Contacts of the helix formed by residues 274 - 286 (chain B) in PDB entry 2QUH
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 CYS 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN 3.2 21.8 - - - +
256A LYS* 3.7 24.7 - - - +
258A VAL 3.2 11.7 - - - +
259A THR* 3.8 6.4 - - + +
202B LEU* 4.5 9.6 - - - -
272B SER 3.9 1.0 + - - -
273B ASP* 1.3 76.3 - - - +
275B ILE* 1.3 62.0 + - - +
276B GLY* 3.0 5.0 + - - -
277B LYS* 3.1 48.4 + - - +
278B ILE* 3.4 9.2 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 3.6 13.5 - - + +
258A VAL* 2.8 43.2 + - + +
259A THR 4.1 8.5 - - - +
260A PHE 4.1 1.1 - - - +
263A VAL* 4.1 17.5 - - + -
278A ILE* 3.2 40.6 - - + +
279A SER* 3.8 20.4 - - - +
281A PRO* 5.2 1.6 - - + -
282A ALA* 4.2 24.2 - - + +
273B ASP 3.7 0.2 + - - -
274B CYS* 1.3 70.8 - - - +
276B GLY* 1.3 64.0 + - - +
278B ILE* 3.5 10.7 + - - +
279B SER* 3.2 22.5 + - - -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 3.3 39.3 + - - +
202B LEU* 3.8 19.4 - - - +
274B CYS* 3.0 2.0 + - - -
275B ILE* 1.3 76.1 - - - +
277B LYS* 1.3 64.0 + - - +
279B SER* 3.2 3.6 + - - -
280B PHE* 3.0 23.4 + - - +
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Residues in contact with LYS 277 (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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202B LEU* 3.7 23.5 - - + +
203B TRP* 3.7 68.2 + - + +
269B PHE* 3.5 14.1 - - + -
273B ASP* 4.2 30.8 + - + +
274B CYS* 3.1 27.3 + - - +
276B GLY* 1.3 73.8 - - - +
278B ILE* 1.3 63.6 + - - +
280B PHE* 3.2 11.1 + - - +
281B PRO* 3.5 10.0 - - - +
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Residues in contact with ILE 278 (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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260A PHE* 3.5 29.8 - - + -
275A ILE* 3.5 27.6 - - + +
278A ILE* 4.4 17.3 - - + -
260B PHE* 3.4 45.5 - - + -
263B VAL* 4.1 7.5 - - + +
269B PHE* 4.1 16.6 - - + -
270B THR 4.3 2.9 - - - +
273B ASP* 3.9 16.4 - - + +
274B CYS 3.4 7.5 + - - +
275B ILE* 3.7 10.1 - - - +
276B GLY 3.2 0.2 - - - -
277B LYS* 1.3 78.4 - - - +
279B SER* 1.3 59.1 + - - +
281B PRO* 3.7 8.0 - - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 3.8 10.6 + - - -
275A ILE* 3.7 21.4 - - - +
279A SER* 3.5 24.4 + - - -
255B GLN* 3.6 19.8 + - - -
275B ILE 3.2 13.1 + - - -
276B GLY 3.7 3.5 + - - -
278B ILE* 1.3 76.2 - - - +
280B PHE* 1.3 66.5 + - - +
281B PRO* 3.4 3.1 - - - -
282B ALA* 3.3 20.5 + - - +
283B ILE* 4.2 3.4 + - - +
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Residues in contact with PHE 280 (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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196B THR* 3.7 13.7 - - + -
198B ASP* 3.9 13.7 - - - -
199B GLU* 3.4 54.1 - - + -
202B LEU* 4.8 6.3 - - + -
203B TRP* 4.0 17.3 - + + -
276B GLY 3.0 13.3 + - - +
277B LYS 3.2 8.0 + - - +
279B SER* 1.3 77.0 - - - +
281B PRO* 1.3 62.7 - - + +
283B ILE* 2.6 58.7 + - + +
284B GLN* 3.4 29.8 + - + -
316B TYR* 3.9 16.6 - + - -
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 5.1 1.8 - - + -
263B VAL* 4.4 2.7 - - + -
267B PHE* 3.6 33.2 - - + -
269B PHE* 4.0 11.7 - - + -
277B LYS 3.5 9.9 - - - +
278B ILE 3.7 5.2 - - - +
279B SER 3.4 4.3 - - - -
280B PHE* 1.3 93.6 - - + +
282B ALA* 1.3 55.1 + - - +
284B GLN* 3.3 3.8 + - - +
285B ALA* 3.0 29.4 + - - +
316B TYR* 4.1 20.0 - - + +
319B MET* 3.5 31.4 - - + +
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Residues in contact with ALA 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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275A ILE* 4.4 6.8 - - + +
251B VAL* 3.9 13.6 - - + +
254B ILE* 3.9 24.2 - - + +
255B GLN* 3.6 28.5 - - + +
279B SER 3.3 12.6 + - - +
280B PHE 2.8 4.9 + - - -
281B PRO* 1.3 74.6 - - - +
283B ILE* 1.3 64.1 + - - +
285B ALA* 3.7 0.9 - - - +
286B ALA* 2.9 27.2 + - - +
319B MET* 5.1 0.6 - - - -
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Residues in contact with ILE 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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248A TYR* 3.9 14.1 - - + +
194B GLN* 3.1 14.2 + - - +
198B ASP* 3.8 7.0 - - - +
237B ASP* 3.6 30.3 - - - +
241B MET* 3.3 28.3 - - + -
247B PHE* 3.8 8.4 - - + -
251B VAL* 3.6 24.2 - - + -
255B GLN* 5.1 3.6 - - - +
279B SER* 4.6 2.0 - - - +
280B PHE* 2.6 38.4 + - + +
282B ALA* 1.3 73.3 - - - +
284B GLN* 1.3 57.4 + - - +
286B ALA* 3.7 2.4 + - - +
287B PRO* 3.0 22.2 - - - +
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Residues in contact with GLN 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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159B TYR* 2.5 27.0 + - - +
194B GLN* 3.5 8.7 - - - +
280B PHE* 3.4 24.0 + - + -
281B PRO 3.3 8.4 + - - +
282B ALA 3.2 0.8 - - - -
283B ILE* 1.3 79.8 - - - +
285B ALA* 1.3 59.1 + - - +
287B PRO* 3.1 5.7 - - - +
313B GLN* 3.0 25.3 + - - -
316B TYR* 3.6 27.8 - - + -
317B PHE* 3.7 17.8 - - + -
818B TRP* 2.7 56.1 + - - +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 4.1 18.2 - - + -
281B PRO 3.0 17.3 + - - +
282B ALA* 3.2 6.0 + - - +
284B GLN* 1.3 77.2 - - - +
286B ALA* 1.3 57.7 + - - +
288B SER* 2.7 35.5 + - - -
289B PHE* 4.0 2.4 - - - -
316B TYR* 4.7 3.1 - - + +
317B PHE* 4.6 1.8 - - - -
319B MET* 5.1 3.4 - - - -
320B THR* 2.9 33.2 - - + +
323B VAL* 5.7 0.2 - - + -
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Residues in contact with ALA 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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247B PHE* 3.9 11.2 - - + -
250B ASN* 4.4 5.2 - - + -
251B VAL* 3.7 27.8 - - + +
254B ILE* 3.6 16.8 - - + +
282B ALA 2.9 16.2 + - - +
283B ILE 3.7 2.2 - - - +
285B ALA* 1.3 76.9 - - - +
287B PRO* 1.3 62.0 - - + +
288B SER 2.9 5.5 + - - -
289B PHE* 3.2 12.1 + - - -
292B SER* 2.9 19.4 + - - -
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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