Contacts of the helix formed by residues 254 - 268 (chain Q) in PDB entry 1U8F
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 254 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253Q ALA* 1.3 75.8 - - - +
255Q TYR* 1.3 67.0 + - - +
256Q ASP* 4.2 9.6 - - + +
257Q ASP* 2.9 32.7 + - - +
258Q ILE* 3.1 10.2 + - - +
305Q ASP* 2.6 37.4 + - - +
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Residues in contact with TYR 255 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253Q ALA 3.7 1.4 + - - -
254Q LYS* 1.3 71.8 - - - +
256Q ASP* 1.3 59.6 + - - +
258Q ILE* 3.0 19.4 + - + +
259Q LYS* 2.9 49.7 + - + +
295Q PHE* 3.8 16.9 - + - -
296Q ASP 4.0 0.5 + - - -
297Q ALA* 2.6 33.7 + - - -
300Q GLY* 3.4 31.5 + - - -
301Q ILE* 4.4 2.9 - - - -
302Q ALA* 4.4 27.3 - - + +
305Q ASP* 5.1 0.4 + - - -
308Q VAL* 5.1 0.9 - - + -
309Q LYS 4.8 0.2 - - - -
310Q LEU* 4.0 21.0 - - + +
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Residues in contact with ASP 256 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254Q LYS* 3.2 7.3 - - + +
255Q TYR* 1.3 80.1 - - - +
257Q ASP* 1.3 59.7 + - - +
259Q LYS* 3.4 29.0 + - - +
260Q LYS* 3.0 43.8 + - - +
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Residues in contact with ASP 257 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168Q PHE* 4.2 6.7 - - + -
253Q ALA* 4.5 9.2 - - + -
254Q LYS* 2.9 37.9 + - - +
256Q ASP* 1.3 76.2 - - - +
258Q ILE* 1.3 65.9 + - - +
260Q LYS* 3.3 16.2 + - - +
261Q VAL* 3.1 29.3 + - + +
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Residues in contact with ILE 258 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164Q ILE* 3.9 22.4 - - + -
168Q PHE* 3.9 17.9 - - + -
249Q LEU* 4.3 12.6 - - + -
253Q ALA* 4.2 7.4 - - + +
254Q LYS 3.1 12.6 + - - +
255Q TYR* 3.0 20.5 + - + +
257Q ASP* 1.3 77.1 - - - +
259Q LYS* 1.3 62.5 + - - +
261Q VAL* 3.1 10.2 - - - +
262Q VAL* 3.1 26.5 + - + +
295Q PHE* 4.2 11.7 - - + -
308Q VAL* 4.2 35.0 - - + -
310Q LEU* 4.2 17.3 - - + -
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Residues in contact with LYS 259 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255Q TYR* 2.9 47.0 + - + +
256Q ASP* 3.5 26.8 + - - +
258Q ILE* 1.3 77.4 - - - +
260Q LYS* 1.3 57.0 + - + +
263Q LYS* 2.9 32.7 + - - +
276Q TYR* 3.3 32.0 - - - +
278Q GLU* 4.0 15.2 + - - +
295Q PHE* 4.2 9.4 - - + -
297Q ALA* 3.9 18.9 - - + +
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Residues in contact with LYS 260 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256Q ASP* 3.0 30.6 + - - +
257Q ASP* 3.6 19.7 - - - +
258Q ILE 3.2 0.4 - - - -
259Q LYS* 1.3 77.1 - - + +
261Q VAL* 1.3 58.3 + - + +
263Q LYS* 3.4 6.3 + - - +
264Q GLN* 3.0 33.1 + - - +
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Residues in contact with VAL 261 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q VAL* 3.9 14.9 - - + +
164Q ILE* 5.1 0.2 - - + -
167Q ASN* 3.7 30.5 + - - +
168Q PHE* 3.6 30.3 - - + -
257Q ASP* 3.1 13.4 + - + +
258Q ILE 3.1 15.7 - - - +
260Q LYS* 1.3 74.3 - - + +
262Q VAL* 1.3 62.8 + - + +
264Q GLN* 3.5 15.6 + - - +
265Q ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 262 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Q LEU* 4.4 8.5 - - + -
163Q VAL* 4.1 11.9 - - + -
164Q ILE* 4.2 23.6 - - + -
258Q ILE* 3.1 23.1 + - + +
259Q LYS 3.9 2.7 - - - +
261Q VAL* 1.3 74.6 - - + +
263Q LYS* 1.3 67.5 + - - +
265Q ALA* 3.1 3.5 + - - +
266Q SER* 2.9 21.5 + - - -
274Q LEU* 4.1 19.8 - - + +
275Q GLY 4.6 1.6 - - - +
276Q TYR* 4.0 6.3 - - + -
295Q PHE* 3.5 39.5 - - + -
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Residues in contact with LYS 263 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259Q LYS 2.9 18.4 + - - +
260Q LYS* 3.8 6.1 - - - +
262Q VAL* 1.3 75.9 - - - +
264Q GLN* 1.3 62.7 + - - +
266Q SER* 2.6 25.8 + - - +
267Q GLU* 3.0 43.3 + - + +
276Q TYR* 3.7 38.8 - - + +
278Q GLU* 4.8 4.5 - - - +
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Residues in contact with GLN 264 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260Q LYS* 3.0 21.3 + - - +
261Q VAL* 3.6 17.1 - - - +
263Q LYS* 1.3 77.5 - - - +
265Q ALA* 1.3 62.1 + - - +
267Q GLU* 3.3 12.0 + - - +
268Q GLY* 3.1 18.7 + - - -
269Q PRO* 4.9 0.5 - - - +
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Residues in contact with ALA 265 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q VAL* 3.7 30.3 - - + -
261Q VAL 3.0 14.7 + - - +
262Q VAL 3.5 7.6 - - - +
264Q GLN* 1.3 78.6 - - - +
266Q SER* 1.3 62.4 + - - +
268Q GLY* 3.1 10.4 + - - +
269Q PRO* 4.8 10.1 - - + -
270Q LEU* 3.3 28.5 + - + +
274Q LEU* 4.1 5.8 - - + -
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Residues in contact with SER 266 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262Q VAL 2.9 11.8 + - - -
263Q LYS* 2.6 22.4 + - - +
265Q ALA* 1.3 76.8 - - - +
267Q GLU* 1.3 62.5 + - - +
268Q GLY 3.4 0.2 - - - -
270Q LEU 4.7 0.4 - - - -
271Q LYS* 3.1 27.7 + - - +
272Q GLY 4.5 0.3 + - - -
274Q LEU* 3.1 28.8 - - - +
275Q GLY* 4.0 4.9 - - - -
276Q TYR* 3.5 25.1 - - - +
291Q HIS* 6.1 0.5 - - - -
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Residues in contact with GLU 267 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263Q LYS* 3.0 49.2 + - + +
264Q GLN* 3.8 9.7 - - - +
265Q ALA 3.1 0.6 - - - -
266Q SER* 1.3 81.9 - - - +
268Q GLY* 1.3 61.5 + - - +
271Q LYS* 4.3 18.2 + - - +
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Residues in contact with GLY 268 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264Q GLN 3.1 8.3 + - - -
265Q ALA 3.1 4.4 + - - -
267Q GLU* 1.3 78.7 - - - +
269Q PRO* 1.3 75.1 - - - +
270Q LEU 3.2 1.3 - - - -
271Q LYS* 3.1 19.9 + - - +
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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