + - - +
303A GLU* 4.0 22.4 - - + +
305A TYR* 3.2 40.2 - - + +
311A PHE* 4.3 4.9 - - + -
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 4.6 0.3 - - - +
170A GLU* 3.2 4.7 - - - -
171A GLY 2.7 31.9 + - - -
173A PHE* 3.5 22.0 - - - -
220A VAL* 4.3 9.2 - - - -
224A VAL* 4.6 6.3 - - - -
288A ILE* 1.3 74.9 - - - +
290A LYS* 1.3 60.6 + - - +
291A VAL* 5.6 0.9 - - - -
299A SER 3.5 5.8 - - - -
300A VAL* 4.5 2.5 - - - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE 3.5 9.0 - - - +
170A GLU* 4.1 18.0 + - + -
224A VAL* 3.9 3.9 - - - +
288A ILE* 3.5 11.9 - - + -
289A GLY* 1.3 74.6 - - - +
291A VAL* 1.3 73.7 + - - +
292A ASP* 5.9 2.2 - - + -
297A SER 4.6 1.6 - - - +
298A VAL* 3.3 5.8 - - - -
299A SER* 2.7 49.2 + - - +
303A GLU* 2.7 40.4 + - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 5.7 0.2 - - + -
168A LYS* 3.5 6.5 - - - +
169A ILE* 2.8 51.7 + - + +
224A VAL* 4.1 10.3 - - + -
227A VAL* 4.5 7.9 - - + -
228A GLY* 4.0 25.4 - - - +
231A SER* 4.3 6.1 - - - -
233A VAL* 4.2 15.5 - - + -
289A GLY 5.6 0.4 - - - -
290A LYS* 1.3 86.0 - - - +
292A ASP* 1.3 64.4 + - - +
293A VAL* 4.1 11.0 - - + -
297A SER 3.8 3.4 - - - -
298A VAL* 4.0 20.9 - - + -
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU 3.7 3.5 - - - +
168A LYS* 3.6 28.5 + - - +
233A VAL* 4.4 0.3 - - - +
290A LYS* 5.9 2.9 - - + -
291A VAL* 1.3 76.5 - - - +
293A VAL* 1.3 57.6 + - - +
294A ALA* 3.3 12.1 + - - +
295A THR* 3.0 44.6 + - - +
296A LYS* 2.8 23.0 + - - -
297A SER* 3.0 21.7 + - - +
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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