Contacts of the strand formed by residues 280 - 288 (chain X) in PDB entry 2Q0Z
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 280 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234X LEU 3.2 9.9 - - - +
235X GLU* 3.9 27.6 - - + +
277X LEU* 3.5 4.9 - - - +
278X GLN* 3.7 4.2 + - - +
279X GLN* 1.3 92.6 + - + +
281X ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X GLN* 3.4 4.3 - - - +
234X LEU* 2.9 34.3 + - + +
275X LEU* 4.0 23.1 - - + -
276X THR 4.7 3.8 - - - +
277X LEU* 3.4 19.3 - - + -
280X LYS* 1.3 78.2 - - - +
282X LYS* 1.3 66.2 + - - +
283X VAL* 5.0 0.7 - - - -
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Residues in contact with LYS 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X VAL 3.3 4.9 - - - +
233X GLN* 3.7 39.2 - - + +
281X ALA* 1.3 76.7 - - - +
283X VAL* 1.3 65.8 + - - +
284X LYS 4.3 0.2 - - - -
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Residues in contact with VAL 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X VAL 3.7 1.2 - - - +
231X LEU* 3.7 1.1 - - - -
232X VAL* 2.8 51.0 + - + +
234X LEU* 4.5 7.4 - - + -
259X VAL* 4.4 17.9 - - + -
273X LYS* 3.9 32.8 - - + +
275X LEU* 3.3 41.3 - - + -
282X LYS* 1.3 81.3 - - - +
284X LYS* 1.3 64.6 + - - +
285X LEU* 4.0 4.0 + - + -
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Residues in contact with LYS 284 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X VAL* 3.6 26.2 - - + +
230X VAL 3.7 2.7 - - - -
231X LEU* 3.7 24.4 - - + +
273X LYS* 2.7 41.0 + - - +
283X VAL* 1.3 75.2 - - - +
285X LEU* 1.3 65.8 + - - +
286X ASP* 5.0 5.5 - - + +
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Residues in contact with LEU 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X VAL* 3.4 4.0 - - - +
230X VAL* 2.8 37.9 + - + +
232X VAL* 5.2 1.3 - - + -
259X VAL* 3.4 39.3 - - + +
260X VAL 4.3 0.4 - - - +
261X ILE* 3.7 40.6 - - + +
271X SER* 4.3 6.1 - - - +
272X ILE 4.1 10.5 - - - +
273X LYS* 3.4 45.8 - - + +
283X VAL* 4.0 4.2 + - + +
284X LYS* 1.3 75.5 - - - +
286X ASP* 1.3 63.9 + - - +
299X LEU* 4.3 3.4 - - + -
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Residues in contact with ASP 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227X PRO* 5.2 7.4 - - + +
228X VAL 3.1 13.0 - - - +
229X VAL* 4.1 17.0 - - + -
271X SER* 2.9 18.1 + - - -
273X LYS* 5.8 2.6 - - - -
284X LYS* 5.0 5.8 - - + +
285X LEU* 1.3 79.6 - - - +
287X PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227X PRO* 3.7 3.5 - - - +
228X VAL* 2.9 68.1 + - + +
230X VAL* 4.6 3.1 - - + -
261X ILE* 3.9 34.5 - - + -
270X ILE* 3.3 33.7 - - + +
271X SER* 3.5 3.1 - - - +
286X ASP* 1.3 82.6 - - - +
288X VAL* 1.3 84.4 + - - +
290X PRO* 4.7 1.8 - - + -
297X TYR* 3.8 47.6 - + - -
315X PHE* 4.6 3.8 - + - -
317X VAL* 5.1 1.1 - - + -
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Residues in contact with VAL 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225X GLY* 3.6 25.4 - - - +
226X GLY 3.7 4.7 - - - -
227X PRO* 5.1 0.2 - - - -
287X PHE* 1.3 87.9 - - - +
289X ALA* 1.3 73.9 + - - +
290X PRO* 3.5 3.6 - - - +
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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