Contacts of the strand formed by residues 283 - 292 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B SER* 4.8 0.5 + - - -
186B THR 5.1 1.4 - - - +
278B ALA* 2.8 27.3 + - + +
279B ALA* 3.5 4.7 + - - -
281B GLU* 3.3 36.8 - - + +
282B ASN* 1.3 81.2 - - - +
284B VAL* 1.3 61.4 + - - +
304B LYS* 3.4 51.1 + - + +
305B TYR* 3.2 14.6 - - - +
306B ASP* 4.0 8.3 - - + +
307B TYR* 3.5 11.1 - - - -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 2.9 43.5 - - - +
186B THR* 4.3 5.8 - - - +
187B SER 5.1 0.4 - - - +
278B ALA* 4.6 1.1 - - - -
283B LYS* 1.3 75.2 - - - +
285B LEU* 1.3 60.8 + - - +
286B ARG* 3.0 29.7 + - + +
303B GLU 3.8 0.2 - - - +
304B LYS* 3.2 6.7 - - - -
305B TYR* 2.7 48.3 + - + +
307B TYR* 4.4 11.2 - - + -
312B ALA* 3.7 27.4 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 3.6 21.8 - - + +
184B PHE* 4.2 13.7 - - + -
185B SER* 2.6 21.5 + - - +
271B LEU* 5.1 1.3 - - + -
274B LEU* 3.7 28.7 - - + -
275B LYS* 3.5 35.7 - - + +
278B ALA* 3.9 13.9 - - + -
284B VAL* 1.3 71.9 - - - +
286B ARG* 1.3 87.0 + - - +
302B ILE* 3.9 13.5 - - + -
303B GLU 3.8 0.7 - - - -
304B LYS* 3.8 26.5 - - + -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.8 21.1 - - + +
178B SER* 6.0 1.6 - - - +
181B PHE* 3.1 25.8 + - - -
182B ASN* 3.5 25.4 + - - +
185B SER 3.0 12.9 + - - -
186B THR* 5.2 2.4 - - - +
284B VAL* 3.0 34.9 - - + +
285B LEU* 1.3 98.6 + - - +
287B PHE* 1.3 60.9 + - - +
288B ILE* 3.7 3.6 + - + +
302B ILE* 3.2 4.0 - - - +
303B GLU* 2.9 32.5 + - - -
305B TYR* 3.9 29.4 - - + -
311B PHE 2.7 26.4 + - - +
312B ALA* 3.9 21.2 + - - +
314B LEU* 5.4 1.0 + - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.8 23.4 - - - +
173B PHE 4.9 0.9 + - - -
174B SER 5.9 0.2 + - - -
177B LEU* 3.6 32.0 + - + +
181B PHE* 3.9 22.4 - + + +
217B GLY* 4.1 10.5 - - - -
220B VAL* 3.6 35.5 - - + +
244B GLN* 3.3 27.6 - - + -
246B LEU* 3.9 27.4 - - + -
286B ARG* 1.3 71.1 - - - +
288B ILE* 1.3 65.6 + - - +
300B VAL* 3.6 15.0 - - + -
301B GLY* 3.8 13.2 - - - -
302B ILE* 3.9 17.7 - - + -
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 5.0 1.8 - - + -
171B GLY 3.2 13.9 - - - +
172B ILE* 3.8 15.0 - - + +
173B PHE 5.9 0.2 - - - -
220B VAL* 5.3 2.7 - - - -
286B ARG* 4.2 4.9 - - + +
287B PHE* 1.3 83.2 - - - +
289B GLY* 1.3 72.7 - - - +
290B LYS* 4.0 16.2 - - + -
299B SER* 5.0 1.1 - - - +
300B VAL* 3.0 8.6 - - - +
301B GLY 2.8 52.5 + - - +
303B GLU* 3.7 26.9 - - + +
305B TYR* 3.7 35.0 - - + +
311B PHE* 4.1 4.3 - - + -
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 6.2 0.2 - - - -
170B GLU* 3.1 7.0 - - - +
171B GLY 2.8 31.9 + - - -
173B PHE* 4.1 11.7 - - - +
220B VAL* 5.4 0.9 - - - -
224B VAL* 3.7 22.7 - - - -
288B ILE* 1.3 76.7 - - - +
290B LYS* 1.3 62.3 + - - +
299B SER 3.5 4.9 - - - -
300B VAL* 4.1 1.8 - - - -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE 3.6 9.6 - - - +
170B GLU* 3.5 20.1 + - - +
224B VAL* 4.0 3.3 - - - +
288B ILE* 4.0 9.0 - - + -
289B GLY* 1.3 74.0 - - - +
291B VAL* 1.3 75.7 + - - +
292B ASP* 5.2 4.0 - - + +
297B SER 5.4 1.1 - - - +
298B VAL* 3.1 5.1 - - - +
299B SER* 2.5 56.0 + - - +
303B GLU* 2.7 34.2 + - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 6.4 0.2 - - + -
168B LYS* 3.6 6.8 - - - +
169B ILE* 3.0 42.2 + - + +
224B VAL* 3.8 15.5 - - + +
227B VAL* 4.9 7.0 - - + -
228B GLY* 3.9 23.6 - - - +
231B SER* 4.7 3.8 - - - -
233B VAL* 3.9 22.9 - - + -
290B LYS* 1.3 80.4 - - - +
292B ASP* 1.3 65.6 + - - +
293B VAL* 4.1 8.3 - - + -
297B SER 3.3 3.6 - - - -
298B VAL* 3.3 27.4 - - + -
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU 3.9 3.3 - - - +
168B LYS* 3.1 31.8 + - + +
233B VAL* 4.5 0.9 - - - +
290B LYS* 5.8 4.5 - - + -
291B VAL* 1.3 75.6 - - - +
293B VAL* 1.3 59.4 + - - +
294B ALA* 3.3 10.4 + - - +
295B THR* 3.2 37.8 + - - +
296B LYS* 2.9 6.6 + - - -
297B SER* 2.6 45.1 + - - +
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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