Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 2QKW
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 ARG 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B LYS 3.8 2.0 + - - -
277B ILE* 1.3 69.7 - - - +
279B PRO* 1.4 66.1 - - + +
280B GLU* 3.2 14.8 + - + +
281B SER* 2.7 27.6 + - - +
282B LEU 3.0 8.8 + - - -
316B LEU 3.4 22.4 - - - +
317B GLN* 3.1 32.9 + - - +
318B GLU* 3.3 31.5 + - - +
319B SER 3.6 23.0 + - - +
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Residues in contact with PRO 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLN* 4.7 13.7 - - - +
277B ILE 3.3 7.6 - - - +
278B ARG* 1.4 90.2 - - + -
280B GLU* 1.3 57.2 + - + +
282B LEU* 3.2 15.8 + - + +
283B ARG* 2.9 29.3 + - - +
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Residues in contact with GLU 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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278B ARG* 3.0 11.7 + - + -
279B PRO* 1.3 81.2 - - + +
281B SER* 1.3 57.1 + - - +
283B ARG* 3.6 9.8 + - + +
284B LYS* 3.1 24.4 + - - +
316B LEU* 3.4 38.5 - - + +
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 3.1 26.5 + - - -
277B ILE* 3.4 1.6 - - - +
278B ARG 2.7 10.2 + - - -
280B GLU* 1.3 72.5 - - - +
282B LEU* 1.3 58.9 + - - +
284B LYS* 3.6 6.9 - - - +
285B PHE* 2.8 37.0 + - - +
313B ALA* 3.3 21.6 - - - +
316B LEU* 3.3 25.6 + - - -
317B GLN* 3.1 9.9 + - - -
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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
----------------------------------------------------------
138B TRP* 5.1 0.4 - - - -
235B LEU* 3.9 29.4 - - + -
260B HIS* 3.5 25.4 - - + +
265B LEU* 5.2 2.9 - - + +
266B GLU 5.1 3.4 - - - +
267B GLN* 3.5 41.5 - - + +
270B ASP* 5.1 6.1 - - - +
277B ILE* 3.6 31.4 - - + +
278B ARG 3.0 3.0 + - - +
279B PRO* 3.3 14.1 - - + +
281B SER* 1.3 78.2 + - - +
283B ARG* 1.3 64.1 + - - +
285B PHE* 4.1 3.9 - - - +
286B GLY* 3.0 18.2 + - - -
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B HIS* 4.2 7.4 + - - -
265B LEU* 3.8 34.9 - - + +
279B PRO 2.9 15.5 + - - +
280B GLU* 3.8 10.7 + - - +
281B SER 3.3 0.2 - - - -
282B LEU* 1.3 77.4 - - - +
284B LYS* 1.3 62.2 + - - +
286B GLY 3.7 0.3 - - - -
287B ASP* 2.8 64.3 + - - +
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Residues in contact with LYS 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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280B GLU 3.1 15.3 + - - +
281B SER 3.6 4.7 - - - +
283B ARG* 1.3 88.7 - - - +
285B PHE* 1.3 57.7 + - - +
287B ASP* 3.4 13.4 + - + +
288B THR* 2.6 39.2 + - - +
308B TRP* 5.4 4.3 - - - -
309B LYS* 3.4 54.0 - - - +
312B TYR* 4.5 15.2 - - + -
313B ALA* 3.8 22.4 - - + +
316B LEU* 4.0 15.9 - - + -
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Residues in contact with PHE 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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138B TRP* 3.5 24.5 - + + -
141B ARG 6.2 0.2 - - - -
142B LEU* 3.5 26.7 - - + -
145B CYS* 4.1 11.9 - - - -
231B LEU* 3.1 52.5 - - + +
232B PHE* 4.6 0.9 - + - -
234B VAL* 4.5 5.6 - - + -
235B LEU* 3.7 26.0 - - + -
281B SER 2.8 20.4 + - - +
282B LEU* 4.1 3.6 - - - +
284B LYS* 1.3 73.4 - - - +
286B GLY* 1.3 60.7 + - - +
288B THR* 3.5 5.5 + - - -
289B ALA* 3.1 26.1 + - + +
310B LEU* 3.6 25.4 - - + -
313B ALA* 4.3 6.7 - - + +
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Residues in contact with GLY 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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232B PHE* 3.8 13.6 - - - -
235B LEU* 5.5 3.1 - - - +
260B HIS* 3.8 21.1 - - - -
282B LEU 3.0 16.8 + - - -
285B PHE* 1.3 77.6 - - - +
287B ASP* 1.3 59.9 + - - +
289B ALA* 3.7 0.8 - - - -
290B VAL* 2.8 36.3 + - - +
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Residues in contact with ASP 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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260B HIS* 4.6 8.1 + - - +
265B LEU* 6.3 0.9 - - + +
283B ARG* 2.8 49.1 + - + +
284B LYS* 3.7 17.6 + - + +
286B GLY* 1.3 73.6 - - - +
288B THR* 1.3 57.7 + - - +
290B VAL* 3.2 9.6 + - - +
291B LYS* 2.9 58.1 + - - +
309B LYS* 5.6 1.0 - - - +
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Residues in contact with THR 288 (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 LEU* 4.7 5.4 - - + -
284B LYS* 2.6 25.7 + - - +
285B PHE* 3.6 5.6 - - - -
287B ASP* 1.3 76.3 + - - +
289B ALA* 1.3 57.8 + - - +
291B LYS* 3.2 8.1 + - - +
292B CYS* 3.0 35.2 + - - -
301B PRO* 4.8 1.7 - - + +
306B VAL* 4.3 27.1 - - + +
309B LYS* 3.5 47.6 - - + +
310B LEU* 5.0 7.0 - - + -
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Residues in contact with ALA 289 (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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228B GLY 4.1 0.8 - - - +
231B LEU* 3.7 36.7 - - + +
232B PHE* 3.3 32.3 - - + -
285B PHE* 3.1 17.4 + - + +
286B GLY 3.8 0.2 - - - +
288B THR* 1.3 77.9 - - - +
290B VAL* 1.3 61.0 + - - +
292B CYS* 3.7 3.4 + - - +
293B LEU* 3.3 26.7 + - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 3.6 18.2 - - + -
257B VAL* 4.3 17.6 - - + +
260B HIS* 3.5 29.2 - - + +
261B ASN* 3.3 32.1 - - + +
286B GLY 2.8 21.6 + - - +
287B ASP* 3.5 9.4 - - - +
288B THR 3.2 0.2 - - - -
289B ALA* 1.3 76.6 - - - +
291B LYS* 1.3 62.1 + - + +
293B LEU* 3.1 21.2 + - - +
294B ALA* 3.6 7.6 + - - -
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Residues in contact with LYS 291 (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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287B ASP* 2.9 43.0 + - - +
288B THR* 3.6 5.8 - - - +
290B VAL* 1.3 77.2 - - + +
292B CYS* 1.3 65.6 + - - +
293B LEU 3.4 0.2 + - - -
294B ALA* 3.5 12.4 + - - +
299B ASP 4.2 5.6 + - - +
300B ARG* 3.5 10.6 - - - -
301B PRO* 3.3 26.0 - - + +
309B LYS* 4.5 22.7 - - - +
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Residues in contact with CYS 292 (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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224B VAL* 3.5 31.6 - - - +
225B TYR* 3.4 12.1 + - - -
227B PHE* 5.1 0.9 - - - -
228B GLY* 3.5 23.3 - - - -
231B LEU* 4.1 17.5 - - - -
288B THR 3.0 20.4 + - - +
289B ALA 3.7 2.2 - - - +
290B VAL 3.2 0.2 - - - -
291B LYS* 1.3 77.8 - - - +
293B LEU* 1.3 59.0 + - - +
294B ALA 3.3 0.2 - - - -
300B ARG* 3.3 23.6 - - - -
301B PRO* 4.0 2.5 - - - -
306B VAL* 3.8 22.9 - - - -
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Residues in contact with LEU 293 (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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225B TYR* 3.3 61.0 - - + +
228B GLY* 3.9 4.9 - - - +
229B VAL* 3.9 13.7 - - + +
232B PHE* 3.5 27.8 - - + -
253B ALA* 3.8 16.2 - - + +
257B VAL* 3.8 23.8 - - + +
289B ALA 3.3 18.2 - - - +
290B VAL 3.1 10.9 + - - +
292B CYS* 1.3 77.9 - - - +
294B ALA* 1.3 66.8 + - - +
295B LEU* 3.3 5.7 + - - +
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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