Contacts of the strand formed by residues 281 - 287 (chain B) in PDB entry 6HYI
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B THR 3.8 11.7 + - - -
279B CYS* 3.1 36.9 + - - +
280B ASN* 1.3 80.8 - - - +
282B LEU* 1.3 60.6 + - - +
283B TYR* 3.1 34.2 - - + -
309B GLY* 3.7 19.4 - - - +
313B LEU* 3.8 7.5 - - - +
334B VAL* 3.8 25.8 - - + -
335B LEU 3.5 8.1 - - - +
336B ASP* 5.0 5.4 - - - -
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Residues in contact with LEU 282 (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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244B LEU* 4.0 4.5 - - + -
245B PHE* 3.8 28.5 - - + -
260B MET* 4.8 0.6 - - + +
281B LYS* 1.3 72.5 - - - +
283B TYR* 1.3 61.3 + - - +
284B ILE* 4.1 9.9 - - + -
307B ALA* 4.0 13.0 - - + -
308B VAL 3.7 14.4 - - - +
310B GLU* 3.7 32.3 - - + +
313B LEU* 3.6 13.4 - - + +
333B TRP 3.6 1.2 - - - +
334B VAL* 3.2 5.4 - - - +
335B LEU* 2.8 51.0 + - + +
340B TYR* 4.0 21.5 - - + -
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Residues in contact with TYR 283 (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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263B ALA* 4.6 1.6 - - + -
265B PHE* 3.8 24.5 - + - -
271B ILE* 3.7 29.1 + - + +
272B MET* 3.8 25.6 - - + -
279B CYS* 4.0 5.1 - - - -
281B LYS* 3.1 42.7 - - + +
282B LEU* 1.3 74.0 - - - +
284B ILE* 1.3 61.4 + - - +
285B ILE* 4.0 2.3 + - + +
306B THR 3.8 0.3 - - - +
307B ALA* 3.1 5.7 - - - +
308B VAL* 2.9 47.3 + - + +
332B ALA* 4.1 18.2 - - + -
333B TRP 3.4 3.8 - - - -
334B VAL* 3.4 31.9 - - + -
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Residues in contact with ILE 284 (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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238B LEU* 4.1 30.3 - - + +
239B LEU* 4.4 4.0 - - + -
242B ASN* 4.2 4.0 - - + +
245B PHE* 3.8 29.6 - - + -
260B MET* 3.5 25.4 - - + -
282B LEU* 4.1 9.4 - - + -
283B TYR* 1.3 75.1 - - - +
285B ILE* 1.3 66.5 + - - +
286B GLN 3.4 0.7 + - - -
305B GLY 4.0 12.8 - - - +
306B THR 3.5 6.7 - - - +
307B ALA* 3.3 29.2 - - + -
332B ALA* 3.3 1.4 - - - -
333B TRP* 2.8 44.4 + - + +
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Residues in contact with ILE 285 (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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238B LEU* 3.8 5.3 - - - +
271B ILE* 5.7 1.6 - - + -
283B TYR* 4.9 4.5 - - + +
284B ILE* 1.3 73.7 - - - +
286B GLN* 1.3 60.0 + - - +
287B SER 3.5 17.7 - - - +
288B GLY 3.3 22.2 - - - +
290B ALA* 5.0 2.2 - - + -
302B LYS* 4.0 21.5 - - + +
303B THR 3.8 7.0 - - - +
304B GLU* 3.9 6.7 - - - -
305B GLY* 2.7 30.7 + - - -
306B THR* 2.9 36.8 + - - +
308B VAL* 4.9 13.0 - - + -
330B LEU* 4.2 26.7 - - + -
331B ILE 3.8 4.9 - - - +
332B ALA* 4.3 3.1 - - + +
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Residues in contact with GLN 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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234B LEU* 3.6 32.1 - - + +
238B LEU* 4.1 12.7 - - + +
262B ARG* 4.9 1.8 + - - +
284B ILE 3.4 3.6 + - - -
285B ILE* 1.3 74.3 - - - +
287B SER* 1.3 64.6 + - - +
304B GLU* 3.5 14.9 - - - +
305B GLY 4.6 0.2 + - - -
331B ILE* 2.8 46.9 + - + +
333B TRP* 2.9 39.8 + - + +
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Residues in contact with SER 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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285B ILE* 3.5 3.3 - - - +
286B GLN* 1.3 84.9 + - - +
288B GLY* 1.3 64.0 + - - +
304B GLU* 4.3 6.3 - - - -
329B GLU 4.7 0.4 - - - -
330B LEU* 3.3 7.9 - - - +
331B ILE* 2.9 50.7 + - - +
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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