Contacts of the helix formed by residues 269 - 281 (chain B) in PDB entry 1QBK
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 ASP 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B VAL* 4.0 18.9 - - + +
267B ASP* 2.7 17.2 + - - +
268B GLN* 1.3 71.3 - - - +
270B GLU* 1.3 67.5 + - - +
271B ASN* 3.5 21.8 + - - +
272B VAL* 2.9 41.8 + - + +
273B ALA 3.4 1.2 + - - -
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Residues in contact with GLU 270 (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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268B GLN 2.8 9.7 + - - +
269B ASP* 1.3 71.6 + - - +
271B ASN* 1.3 64.6 + - - +
272B VAL 3.0 1.6 + - - -
273B ALA* 3.2 14.7 + - - +
274B LEU* 3.2 11.6 + - - +
310B TYR* 2.7 52.6 + - + -
374B ASN* 4.3 6.1 - - - +
375B LEU* 3.2 25.2 + - + +
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Residues in contact with ASN 271 (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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231B VAL* 5.8 0.2 - - - +
232B ARG* 5.5 3.4 - - - +
235B VAL* 3.6 27.5 - - - +
269B ASP* 3.2 20.3 + - - +
270B GLU* 1.3 79.2 - - - +
272B VAL* 1.3 65.2 + - - +
274B LEU* 3.7 8.1 + - - +
275B GLU* 3.5 12.3 + - - +
143C ASN* 4.5 17.9 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL* 4.7 2.5 - - + +
234B ASN* 3.4 22.4 - - - +
235B VAL* 3.2 33.9 - - + -
238B ALA* 5.1 3.1 - - + -
264B ARG* 4.0 12.1 - - + +
267B ASP* 2.9 34.8 - - - +
269B ASP* 2.9 30.1 + - + +
271B ASN* 1.3 72.1 - - - +
273B ALA* 1.3 56.3 + - - +
274B LEU 3.0 1.6 - - - -
275B GLU* 2.6 29.3 + - - +
276B ALA 2.9 8.1 + - - -
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Residues in contact with ALA 273 (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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265B THR* 2.8 34.1 - - - +
266B GLN 5.1 0.4 - - - -
267B ASP* 3.4 12.6 + - - +
269B ASP 3.4 4.2 + - - +
270B GLU* 3.2 9.8 + - - +
272B VAL* 1.3 78.3 - - - +
274B LEU* 1.3 53.9 + - - +
276B ALA 3.6 0.2 - - - -
277B CYS* 2.7 38.3 + - - +
375B LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 274 (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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270B GLU* 3.2 11.8 + - - +
271B ASN* 3.8 10.8 - - - +
272B VAL 2.8 5.1 + - - -
273B ALA* 1.3 71.6 - - - +
275B GLU* 1.3 58.9 + - - +
276B ALA 3.0 4.9 - - - -
278B GLU* 2.8 42.5 + - + +
373B TRP* 3.3 24.7 - - + +
374B ASN* 3.1 37.7 - - - +
375B LEU* 3.3 19.7 - - + +
378B CYS* 4.9 6.7 - - + -
140C ARG* 5.3 5.6 - - - +
143C ASN* 4.0 28.7 - - - +
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Residues in contact with GLU 275 (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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235B VAL* 3.4 41.7 - - + +
236B CYS* 5.3 0.7 - - - -
238B ALA* 3.5 5.3 - - + +
239B LEU* 3.3 25.5 - - + +
271B ASN* 3.5 4.3 + - - +
272B VAL 2.6 14.3 + - - +
274B LEU* 1.3 75.8 - - - +
276B ALA* 1.3 54.8 + - - +
278B GLU* 3.6 3.1 - - - +
279B PHE* 3.0 48.4 - - + +
141C LYS* 2.9 32.2 + - - +
143C ASN* 5.4 3.0 - - - +
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Residues in contact with ALA 276 (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 ALA* 4.2 11.0 - - + -
242B LEU* 5.3 0.2 - - - +
261B MSE 3.2 23.8 - - + -
264B ARG 3.7 6.5 - - - +
265B THR* 2.9 24.5 - - - +
272B VAL 2.9 7.7 + - - +
273B ALA 3.5 5.6 - - - +
274B LEU 3.0 0.8 - - - -
275B GLU* 1.3 75.7 - - - +
277B CYS* 1.3 58.6 + - - +
278B GLU 2.9 1.9 + - - -
279B PHE 3.0 3.3 + - - -
280B TRP* 2.6 37.6 + - - +
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Residues in contact with CYS 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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265B THR* 2.7 30.1 + - + -
273B ALA 2.7 20.3 + - - +
276B ALA* 1.3 68.7 - - - +
278B GLU* 1.3 68.6 + - - +
280B TRP* 4.0 4.3 - - - -
281B LEU* 3.1 38.1 + - - +
303B VAL* 5.8 3.1 - - - -
306B ASN* 5.2 4.0 - - - +
375B LEU* 4.0 11.7 - - + -
378B CYS* 3.7 36.9 - - - -
379B SER* 4.6 4.9 - - - -
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Residues in contact with GLU 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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274B LEU* 2.8 28.1 + - + +
275B GLU* 3.6 6.2 - - - +
276B ALA 2.9 0.4 + - - -
277B CYS* 1.3 81.1 - - - +
279B PHE* 1.3 87.2 + - + +
280B TRP 2.7 11.8 + - - -
281B LEU 3.5 8.3 + - - +
282B THR* 3.5 9.5 + - - -
378B CYS* 3.6 23.7 - - - -
140C ARG* 3.1 44.5 + - - +
141C LYS* 3.5 10.5 + - - -
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Residues in contact with PHE 279 (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 ALA 4.5 2.5 - - - +
239B LEU* 3.5 39.7 - - + -
242B LEU* 2.7 46.2 - - + +
243B LEU* 5.4 1.8 - - + -
275B GLU* 3.0 40.8 + - - +
276B ALA 3.0 3.2 + - - +
278B GLU* 1.3 101.8 - - + +
280B TRP* 1.3 53.6 + - - +
282B THR* 3.2 16.4 + - - -
141C LYS* 3.0 39.7 - - + -
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Residues in contact with TRP 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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242B LEU* 3.2 43.4 - - + +
257B ILE* 5.6 1.6 - - - +
258B VAL* 4.0 30.0 - - + +
261B MSE 3.7 19.8 - - + +
262B LEU* 3.6 26.0 - - + -
265B THR* 4.4 15.7 - - + +
276B ALA* 2.6 24.1 + - - +
277B CYS* 3.3 3.4 - - - +
278B GLU 2.7 4.2 + - - -
279B PHE* 1.3 72.5 - - - +
281B LEU* 1.3 81.1 + - + +
282B THR* 2.4 24.2 + - - -
283B LEU* 5.2 1.9 - - - +
299B LYS* 2.7 54.1 - - + -
302B PRO* 6.2 0.2 - - + -
303B VAL* 5.5 1.3 - - + -
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Residues in contact with LEU 281 (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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265B THR* 5.9 0.2 - - + -
277B CYS* 3.1 35.2 + - - +
278B GLU 4.0 3.9 - - - +
280B TRP* 1.3 118.4 - - + +
282B THR* 1.3 58.3 + - - +
283B LEU* 3.4 27.4 + - + +
299B LYS* 3.6 22.4 - - + -
303B VAL* 5.1 8.5 - - + -
382B ALA* 3.3 38.7 - - + +
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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