Contacts of the strand formed by residues 286 - 292 (chain B) in PDB entry 3BEQ
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 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B VAL* 4.1 2.2 - - - +
282B PRO* 3.4 5.2 - - - +
283B ASP 2.8 32.7 + - - +
284B THR 4.0 7.2 - - - +
285B GLY* 1.3 83.5 - - - +
287B VAL* 1.3 67.5 + - - +
304B SER* 4.5 5.9 + - - -
305B PHE* 3.3 27.3 - - - +
306B ASP* 4.0 18.2 - - + +
311B ASP 5.4 1.1 + - - -
313B GLN* 4.3 16.6 + - - +
1006B GOL 3.7 31.8 + - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 3.8 29.2 - - + -
233B VAL* 4.1 9.9 - - + -
238B PHE* 3.9 26.2 - - + -
280B CYS* 4.0 4.0 - - + -
281B TYR 3.4 9.9 - - - +
282B PRO* 4.5 0.7 - - + -
286B LYS* 1.3 83.4 - - - +
288B MET* 1.3 62.2 + - - +
289B CYS* 4.0 14.4 - - - -
303B VAL 4.1 0.2 - - - +
304B SER* 3.1 7.4 - - - -
305B PHE* 3.0 58.5 + - + +
306B ASP 6.4 0.4 - - - -
1006B GOL 3.9 3.4 - - - -
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Residues in contact with MET 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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280B CYS* 3.2 1.2 - - - -
281B TYR* 2.9 72.5 + - + +
287B VAL* 1.3 73.7 - - - +
289B CYS* 1.3 77.8 + - - +
290B VAL* 4.5 1.8 - - + -
302B TRP* 3.9 11.0 - - + -
303B VAL 3.8 4.0 - - - +
304B SER* 3.6 23.8 - - - +
355B ARG* 4.0 9.0 - - - +
383B TRP* 3.6 38.6 - - + +
1006B GOL 3.4 28.4 - - - +
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Residues in contact with CYS 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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240B ILE* 3.9 13.2 - - - -
278B CYS* 4.2 0.7 - - + -
279B SER 3.3 4.0 - - - +
280B CYS* 2.1 47.1 - - - -
287B VAL* 4.0 2.2 - - - -
288B MET* 1.3 75.7 - - - +
290B VAL* 1.3 62.7 + - - +
291B CYS* 4.0 9.8 - - - -
302B TRP* 3.0 8.8 - - - +
303B VAL* 2.8 50.0 + - + +
305B PHE* 3.9 19.7 - - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B SER* 2.8 35.5 + - - +
281B TYR* 5.2 0.4 - - + -
288B MET* 4.5 5.4 - - + -
289B CYS* 1.3 76.8 - - - +
291B CYS* 1.3 63.7 + - - +
300B ARG* 3.5 35.9 - - + -
301B PRO 3.6 3.6 - - - +
302B TRP* 4.3 2.5 - - + -
317B ILE* 4.0 8.3 - - + -
351B GLY 3.6 4.2 - - - +
352B PHE 3.9 0.9 - - - -
353B SER* 3.6 42.0 - - - +
383B TRP* 3.9 27.4 - - + -
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Residues in contact with CYS 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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275B TYR* 3.6 17.0 - - + -
276B GLU 3.4 10.1 - - - +
277B GLU 4.4 2.0 - - - -
278B CYS* 2.2 49.8 - - - +
289B CYS* 4.0 9.2 - - - -
290B VAL* 1.3 83.4 - - - +
292B ARG* 1.3 62.2 + - - +
300B ARG* 2.9 34.9 + - - +
301B PRO* 2.8 26.1 + - + +
303B VAL* 4.7 0.2 - - - -
351B GLY 5.0 1.3 - - - -
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Residues in contact with ARG 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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274B HIS 3.4 5.3 - - - +
275B TYR 3.7 0.5 - - - -
276B GLU* 2.9 50.1 + - + +
277B GLU* 2.7 39.6 + - + +
291B CYS* 1.3 80.0 - - - +
293B ASP* 1.3 66.5 + - - +
294B ASN* 2.8 31.3 + - - +
300B ARG* 3.7 5.4 - - - +
301B PRO* 4.1 0.2 - - - -
324B ASP* 4.6 1.3 - - - +
347B ASN* 3.5 9.5 + - - -
348B GLY* 3.1 29.7 + - - -
349B ILE* 3.8 31.4 - - - +
350B LYS* 4.6 1.6 - - - -
371B ARG* 4.0 5.1 - - - +
406B TYR* 3.1 18.4 + - - -
1004B GOL 3.5 21.2 - - - -
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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