Contacts of the strand formed by residues 285 - 292 (chain B) in PDB entry 2Q2U
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 ARG 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B ASP* 2.6 40.0 + - - -
75B PHE* 3.8 29.6 - - - -
161B GLU* 4.4 6.1 + - - -
275B TYR* 3.6 1.4 - - - +
276B PHE* 2.9 41.7 + - - +
278B MET 3.1 23.8 + - - +
279B GLY* 3.5 27.4 - - - +
280B SER* 2.9 10.8 + - - +
283B CYS 5.1 0.2 - - - +
284B PRO* 1.3 71.5 - - - +
286B PHE* 1.3 112.4 + - + +
287B PRO 3.3 1.7 - - - -
12G G 4.9 5.4 - - - +
13G G 5.6 7.4 - - - +
14G G 6.5 0.9 - - - -
31H C 4.6 6.7 + - - +
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Residues in contact with PHE 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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161B GLU* 4.6 3.8 - - - -
188B LYS* 4.0 17.7 - - - -
190B PHE* 3.6 26.6 - + + -
274B LYS 3.7 1.9 - - - +
276B PHE* 3.7 28.7 - + + -
285B ARG* 1.3 110.7 - - - +
287B PRO* 1.3 75.8 - - - +
288B VAL* 3.2 14.4 + - - +
11G G 6.3 0.4 - - - +
12G G 3.5 32.1 + + - +
13G G 5.5 0.6 + - - -
31H C 3.7 12.8 - - + -
32H C 3.7 31.9 - - + -
33H A 4.1 11.9 - - - -
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Residues in contact with PRO 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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245B PHE* 3.9 26.9 - - + -
246B SER 3.6 18.6 - - - +
247B ILE* 4.0 13.7 - - + +
248B GLY 5.2 0.2 + - - -
249B THR* 3.3 18.4 - - - +
273B PHE* 5.0 1.1 - - + -
274B LYS 3.6 7.4 - - - +
275B TYR* 4.2 4.9 - - + -
284B PRO* 3.8 16.6 - - + +
285B ARG 3.3 3.9 - - - -
286B PHE* 1.3 89.7 - - - +
288B VAL* 1.3 58.8 + - - +
12G G 4.2 25.4 - - - +
13G G 4.9 4.7 - - - -
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Residues in contact with VAL 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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190B PHE* 4.4 1.1 - - + -
247B ILE* 4.3 0.7 - - - -
249B THR* 4.0 6.3 - - + -
250B GLY* 4.2 6.5 - - - -
273B PHE* 3.2 5.6 - - - +
274B LYS* 2.8 56.6 + - + -
286B PHE 3.3 15.7 - - - +
287B PRO* 1.3 75.2 - - - +
289B PHE* 1.3 74.2 + - - +
290B ILE* 3.9 1.9 - - + +
33H A 3.5 32.1 - - - +
34H C 3.5 29.6 - - - +
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Residues in contact with PHE 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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236B ILE* 4.7 2.7 - - + -
247B ILE* 3.6 11.5 - - + +
249B THR 3.3 19.5 + - - +
250B GLY* 3.7 21.6 - - - +
251B PHE* 3.5 34.5 - + + -
255B GLN* 3.8 23.8 - - - -
259B PHE* 3.9 19.5 - + - -
271B VAL* 3.8 24.9 - - + -
272B LYS 3.9 8.7 - - - -
273B PHE* 4.1 2.0 - - + -
288B VAL* 1.3 85.9 - - - +
290B ILE* 1.3 66.2 + - - +
291B GLY* 3.4 40.8 - - - -
292B ILE* 3.9 3.4 - - + -
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Residues in contact with ILE 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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192B ASP* 3.5 24.7 - - - +
255B GLN* 5.3 1.7 + - - -
272B LYS* 3.1 27.4 + - + +
273B PHE* 3.7 10.8 - - - +
274B LYS* 3.6 31.9 - - + +
288B VAL* 3.9 4.5 - - + +
289B PHE* 1.3 88.7 - - - +
291B GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 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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255B GLN* 5.8 0.7 - - - -
271B VAL* 3.4 2.9 - - - +
272B LYS* 2.7 43.4 + - - +
289B PHE* 3.4 17.5 - - - -
290B ILE* 1.3 83.6 - - - +
292B ILE* 1.3 59.5 + - - -
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Residues in contact with ILE 292 (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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255B GLN* 6.3 0.4 - - - +
259B PHE* 3.8 22.0 - - + -
266B TYR* 3.6 39.9 - - + +
269B LYS* 4.6 14.4 - - + +
270B MET 3.7 11.4 - - - +
271B VAL* 4.1 9.9 - - + -
272B LYS* 3.7 9.4 + - - -
289B PHE* 4.2 3.6 - - + -
291B GLY* 1.3 76.0 - - - -
293B ARG* 1.3 84.7 + - + +
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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